Quantitative Microbial Risk Assessment Tutorial - Primer

EPA Science Inventory

This document provides a Quantitative Microbial Risk Assessment (QMRA) primer that organizes QMRA tutorials. The tutorials describe functionality of a QMRA infrastructure, guide the user through software use and assessment options, provide step-by-step instructions for implementi...

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, an...

Using Integrated Environmental Modeling to Automate a Process-Based Quantitative Microbial Risk Assessment (presentation)

EPA Science Inventory

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and...

Using integrated environmental modeling to automate a process-based Quantitative Microbial Risk Assessment

USDA-ARS?s Scientific Manuscript database

Integrated Environmental Modeling (IEM) organizes multidisciplinary knowledge that explains and predicts environmental-system response to stressors. A Quantitative Microbial Risk Assessment (QMRA) is an approach integrating a range of disparate data (fate/transport, exposure, and human health effect...

A quantitative microbial risk assessment for center pivot irrigation of dairy wastewaters

USDA-ARS?s Scientific Manuscript database

In the western United States where livestock wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks from inhaling pathogens aerosolized dur...

An integrated environmental modeling framework for performing Quantitative Microbial Risk Assessments

EPA Science Inventory

Standardized methods are often used to assess the likelihood of a human-health effect from exposure to a specified hazard, and inform opinions and decisions about risk management and communication. A Quantitative Microbial Risk Assessment (QMRA) is specifically adapted to detail ...

Cultivation and Characterization of Oil-Degrading Microbes and the Environmental Controls on Hydrocarbon Biodegradation Patterns

NASA Astrophysics Data System (ADS)

Redmond, M. C.

2016-02-01

The Deepwater Horizon oil spill highlighted the ability of microbes to degrade hydrocarbons in both cold, deep water and at the warm sea surface. However, the temperature and differing hydrocarbons in the deep ocean and sea surface led to different microbial communities and biodegradation patterns. In order to develop a better understanding of the factors that control microbial community composition and biodegradation patterns, we conducted laboratory microcosm studies with seawater samples from coastal South Carolina and hydrocarbon seeps in the Gulf of Mexico, incubated with different hydrocarbons, at different temperatures, and in static or shaking incubation conditions. We analyzed microbial community composition after three weeks and used successive transfers on liquid and then solid media to isolate cultures. More rapid growth was observed at 28 degrees than 4 degrees, with hexadecane compared to benzene, cyclohexane, or crude oil, and in shaking incubations compared to static. However, we were able to successfully culture microbes under all conditions. Physiological and genetic characterization of isolated strains is ongoing, and will be combined with assessment of hydrocarbon substrate preferences and kinetics under different environmental conditions.

New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods

EPA Science Inventory

Binary sensitivity and specificity metrics are not adequate to describe the performance of quantitative microbial source tracking methods because the estimates depend on the amount of material tested and limit of detection. We introduce a new framework to compare the performance ...

Use of Quantitative Microbial Risk Assessment to Improve Interpretation of a Recreational Water Epidemiological Study

EPA Science Inventory

We conducted a supplemental water quality monitoring study and quantitative microbial risk assessment (QMRA) to complement the United States Environmental Protection Agency’s (U.S. EPA) National Epidemiological and Environmental Assessment of Recreational Water study at Boquerón ...

An integrated environmental modeling framework for performing quantitative microbial risk assessments

USDA-ARS?s Scientific Manuscript database

Standardized methods are often used to assess the likelihood of a human-health effect from exposure to a specified hazard, and inform opinions and decisions about risk management and communication. A Quantitative Microbial Risk Assessment (QMRA) is specifically adapted to detail potential human-heal...

Focal Point Theory Models for Dissecting Dynamic Duality Problems of Microbial Infections

PubMed Central

Huang, S.-H.; Zhou, W.; Jong, A.

2008-01-01

Extending along the dynamic continuum from conflict to cooperation, microbial infections always involve symbiosis (Sym) and pathogenesis (Pat). There exists a dynamic Sym-Pat duality (DSPD) in microbial infection that is the most fundamental problem in infectomics. DSPD is encoded by the genomes of both the microbes and their hosts. Three focal point (FP) theory-based game models (pure cooperative, dilemma, and pure conflict) are proposed for resolving those problems. Our health is associated with the dynamic interactions of three microbial communities (nonpathogenic microbiota (NP) (Cooperation), conditional pathogens (CP) (Dilemma), and unconditional pathogens (UP) (Conflict)) with the hosts at different health statuses. Sym and Pat can be quantitated by measuring symbiotic index (SI), which is quantitative fitness for the symbiotic partnership, and pathogenic index (PI), which is quantitative damage to the symbiotic partnership, respectively. Symbiotic point (SP), which bears analogy to FP, is a function of SI and PI. SP-converting and specific pathogen-targeting strategies can be used for the rational control of microbial infections. PMID:18350122

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

PubMed

von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

2013-10-01

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

Agreement between quantitative microbial risk assessment and epidemiology at low doses during waterborne outbreaks of protozoan disease

USDA-ARS?s Scientific Manuscript database

Quantitative microbial risk assessment (QMRA) is a valuable complement to epidemiology for understanding the health impacts of waterborne pathogens. The approach works by extrapolating available data in two ways. First, dose-response data are typically extrapolated from feeding studies, which use ...

ESTIMATION OF MICROBIAL REDUCTIVE TRANSFORMATION RATES FOR CHLORINATED BENZENES AND PHENOLS USING A QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP APPROACH

EPA Science Inventory

A set of literature data was used to derive several quantitative structure-activity relationships (QSARs) to predict the rate constants for the microbial reductive dehalogenation of chlorinated aromatics. Dechlorination rate constants for 25 chloroaromatics were corrected for th...

Influence of Dynamic Hydraulic Conditions on Nitrogen Cycling in Column Experiments

NASA Astrophysics Data System (ADS)

Gassen, Niklas; von Netzer, Frederick; Ryabenko, Evgenia; Lüders, Tillmann; Stumpp, Christine

2015-04-01

In order to improve management strategies of agricultural nitrogen input, it is of major importance to further understand which factors influence turnover processes within the nitrogen cycle. Many studies have focused on the fate of nitrate in hydrological systems, but up to date only little is known about the influence of dynamic hydraulic conditions on the fate of nitrate at the soil-groundwater interface. We conducted column experiments with natural sediment and compared a system with a fluctuating water table to systems with different water content and static conditions under the constant input of ammonia into the system. We used hydrochemical methods in order to trace nitrogen species, 15N isotope methods to get information about dominating turnover processes and microbial community analysis in order to connect hydrochemical and microbial information. We found that added ammonia was removed more effectively under dynamic hydraulic conditions than under static conditions. Furthermore, denitrification is the dominant process under saturated, static conditions, while nitrification is more important under unsaturated, static conditions. We conclude that a fluctuating water table creates hot spots where both nitrification and denitrification processes can occur spatially close to each other and therefore remove nitrogen more effectively from the system. Furthermore, the fluctuating water table enhances the exchange of solutes and triggers hot moments of solute turnover. Therefore we conclude that a fluctuating water table can amplify hot spots and trigger hot moments of nitrogen cycling.

Quantitative microbiome profiling links gut community variation to microbial load.

PubMed

Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

2017-11-23

Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

PubMed

Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment. Published by Elsevier B.V.

Effects of Static or Oscillating Dietary Crude Protein Levels on Fermentation Dynamics of Beef Cattle Diets Using a Dual-Flow Continuous Culture System

PubMed Central

Benedeti, Pedro Del Bianco; da Silva, Lorrayny Galoro; de Paula, Eduardo Marostegan; Monteiro, Hugo Fernando; Shenkoru, Teshome; Santos, Stefanie Alvarenga; Poulson, Simon Roger

2016-01-01

The objective of this study was to evaluate the effects of increasing dietary crude protein (CP) levels and also comparing the effects of static versus oscillating dietary CP on ruminal nutrient digestibility, ruminal fermentation, nitrogen (N) metabolism, and microbial efficiency in beef cattle diets using a dual-flow continuous culture system. Eight fermenters (1,223 ± 21 mL) were used in a replicated 4 x 4 Latin square design with periods lasting 12 d each (8 d for adaptation and 4 d for sampling). Dietary treatments were: 1) 10% CP, 2) 12% CP, 3) 14% CP, and 4) 10 and 14% CP diets oscillating at 48-h intervals. Experimental diets consisted of 50% orchard hay and 50% concentrate. Fermenters were fed 72 g/d and solid and liquid dilution rates were adjusted to 5.5 and 11%/h, respectively. Data were analyzed using the MIXED procedure in SAS with α = 0.05. Apparent and true ruminal digestibilities of dry matter and organic matter were not affected (P > 0.05) by increasing dietary CP, nor by oscillating dietary CP. Total volatile fatty acids concentration and molar proportions of acetate, propionate, butyrate, valerate, iso-butyrate and iso-valerate were not affected (P > 0.05) by increasing or oscillating dietary CP. Ruminal NH3-N concentration increased linearly (P < 0.01) in response to increasing dietary CP. Total N, non-ammonia N, and rumen undegraded protein flows did not differ among treatments or between oscillating dietary CP and static 12% CP. Microbial N and NH3-N flows and microbial efficiency did not differ when comparing oscillating versus static CP (P > 0.05). However, there was a quadratic effect (P < 0.05) for these variables when dietary CP was increased. These results indicate that either ruminal microorganisms do not respond to oscillating CP levels or are capable of coping with 48-h periods of undernourishment. PMID:28036405

Smoking cessation alters intestinal microbiota: insights from quantitative investigations on human fecal samples using FISH.

PubMed

Biedermann, Luc; Brülisauer, Karin; Zeitz, Jonas; Frei, Pascal; Scharl, Michael; Vavricka, Stephan R; Fried, Michael; Loessner, Martin J; Rogler, Gerhard; Schuppler, Markus

2014-09-01

There has been a dramatic increase in investigations on the potential mechanistic role of the intestinal microbiota in various diseases and factors modulating intestinal microbial composition. We recently reported on intestinal microbial shifts after smoking cessation in humans. In this study, we aimed to conduct further microbial analyses and verify our previous results obtained by pyrosequencing using a direct quantitative microbial approach. Stool samples of healthy smoking human subjects undergoing controlled smoking cessation during a 9-week observational period were analyzed and compared with 2 control groups, ongoing smoking and nonsmoking subjects. Fluorescence in situ hybridization was applied to quantify specific bacterial groups. Intestinal microbiota composition was substantially altered after smoking cessation as characterized by an increase in key representatives from the phyla of Firmicutes (Clostridium coccoides, Eubacterium rectale, and Clostridium leptum subgroup) and Actinobacteria (HGC bacteria and Bifidobacteria) as well as a decrease in Bacteroidetes (Prevotella spp. and Bacteroides spp.) and Proteobacteria (β- and γ-subgroup of Proteobacteria). As determined by fluorescence in situ hybridization, an independent direct quantitative microbial approach, we could confirm that intestinal microbiota composition in humans is influenced by smoking. The characteristics of observed microbial shifts suggest a potential mechanistic association to alterations in body weight subsequent to smoking cessation. More importantly, regarding previously described microbial hallmarks of dysbiosis in inflammatory bowel diseases, a variety of observed microbial alterations after smoking cessation deserve further consideration in view of the divergent effect of smoking on the clinical course of Crohn's disease and ulcerative colitis.

Potential of the waste from beer fermentation broth for bio-ethanol production without any additional enzyme, microbial cells and carbohydrates.

PubMed

Ha, Jung Hwan; Shah, Nasrullah; Ul-Islam, Mazhar; Park, Joong Kon

2011-08-10

The potential of the waste from beer fermentation broth (WBFB) for the production of bio-ethanol using a simultaneous saccharification and fermentation process without any extra additions of saccharification enzymes, microbial cells or carbohydrate was tested. The major microbial cells in WBFB were isolated and identified. The variations in compositions of WBFB with stock time were investigated. There was residual activity of starch hydrolyzing enzymes in WBFB. The effects of reaction modes e.g. static and shaking on bio-ethanol production were studied. After 7 days of cultivation using the supernatant of WBFB at 30 °C the ethanol concentration reached 103.8 g/L in shaking culture and 91.5 g/L in static culture. Agitation experiments conducted at a temperature-profile process in which temperature was increased from 25 to 67 °C shortened the simultaneous process time. The original WBFB was more useful than the supernatant of WBFB in getting the higher concentration of ethanol and reducing the fermentation time. From this whole study it was found that WBFB is a cheap and suitable source for bio-ethanol production. Copyright © 2011 Elsevier Inc. All rights reserved.

MECHANISMS OF MICROBIAL MOVEMENT IN SUBSURFACE MATERIALS

EPA Science Inventory

The biological factors important in the penetration of Escherichia coli through anaerobic, nutrient-saturated, Ottawa sand-packed cores were studied under static conditions. In cores saturated with galactose-peptone medium, motile strains of E. coli penetrated four times faster t...

Application of a weak magnetic field to improve microbial fuel cell performance.

PubMed

Tong, Zhong-Hua; Yu, Han-Qing; Li, Wen-Wei; Wang, Yun-Kun; Sun, Min; Liu, Xian-Wei; Sheng, Guo-Ping

2015-12-01

Microbial fuel cells (MFCs) have emerged as a promising technology for wastewater treatment with concomitant energy production but the performance is usually limited by low microbial activities. This has spurred intensive research interest for microbial enhancement. This study demonstrated an interesting stimulation effect of a static magnetic field (MF) on sludge-inoculated MFCs and explored into the mechanisms. The implementation of a 100-mT MF accelerated the reactor startup and led to increased electricity generation. Under the MF exposure, the activation loss of the MFC was decreased, but there was no increased secretion of redox mediators. Thus, the MF effect was mainly due to enhanced bioelectrochemical activities of anodic microorganisms, which are likely attributed to the oxidative stress and magnetohydrodynamic effects under an MF exposure. This work implies that weak MF may be applied as a simple and effective approach to stimulate microbial activities for various bioelectrochemical energy production and decontamination applications.

Static headspace gas chromatographic method for quantitative determination of residual solvents in pharmaceutical drug substances according to european pharmacopoeia requirements.

PubMed

Otero, Raquel; Carrera, Guillem; Dulsat, Joan Francesc; Fábregas, José Luís; Claramunt, Juan

2004-11-19

A static headspace (HS) gas chromatographic method for quantitative determination of residual solvents in a drug substance has been developed according to European Pharmacopoeia general procedure. A water-dimethylformamide mixture is proposed as sample solvent to obtain good sensitivity and recovery. The standard addition technique with internal standard quantitation was used for ethanol, tetrahydrofuran and toluene determination. Validation was performed within the requirements of ICH validation guidelines Q2A and Q2B. Selectivity was tested for 36 solvents, and system suitability requirements described in the European Pharmacopoeia were checked. Limits of detection and quantitation, precision, linearity, accuracy, intermediate precision and robustness were determined, and excellent results were obtained.

Detection of Fatty Acids from Intact Microorganisms by Molecular Beam Static Secondary Ion Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ingram, Jani Cheri; Lehman, Richard Michael; Bauer, William Francis

We report the use of a surface analysis approach, static secondary ion mass spectrometry (SIMS) equipped with a molecular (ReO4-) ion primary beam, to analyze the surface of intact microbial cells. SIMS spectra of 28 microorganisms were compared to fatty acid profiles determined by gas chromatographic analysis of transesterfied fatty acids extracted from the same organisms. The results indicate that surface bombardment using the molecular primary beam cleaved the ester linkage characteristic of bacteria at the glycerophosphate backbone of the phospholipid components of the cell membrane. This cleavage enables direct detection of the fatty acid conjugate base of intact microorganismsmore » by static SIMS. The limit of detection for this approach is approximately 107 bacterial cells/cm2. Multivariate statistical methods were applied in a graded approach to the SIMS microbial data. The results showed that the full data set could initially be statistically grouped based upon major differences in biochemical composition of the cell wall. The gram-positive bacteria were further statistically analyzed, followed by final analysis of a specific bacterial genus that was successfully grouped by species. Additionally, the use of SIMS to detect microbes on mineral surfaces is demonstrated by an analysis of Shewanella oneidensis on crushed hematite. The results of this study provide evidence for the potential of static SIMS to rapidly detect bacterial species based on ion fragments originating from cell membrane lipids directly from sample surfaces.« less

An approach to mitigating soil CO2 emission by biochemically inhibiting cellulolytic microbial populations through mediation via the medicinal herb Isatis indigotica

NASA Astrophysics Data System (ADS)

Wu, Hong-Sheng; Chen, Su-Yun; Li, Ji; Liu, Dong-Yang; Zhou, Ji; Xu, Ya; Shang, Xiao-Xia; Wei, Dong-yang; Yu, Lu-ji; Fang, Xiao-hang; Li, Shun-yi; Wang, Ke-ke

2017-06-01

Greenhouse gases (GHGs, particularly carbon dioxide (CO2)) emissions from soil under wheat production are a significant source of agricultural carbon emissions that have not been mitigated effectively. A field experiment and a static incubation study in a lab were conducted to stimulate wheat growth and investigate its potential to reduce CO2 emissions from soil through intercropping with a traditional Chinese medicinal herb called Isatis indigotica. This work was conducted by adding I. indigotica root exudates based on the quantitative real-time PCR (qPCR) analysis of the DNA copy number of the rhizosphere or bulk soil microbial populations. This addition was performed in relation to the CO2 formation by cellulolytic microorganisms (Penicillium oxalicum, fungi and Ruminococcus albus) to elucidate the microbial ecological basis for the molecular mechanism that decreases CO2 emissions from wheat fields using I. indigotica. The results showed that the panicle weight and full grains per panicle measured through intercropping with I. indigotica (NPKWR) increased by 39% and 28.6%, respectively, compared to that of the CK (NPKW). Intercropping with I. indigotica significantly decreased the CO2 emissions from soil under wheat cultivation. Compared with CK, the total CO2 emission flux during the wheat growth period in the I. indigotica (NPKWR) intercropping treatment decreased by 29.26%. The intensity of CO2 emissions per kg of harvested wheat grain declined from 7.53 kg CO2/kg grain in the NPKW (CK) treatment to 5.55 kg CO2/kg grain in the NPKWR treatment. The qPCR analysis showed that the DNA copy number of the microbial populations of cellulolytic microorganisms (P. oxalicum, fungi and R. albus) in the field rhizosphere around I. indigotica or in the bulk soil under laboratory incubation was significantly lower than that of CK. This finding indicated that root exudates from I. indigotica inhibited the activity and number of cellulolytic microbial populations, which led to decreased CO2 emissions, suggesting this plant's potential role in mitigating agricultural GHGs and in supporting agroecology.

Confirmatory and quantitative analysis of beta-lactam antibiotics in bovine kidney tissue by dispersive solid-phase extraction and liquid chromatography-tandem mass spectrometry.

PubMed

Fagerquist, Clifton K; Lightfield, Alan R; Lehotay, Steven J

2005-03-01

A simple, rapid, rugged, sensitive, and specific method for the confirmation and quantitation of 10 beta-lactam antibiotics in fortified and incurred bovine kidney tissue has been developed. The method uses a simple solvent extraction, dispersive solid-phase extraction (dispersive-SPE) cleanup, and liquid chromatography-tandem mass spectrometry (LC/MS/MS) for confirmation and quantitation. Dispersive-SPE greatly simplifies and accelerates sample cleanup and improves overall recoveries compared with conventional SPE cleanup. The beta-lactam antibiotics tested were as follows: deacetylcephapirin (an antimicrobial metabolite of cephapirin), amoxicillin, desfuroylceftiofur cysteine disulfide (DCCD, an antimicrobial metabolite of ceftiofur), ampicillin, cefazolin, penicillin G, oxacillin, cloxacillin, naficillin, and dicloxacillin. Average recoveries of fortified samples were 70% or better for all beta-lactams except DCCD, which had an average recovery of 58%. The LC/MS/MS method was able to demonstrate quantitative recoveries at established tolerance levels and provide confirmatory data for unambiguous analyte identification. The method was also tested on 30 incurred bovine kidney samples obtained from the USDA Food Safety and Inspection Service, which had previously tested the samples using the approved semiquantitative microbial assay. The results from the quantitative LC/MS/MS analysis were in general agreement with the microbial assay for 23 samples although the LC/MS/MS method was superior in that it could specifically identify which beta-lactam was present and quantitate its concentration, whereas the microbial assay could only identify the type of beta-lactam present and report a concentration with respect to the microbial inhibition of a penicillin G standard. In addition, for 6 of the 23 samples, LC/MS/MS analysis detected a penicillin and a cephalosporin beta-lactam, whereas the microbial assay detected only a penicillin beta-lactam. For samples that do not fall into the "general agreement" category, the most serious discrepancy involves two samples where the LC/MS/MS method detected a violative level of a cephalosporin beta-lactam (deacetylcephapirin) in the first sample and a possibly violative level of desfuroylceftiofur in the second, whereas the microbial assay identified the two samples as having only violative levels of a penicillin beta-lactam.

Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage▿

PubMed Central

Kock, Dagmar; Schippers, Axel

2008-01-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage.

PubMed

Kock, Dagmar; Schippers, Axel

2008-08-01

The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 10(9) cells g(-1) dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

Speckle dynamics under ergodicity breaking

NASA Astrophysics Data System (ADS)

Sdobnov, Anton; Bykov, Alexander; Molodij, Guillaume; Kalchenko, Vyacheslav; Jarvinen, Topias; Popov, Alexey; Kordas, Krisztian; Meglinski, Igor

2018-04-01

Laser speckle contrast imaging (LSCI) is a well-known and versatile approach for the non-invasive visualization of flows and microcirculation localized in turbid scattering media, including biological tissues. In most conventional implementations of LSCI the ergodic regime is typically assumed valid. However, most composite turbid scattering media, especially biological tissues, are non-ergodic, containing a mixture of dynamic and static centers of light scattering. In the current study, we examined the speckle contrast in different dynamic conditions with the aim of assessing limitations in the quantitative interpretation of speckle contrast images. Based on a simple phenomenological approach, we introduced a coefficient of speckle dynamics to quantitatively assess the ratio of the dynamic part of a scattering medium to the static one. The introduced coefficient allows one to distinguish real changes in motion from the mere appearance of static components in the field of view. As examples of systems with static/dynamic transitions, thawing and heating of Intralipid samples were studied by the LSCI approach.

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

NASA Astrophysics Data System (ADS)

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.

Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.

PubMed

Kim, Jaai; Lim, Juntaek; Lee, Changsoo

2013-12-01

Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results. Copyright © 2013 Elsevier Inc. All rights reserved.

Biofilm initiation and growth of Pseudomonas aeruginosa on 316L stainless steel in low gravity in orbital space flight

NASA Astrophysics Data System (ADS)

Todd, Paul; Pierson, Duane L.; Allen, Britt; Silverstein, JoAnn

The formation of biofilms by water microorganisms such as Pseudomonas aeruginosa in spacecraft water systems has been a matter of concern for long-duration space flight. Crewed spacecraft plumbing includes internal surfaces made of 316L stainless steel. Experiments were therefore undertaken to compare the ability of P. aeruginosa to grow in suspension, attach to stainless steel and to grow on stainless steel in low gravity on the space shuttle. Four categories of cultures were studied during two space shuttle flights (STS-69 and STS-77). Cultures on the ground were held in static horizontal or vertical cylindrical containers or were tumbled on a clinostat and activated under conditions identical to those for the flown cultures. The containers used on the ground and in flight were BioServe Space Technologies’ Fluid Processing Apparatus (FPA), an open-ended test tube with rubber septa that allows robotic addition of bacteria to culture media to initiate experiments and the addition of fixative to conclude experiments. Planktonic growth was monitored by spectrophotometry, and biofilms were characterized quantitatively by epifluorescence and scanning electron microscopy. In these experiments it was found that: (1) Planktonic growth in flown cultures was more extensive than in static cultures, as seen repeatedly in the history of space microbiology, and closely resembled the growth of tumbled cultures. (2) Conversely, the attachment of cells in flown cultures was as much as 8 times that in tumbled cultures but not significantly different from that in static horizontal and vertical cultures, consistent with the notion that flowing fluid reduces microbial attachment. (3) The final surface coverage in 8 days was the same for flown and static cultures but less by a factor of 15 in tumbled cultures, where coverage declined during the preceding 4 days. It is concluded that cell attachment to 316L stainless steel in the low gravity of orbital space flight is similar to that found in stagnant cultures at 1 x g. Research was supported by NASA contract NAGW-1197 to the University of Colorado.

49 CFR 238.203 - Static end strength.

Code of Federal Regulations, 2014 CFR

2014-10-01

... inches by 24 inches. The alternative specified in this paragraph is not applicable to a cab car or an MU... use of the equipment; and (v) A quantitative risk assessment, incorporating the design information... Equipment § 238.203 Static end strength. (a)(1) Except as further specified in this paragraph or in...

49 CFR 238.203 - Static end strength.

Code of Federal Regulations, 2013 CFR

2013-10-01

... inches by 24 inches. The alternative specified in this paragraph is not applicable to a cab car or an MU... use of the equipment; and (v) A quantitative risk assessment, incorporating the design information... Equipment § 238.203 Static end strength. (a)(1) Except as further specified in this paragraph or in...

49 CFR 238.203 - Static end strength.

Code of Federal Regulations, 2012 CFR

2012-10-01

... inches by 24 inches. The alternative specified in this paragraph is not applicable to a cab car or an MU... use of the equipment; and (v) A quantitative risk assessment, incorporating the design information... Equipment § 238.203 Static end strength. (a)(1) Except as further specified in this paragraph or in...

Quantitative comparison of the in situ microbial communities in different biomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, D.C.; Ringelberg, D.B.; Palmer, R.J.

1995-12-31

A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedlymore » documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/« less

DMPP-added nitrogen fertilizer affects soil N2O emission and microbial activity in Southern Italy

NASA Astrophysics Data System (ADS)

Vitale, Luca; De Marco, Anna; Maglione, Giuseppe; Polimeno, Franca; Di Tommasi, Paul; Magliulo, Vincenzo

2014-05-01

Arable sites contributes to global N2O emission due to massive utilization of nitrogen fertilizers. N2O derives from the biological processes such as nitrification and denitrification influenced by soil nitrogen availability. The use of nitrogen fertilizers added with nitrification inhibitors represents one among the proposed strategy to reduce soil N2O emission form arable sites. The aim of this work was to evaluate the effects of 3,4-dimethylphyrazole phosphate (DMPP), a nitrification inhibitor, on N2O emission and microbial activity of a soil cropped to potato in Southern Italy. The experiment was a randomized block design with two treatments applied and three replicates: control (C) and DMPP (Entec®, K+S Nitrogen) plots, both supplied with the same amount of ammonium nitrate. The nitrogen fertilizer was supplied in three events: at 0 Day After Sowing (DAS; 100 kg N ha-1), at 57 DAS (30 kg N ha-1), and at 71 DAS (30 kg N ha-1). Soil N2O emission was monitored by both dynamic and static chambers. Static chambers were located both on hills and furrows whereas dynamic chambers were located on furrows. Air samples were collected from chambers at different times and analysed by a gas chromatograph (SRI 8610C, Gas Chromatograph). Fluxes were estimated as a linear interpolation of N2O changes over a 30 min time. Microbial biomass and basal respiration were determined as CO2 evolution, analysed by means of an IRGA (Li6200, Licor), on 2 g of fresh soil over a 4h incubation time. Microbial biomass was determined by Substrate Induced Respiration method. Data show no statistical differences in N2O fluxes measured with either dynamic chambers between C and DMPP plots in studied period. However, after the first fertilization event, when the fertilizer was applied as 100 kg N ha-1, the average N2O fluxes measured with static chambers were higher in DMPP plots compared to C plots. In the same period, the microbial biomass significantly decreased in DMPP plots as compared to C plots, whereas an opposite trend for basal respiration was observed, thus evidencing a stressful condition for nitrifying microbial population. After 57 and 71 DAS, when fertilizer was applied as 30 kg N ha-1, the microbial biomass was similar between C and DMPP plots, whereas basal respiration resulted statistically lower in DMPP plots than C plots. During these periods, average DMPP N2O fluxes were also comparable or lower. In conclusion, our data evidence a stressful condition for soil microbes and in particular for nitrifiers when a higher DMPP quantity is supplied. On the contrary, when lower quantities of DMPP-added fertilizers are supplied (e.s. 30 kg N ha-1) effectiveness of DMPP in reducing soil N2O emission is guaranteed by reducing the nitrifiers activity without negatively affecting their growth.

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate.

PubMed

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans , and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations.

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

PubMed Central

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations. PMID:28066365

Relating Anaerobic Digestion Microbial Community and Process Function.

PubMed

Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

2015-01-01

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Quantitative exploration of the contribution of settlement, growth, dispersal and grazing to the accumulation of natural marine biofilms on antifouling and fouling-release coatings

PubMed Central

Van Mooy, Benjamin A. S.; Hmelo, Laura R.; Fredricks, Helen F.; Ossolinski, Justin E.; Pedler, Byron E.; Bogorff, Daniel J.; Smith, Peter J.S.

2014-01-01

The accumulation of microbial biofilms on ships' hulls negatively affects ships' performance and efficiency while also moderating the establishment of even more detrimental hard-fouling communities. However, there is little quantitative information on how the accumulation rate of microbial biofilms is impacted by the balance of the rates of cell settlement, in situ production (ie growth), dispersal to surrounding waters and mortality induced by grazers. These rates were quantified on test panels coated with copper-based antifouling or polymer-based fouling-release coatings by using phospholipids as molecular proxies for microbial biomass. The results confirmed the accepted modes of efficacy of these two types of coatings. In a more extensive set of experiments with only the fouling-release coatings, it was found that seasonally averaged cellular production rates were 1.5 ± 0.5 times greater than settlement and the dispersal rates were 2.7 ± 0.8 greater than grazing. The results of this study quantitatively describe the dynamic balance of processes leading to microbial biofilm accumulation on coatings designed for ships' hulls. PMID:24417212

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities. PMID:21346791

Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants.

PubMed

Sanders, Jon G; Lukasik, Piotr; Frederickson, Megan E; Russell, Jacob A; Koga, Ryuichi; Knight, Rob; Pierce, Naomi E

2017-10-01

Abundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative polymerase chain reaction as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results provide quantitative context to the potential role of bacteria in facilitating the ants' dominance of the tropical rainforest canopy, and have broad implications for the interpretation of sequence-based surveys of microbial diversity. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

SPECIES-SPECIFIC DETECTION OF HYDROCARBON UTILIZING BACTERIA. (R825810)

EPA Science Inventory

Rapid detection and quantitative assessment of specific microbial species in environmental samples is desirable for monitoring changes in ecosystems and for tracking natural or introduced microbial species during bioremediation of contaminated sites. In the interests of develo...

Fabrication of Slippery Lubricant-Infused Porous Surface for Inhibition of Microbially Influenced Corrosion.

PubMed

Wang, Peng; Zhang, Dun; Lu, Zhou; Sun, Shimei

2016-01-20

Microbially influenced corrosion (MIC) accelerates the failure of metal in a marine environment. In this research, slippery lubricant-infused porous surface (SLIPS) was designed on aluminum, and its great potential for inhibiting MIC induced by sulfate-reducing bacteria (SRB) was demonstrated in a simulated marine environment. The inhibition mechanism of SLIPS to MIC was proposed based on its effective roles in the suppression of SRB settlement and isolation effect to corrosive metabolites. The liquid-like property is demonstrated to be the major contributor to the suppression effect of SLIPS to SRB settlement. The effects of environmental factors (static and dynamic conditions) and lubricant type to SRB settlement over SLIPS were also investigated. It was indicated that the as-fabricated SLIPS can inhibit the SRB settlement in both static and dynamic marine conditions, and lubricant type presents a negligible effect on the SRB settlement. These results will provide a series of foundational data for the future practical application of SLIPS in the marine environment, and also a lubricant selecting instruction to construct SLIPS for MIC control.

Statistical differences between relative quantitative molecular fingerprints from microbial communities.

PubMed

Portillo, M C; Gonzalez, J M

2008-08-01

Molecular fingerprints of microbial communities are a common method for the analysis and comparison of environmental samples. The significance of differences between microbial community fingerprints was analyzed considering the presence of different phylotypes and their relative abundance. A method is proposed by simulating coverage of the analyzed communities as a function of sampling size applying a Cramér-von Mises statistic. Comparisons were performed by a Monte Carlo testing procedure. As an example, this procedure was used to compare several sediment samples from freshwater ponds using a relative quantitative PCR-DGGE profiling technique. The method was able to discriminate among different samples based on their molecular fingerprints, and confirmed the lack of differences between aliquots from a single sample.

Source-to-Outcome Microbial Exposure and Risk Modeling Framework

EPA Science Inventory

A Quantitative Microbial Risk Assessment (QMRA) is a computer-based data-delivery and modeling approach that integrates interdisciplinary fate/transport, exposure, and impact models and databases to characterize potential health impacts/risks due to pathogens. As such, a QMRA ex...

QUANTITATIVE RISK ASSESSMENT FOR MICROBIAL AGENTS

EPA Science Inventory

Compared to chemical risk assessment, the process for microbial agents and infectious disease is more complex because of host factors and the variety of settings in which disease transmission can occur. While the National Academy of Science has established a paradigm for performi...

mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

PubMed Central

Bodrossy, Levente; Stralis-Pavese, Nancy; Konrad-Köszler, Marianne; Weilharter, Alexandra; Reichenauer, Thomas G.; Schöfer, David; Sessitsch, Angela

2006-01-01

A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities. PMID:16461725

CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution.

PubMed

Gross, Colin A; Reddy, Chandan K; Dazzo, Frank B

2010-02-01

Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at http://cme.msu.edu/cmeias/ . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most, thereby strengthening quantitative microscopy-based approaches to advance microbial ecology in situ at individual single-cell resolution.

No significant correlation between the intensity of static stretching and subject's perception of pain.

PubMed

Lim, Wootaek; Park, Hyunju

2017-10-01

[Purpose] The purpose of this study was to determine whether the intensity of static stretching measured quantitatively is related to subjects' perception of pain. [Subjects and Methods] Sixty-eight participants were recruited. Static stretching was performed once for 30 seconds while maintaining the knee at 0° flexion and was continued to the point where pain was recognized. The intensity of stretching exerted by the practitioner was quantitatively measured by using a handheld dynamometer (HHD). A subject's pain scaled on one's perception was measured by using the visual analog scale (VAS). [Results] No significant correlation was found between the intensity of stretching and the VAS score representing the subject's pain scaled on one's perception. In this study, the most frequent VAS score was 7, and the mean VAS score was 5.57 ± 1.77. The stretching intensity measured by using a HHD ranged from 28.4 to 133.0 N (mean, 72.04 ± 22.37 N). [Conclusion] This study showed that the intensity of stretching quantitatively measured by using HHD did not correlate with the degree of pain reported by the subjects. Therefore, subjective responses cannot guarantee a consistent application of intensity.

Quantitative Metaproteomics and Activity-Based Probe Enrichment Reveals Significant Alterations in Protein Expression from a Mouse Model of Inflammatory Bowel Disease.

PubMed

Mayers, Michael D; Moon, Clara; Stupp, Gregory S; Su, Andrew I; Wolan, Dennis W

2017-02-03

Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity of the samples. We introduce two new methodologies to improve metaproteomic studies of microbiome samples. These methods include the stable isotope labeling in mammals to permit protein quantitation across two mouse cohorts as well as the application of activity-based probes to enrich and analyze both host and microbial proteins with specific functionalities. We used these technologies to study the microbiota from the adoptive T cell transfer mouse model of inflammatory bowel disease (IBD) and compare these samples to an isogenic control, thereby limiting genetic and environmental variables that influence microbiome composition. The data generated highlight quantitative alterations in both host and microbial proteins due to intestinal inflammation and corroborates the observed phylogenetic changes in bacteria that accompany IBD in humans and mouse models. The combination of isotope labeling with shotgun proteomics resulted in the total identification of 4434 protein clusters expressed in the microbial proteomic environment, 276 of which demonstrated differential abundance between control and IBD mice. Notably, application of a novel cysteine-reactive probe uncovered several microbial proteases and hydrolases overrepresented in the IBD mice. Implementation of these methods demonstrated that substantial insights into the identity and dysregulation of host and microbial proteins altered in IBD can be accomplished and can be used in the interrogation of other microbiome-related diseases.

Quantitative Relationships between Photosynthetic, Nitrogen Fixing, and Fermentative H2 Metabolism in a Photosynthetic Microbial Mat

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Albert, Daniel B.; Bebout, Brad M.; Turk, Kendra A.; DesMarais, David J.

2004-01-01

The ultimate potential of any microbial ecosystem to contribute chemically to its environment - and therefore, to impact planetary biogeochemistry or to generate recognizable biosignatures - depends not only on the individual metabolic capabilities of constituent organisms, but also on how those capabilities are expressed through interactions with neighboring organisms. This is particularly important for microbial mats, which compress an extremely broad range of metabolic potential into a small and dynamic system. H2 participates in many of these metabolic processes, including the major elemental cycling processes of photosynthesis, nitrogen fixation, sulfate reduction, and fermentation, and may therefore serve as a mediator of microbial interactions within the mat system. Collectively, the requirements of energy, electron transfer, and biomass element stoichiometry suggest quantitative relationships among the major element cycling processes, as regards H2 metabolism We determined experimentally the major contributions to 32 cycling in hypersaline microbial mats from Baja California, Mexico, and compared them to predicted relationships. Fermentation under dark, anoxic conditions is quantitatively the most important mechanism of H2 production, consistent with expectations for non-heterocystous mats such as those under study. Up to 16% of reducing equivalents fixed by photosynthesis during the day may be released by this mechanism. The direct contribution of nitrogen fixation to H2 production is small in comparison, but this process may indirectly stimulate substantial H2 generation, by requiring higher rates of fermentation. Sulfate reduction, aerobic consumption, diffusive and ebulitive loss, and possibly H2-based photoreduction of CO2 serve as the principal H2 sinks. Collectively, these processes interact to create an orders-of-magnitude daily variation in H2 concentrations and fluxes, and thereby in the oxidation-reduction potential that is imposed on microbial processes occuring within the mat matrix.

[Determination of sugars, organic acids and alcohols in microbial consortium fermentation broth from cellulose using high performance liquid chromatography].

PubMed

Jiang, Yan; Fan, Guifang; Du, Ran; Li, Peipei; Jiang, Li

2015-08-01

A high performance liquid chromatographic method was established for the determination of metabolites (sugars, organic acids and alcohols) in microbial consortium fermentation broth from cellulose. Sulfate was first added in the samples to precipitate calcium ions in microbial consortium culture medium and lower the pH of the solution to avoid the dissociation of organic acids, then the filtrates were effectively separated using high performance liquid chromatography. Cellobiose, glucose, ethanol, butanol, glycerol, acetic acid and butyric acid were quantitatively analyzed. The detection limits were in the range of 0.10-2.00 mg/L. The linear correlation coefficients were greater than 0.999 6 in the range of 0.020 to 1.000 g/L. The recoveries were in the range of 85.41%-115.60% with the relative standard deviations of 0.22% -4.62% (n = 6). This method is accurate for the quantitative analysis of the alcohols, organic acids and saccharides in microbial consortium fermentation broth from cellulose.

Heat and Mass Transfer Measurements for Tray-Fermented Fungal Products

NASA Astrophysics Data System (ADS)

Jou, R.-Y.; Lo, C.-T.

2011-01-01

In this study, heat and mass transfer in static tray fermentation, which is widely used in solid-state fermentation (SSF) to produce fungal products, such as enzymes or koji, is investigated. Specifically, kinetic models of transport phenomena in the whole-tray chamber are emphasized. The effects of temperature, moisture, and humidity on microbial growth in large-scale static tray fermentation are essential to scale-up SSF and achieve uniform fermentation. In addition, heat and mass transfer of static tray fermentation of Trichoderma fungi with two tray setups—traditional linen coverings and stacks in a temperature-humidity chamber is examined. In both these setups, the following factors of fermentation were measured: air velocity, air temperature, illumination, pH, carbon dioxide (CO2) concentration, and substrate temperature, and the effects of bed height, moisture of substrate, and relative humidity of air are studied. A thin (1 cm) bed at 28 °C and 95 % relative humidity is found to be optimum. Furthermore, mixing was essential for achieving uniform fermentation of Trichoderma fungi. This study has important applications in large-scale static tray fermentation of fungi.

Investigating the Magnetic Interaction with Geomag and Tracker Video Analysis: Static Equilibrium and Anharmonic Dynamics

ERIC Educational Resources Information Center

Onorato, P.; Mascheretti, P.; DeAmbrosis, A.

2012-01-01

In this paper, we describe how simple experiments realizable by using easily found and low-cost materials allow students to explore quantitatively the magnetic interaction thanks to the help of an Open Source Physics tool, the Tracker Video Analysis software. The static equilibrium of a "column" of permanents magnets is carefully investigated by…

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

DOE PAGES

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

2016-11-28

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes producemore » chemically diverse, stable SOM. As a result, we show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.« less

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes producemore » chemically diverse, stable SOM. As a result, we show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.« less

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

NASA Astrophysics Data System (ADS)

Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart

2016-11-01

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls.

PubMed

Kallenbach, Cynthia M; Frey, Serita D; Grandy, A Stuart

2016-11-28

Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

PubMed Central

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

How to Study Biofilms after Microbial Colonization of Materials Used in Orthopaedic Implants.

PubMed

Drago, Lorenzo; Agrappi, Serse; Bortolin, Monica; Toscano, Marco; Romanò, Carlo Luca; De Vecchi, Elena

2016-02-26

Over the years, various techniques have been proposed for the quantitative evaluation of microbial biofilms. Spectrophotometry after crystal violet staining is a widespread method for biofilm evaluation, but several data indicate that it does not guarantee a good specificity, although it is rather easy to use and cost saving. Confocal laser microscopy is one of the most sensitive and specific tools to study biofilms, and it is largely used for research. However, in some cases, no quantitative measurement of the matrix thickness or of the amount of embedded microorganisms has been performed, due to limitation in availability of dedicated software. For this reason, we have developed a protocol to evaluate the microbial biofilm formed on sandblasted titanium used for orthopaedic implants, that allows measurement of biomass volume and the amount of included cells. Results indicate good reproducibility in terms of measurement of biomass and microbial cells. Moreover, this protocol has proved to be applicable for evaluation of the efficacy of different anti-biofilm treatments used in the orthopaedic setting. Summing up, the protocol here described is a valid and inexpensive method for the study of microbial biofilm on prosthetic implant materials.

Abundance and diversity of microbial inhabitants in European spacecraft-associated clean rooms.

PubMed

Stieglmeier, Michaela; Rettberg, Petra; Barczyk, Simon; Bohmeier, Maria; Pukall, Rüdiger; Wirth, Reinhard; Moissl-Eichinger, Christine

2012-06-01

The determination of the microbial load of a spacecraft en route to interesting extraterrestrial environments is mandatory and currently based on the culturable, heat-shock-surviving portion of microbial contaminants. Our study compared these classical bioburden measurements as required by NASA's and ESA's guidelines for the microbial examination of flight hardware, with molecular analysis methods (16S rRNA gene cloning and quantitative PCR) to further develop our understanding of the diversity and abundance of the microbial communities of spacecraft-associated clean rooms. Three samplings of the Herschel Space Observatory and its surrounding clean rooms were performed in two different European facilities. Molecular analyses detected a broad diversity of microbes typically found in the human microbiome with three bacterial genera (Staphylococcus, Propionibacterium, and Brevundimonas) common to all three locations. Bioburden measurements revealed a low, but heterogeneous, abundance of spore-forming and other heat-resistant microorganisms. Total cell numbers estimated by quantitative real-time PCR were typically 3 orders of magnitude greater than those determined by viable counts, which indicates a tendency for traditional methods to underestimate the extent of clean room bioburden. Furthermore, the molecular methods allowed the detection of a much broader diversity than traditional culture-based methods.

Using Facebook as a LMS?

ERIC Educational Resources Information Center

Arabacioglu, Taner; Akar-Vural, Ruken

2014-01-01

The main purpose of this research was to compare the communication media according to effective teaching. For this purpose, in the research, the mixed method, including quantitative and qualitative data collecting techniques, was applied. For the quantitative part of the research, the static group comparison design was implemented as one of the…

Test–retest repeatability of human speech biomarkers from static and real-time dynamic magnetic resonance imaging

PubMed Central

Töger, Johannes; Sorensen, Tanner; Somandepalli, Krishna; Toutios, Asterios; Lingala, Sajan Goud; Narayanan, Shrikanth; Nayak, Krishna

2017-01-01

Static anatomical and real-time dynamic magnetic resonance imaging (RT-MRI) of the upper airway is a valuable method for studying speech production in research and clinical settings. The test–retest repeatability of quantitative imaging biomarkers is an important parameter, since it limits the effect sizes and intragroup differences that can be studied. Therefore, this study aims to present a framework for determining the test–retest repeatability of quantitative speech biomarkers from static MRI and RT-MRI, and apply the framework to healthy volunteers. Subjects (n = 8, 4 females, 4 males) are imaged in two scans on the same day, including static images and dynamic RT-MRI of speech tasks. The inter-study agreement is quantified using intraclass correlation coefficient (ICC) and mean within-subject standard deviation (σe). Inter-study agreement is strong to very strong for static measures (ICC: min/median/max 0.71/0.89/0.98, σe: 0.90/2.20/6.72 mm), poor to strong for dynamic RT-MRI measures of articulator motion range (ICC: 0.26/0.75/0.90, σe: 1.6/2.5/3.6 mm), and poor to very strong for velocities (ICC: 0.21/0.56/0.93, σe: 2.2/4.4/16.7 cm/s). In conclusion, this study characterizes repeatability of static and dynamic MRI-derived speech biomarkers using state-of-the-art imaging. The introduced framework can be used to guide future development of speech biomarkers. Test–retest MRI data are provided free for research use. PMID:28599561

Quantitative Analysis of Electrochemical and Electrode Stability with Low Self-Discharge Lithium-Sulfur Batteries

DOE PAGES

Chung, Sheng-Heng; Han, Pauline; Manthiram, Arumugam

2017-06-07

The viability of employing high-capacity sulfur cathodes in building high-energy-density lithium-sulfur batteries is limited by rapid self-discharge, short shelf life, and severe structural degradation during cell resting (static instability). Unfortunately, the static instability has largely been ignored in the literature. We present in this letter a longterm self-discharge study by quantitatively analyzing the control lithium-sulfur batteries with a conventional cathode configuration, which provides meaningful insights into the cathode failure mechanisms during resting. Lastly, utilizing the understanding obtained with the control cells, we design and present low self-discharge (LSD) lithium-sulfur batteries for investigating the long-term self-discharge effect and electrode stability.

Quantitative Analysis of Electrochemical and Electrode Stability with Low Self-Discharge Lithium-Sulfur Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, Sheng-Heng; Han, Pauline; Manthiram, Arumugam

The viability of employing high-capacity sulfur cathodes in building high-energy-density lithium-sulfur batteries is limited by rapid self-discharge, short shelf life, and severe structural degradation during cell resting (static instability). Unfortunately, the static instability has largely been ignored in the literature. We present in this letter a longterm self-discharge study by quantitatively analyzing the control lithium-sulfur batteries with a conventional cathode configuration, which provides meaningful insights into the cathode failure mechanisms during resting. Lastly, utilizing the understanding obtained with the control cells, we design and present low self-discharge (LSD) lithium-sulfur batteries for investigating the long-term self-discharge effect and electrode stability.

Interactions Between Mineral Surfaces, Substrates, Enzymes, and Microbes Result in Hysteretic Temperature Sensitivities and Microbial Carbon Use Efficiencies and Weaker Predicted Carbon-Climate Feedbacks

NASA Astrophysics Data System (ADS)

Riley, W. J.; Tang, J.

2014-12-01

We hypothesize that the large observed variability in decomposition temperature sensitivity and carbon use efficiency arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. To test this hypothesis, we developed a numerical model that integrates the Dynamic Energy Budget concept for microbial physiology, microbial trait-based community structure and competition, process-specific thermodynamically ­­based temperature sensitivity, a non-linear mineral sorption isotherm, and enzyme dynamics. We show, because mineral surfaces interact with substrates, enzymes, and microbes, both temperature sensitivity and microbial carbon use efficiency are hysteretic and highly variable. Further, by mimicking the traditional approach to interpreting soil incubation observations, we demonstrate that the conventional labile and recalcitrant substrate characterization for temperature sensitivity is flawed. In a 4 K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker carbon-climate feedbacks than did the static temperature sensitivity and carbon use efficiency model when forced with yearly, daily, and hourly variable temperatures. These results imply that current earth system models likely over-estimate the response of soil carbon stocks to global warming.

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

PubMed

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Comparative Ecology of H2 Cycling in Organotrophic and Phototrophic Ecosystems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Bebout, Brad M.; Martens, Christopher S.; DesMarais, David J.; DeVincenzi, Don (Technical Monitor)

2001-01-01

The simple biochemistry of H2 is critical to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. The sensitivity of these many processes to H2 can be described quantitatively, at a basic thermodynamic level. This shared dependence on H2 may provide a means for interpreting the ecology and system-level biogeochemistry of widely variant microbial ecosystems on a common (and quantitative) level. Understanding the factors that control H2 itself is a critical prerequisite. Here, we examine two ecosystems that vary widely with respect to H2 cycling. In anoxic, 'organotrophic' sediments from Cape Lookout Bight (North Carolina, USA), H2 partial pressures are strictly maintained at low, steady-state levels by H2-consuming organisms, in a fashion that can be quantitatively predicted by simple thermodynamic calculations. In phototrophic microbial mats from Baja, Mexico, H2 partial pressures are instead controlled by the activity of light-sensitive H2-producing organisms. In consequence, H2 partial pressures within the system fluctuate by orders of magnitude on hour-long time scales. The differences in H2 cycling subsequently impact H2-sensitive microbial processes, such as methanogenesis. For example, the presence of sulfate in the organotrophic system always yielded low levels of H2 that were inhibitory to methanogenesis; however, the elevated levels of H2 in the phototrophic system favored methane production at significant levels, even in the presence of high sulfate concentrations. The myriad of other H2-sensitive microbial processes are expected to exhibit similar behavior.

Quantitative Microbial Risk Assessment Tutorial: Publishing a Microbial Density Time Series as a Txt File

EPA Science Inventory

A SARA Timeseries Utility supports analysis and management of time-varying environmental data including listing, graphing, computing statistics, computing meteorological data and saving in a WDM or text file. File formats supported include WDM, HSPF Binary (.hbn), USGS RDB, and T...

An Open-Ended Investigative Microbial Ecology Laboratory for Introductory Biology

ERIC Educational Resources Information Center

Jones-Held, Susan; Paoletti, Robert; Glick, David; Held, Michael E.

2010-01-01

In this article we describe a multi-week investigative laboratory in microbial ecology/diversity and nitrogen cycling that we have used in our introductory biology course. This module encourages active student involvement in experimental design, using the scientific literature and quantitative analysis of large data sets. Students analyze soil…

Development and Evaluation of a Quantitative PCR Assay Targeting Sandhill Crane (Grus canadensis) Fecal Pollution

EPA Science Inventory

While the microbial water quality in the Platte River is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. Here we characterized microbial populations in crane feces using phylogenetic analysis of 16S rRNA gen...

Review of pathogen treatment reductions for onsite non-potable reuse of alternative source waters

EPA Science Inventory

Communities face a challenge when implementing onsite reuse of collected waters for non-potable purposes given the lack of national microbial standards. Quantitative Microbial Risk Assessment (QMRA) can be used to predict the pathogen risks associated with the non-potable reuse o...

Impact of a static magnetic field on the electricity production of Shewanella-inoculated microbial fuel cells.

PubMed

Li, Wen-Wei; Sheng, Guo-Ping; Liu, Xian-Wei; Cai, Pei-Jie; Sun, Min; Xiao, Xiang; Wang, Yun-Kun; Tong, Zhong-Hua; Dong, Fang; Yu, Han-Qing

2011-06-15

The electricity production of Shewanella-inoculated microbial fuel cells (MFCs) under magnetic field (MF) exposure was investigated in different reactor systems. The persistency of the MF effect and the influences of MF intensity and direction on MFC performance were also studied. Application of a 100-mT static MF to the MFCs improved electricity production considerably, with an increase in the maximum voltage by 20-27% in both single- and two-chamber MFCs, while a more conspicuous improvement in the electricity generation was observed in a three-electrode cell. The MF effects were found to be immediate and reversible, and adverse effects seemed to occur when the MF was suddenly removed. The medium components analysis demonstrated that the application of MF led to an enhanced bioelectrochemical activity of Shewanella, and no significant promotion in mediator secretion was found. The improvement in the electricity production of MFCs under MF was mainly attributed to the enhanced bioelectrochemical activity, possibly through the oxidative stress mechanism. An accelerated cell growth under MF might also contribute to the enhanced substrate degradation and power generation. Copyright © 2010 Elsevier B.V. All rights reserved.

Simulations of Carnival Rides and Rube Goldberg Machines for the Visualization of Concepts of Statics and Dynamics

ERIC Educational Resources Information Center

Howard, William; Williams, Richard; Yao, Jason

2010-01-01

Solid modeling is widely used as a teaching tool in summer activities with high school students. The addition of motion analysis allows concepts from statics and dynamics to be introduced to students in both qualitative and quantitative ways. Two sets of solid modeling projects--carnival rides and Rube Goldberg machines--are shown to allow the…

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microbial ecology that can play a role in animal health and productivity, but the magnitude of these changes remains unknown. The objective of this study was ...

Microbial response to modified precipitation patterns in tallgrass prairie soil: molecular mechanisms, activity rates and organic matter dynamics

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; David, M.; Bottomley, P.; Hettich, R. L.; Jansson, J.; Jumpponen, A.; Rice, C. W.; Tringe, S.; VerBerkmoes, N. C.; Myrold, D.

2011-12-01

A significant amount of carbon (C) is processed and stored in prairie soils: grasslands cover 6.1-7.4% of the earth's land surface and hold 7.3-11.4% of global soil C. Global change models predict that the future precipitation regime across the North American Great Plains will entail less frequent but larger rainfall events. The response of prairie soil microbial C processing and allocation to this scenario of higher hydrologic variability is not known, but will be a key determiner of the future capacity for prairie soil C sequestration. We are approaching this problem by assessing soil microbial function (respiration, C utilization efficiency, extracellular enzyme activity) and molecular indicators of dominant C allocation pathways (soil transcriptome, proteome and metabolome) under ambient and experimentally modified precipitation regimes. The rainfall manipulation plots (RaMPs) at the Konza Prairie Long-Term Ecological Research (LTER) site in eastern Kansas, USA is a replicated field manipulation of the magnitude and frequency of natural precipitation that was established in 1998. We collected soil before, during and after a rainfall event in both ambient and modified precipitation treatments and measured the microbial response. Microbial respiration doubled in both treatments during the water addition, and cellobiohydrolase enzyme potential activity (a catalyst of cellulose hydrolysis) increased slightly, but no significant effect of altered precipitation treatment has emerged. The fungal and bacterial ribosomal gene composition was also similar between precipitation treatments. Although pools of genes and extracellular enzymes may be relatively static during short-term dynamic conditions, transcript and intracellular protein abundances may be more indicative of the active microbial metabolic response to rapid shifts in soil moisture. Thus, analysis of transcript and protein composition is underway. In addition, we have implemented a series of lab experiments to optimize and link transcript and protein recovery and analysis procedures using the model soil bacterium Arthrobacter chlorophenicolus strain A6 (ArtchA6). Konza prairie soil was inoculated with ArchA6 and incubated for 72 h with no supplemental C, with acetate or with 4-chlorophenol (a xenobiotic compound that ArtchA6 can utilize as its sole C source), then RNA and protein were extracted from the soil. Quantitatively representative recovery of ArtchA6 genes, rRNA, mRNA and protein was successful. The ratio of ArtchA6 isocitrate lyase (icl, indicative of 2-C metabolism) to succinyl CoA synthetase (suCAB, indicative of total respiratory activity) transcript was highest in soils amended with acetate. Proteomic signatures were distinct in soils with different supplemental C sources. This experiment confirms our capability of recovering transcript and protein from the study soil and of identifying the functional molecules representative of distinct C metabolism pathways.

Comparison of whole-cell fatty acid (MIDI) or phospholipid fatty acid (PLFA) extractants as biomarkers to profile soil microbial communities.

PubMed

Fernandes, Marcelo F; Saxena, Jyotisna; Dick, Richard P

2013-07-01

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.

Investigations into the metabolic diversity of microorganisms as part of microbial diversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leadbetter, Jared

DOE funds supported a key portion of the MBL Microbial Diversity (Woods Hole) program across 6 complete summers. The initial 4 years of the funded period were overseen by two co-Directors, Daniel Buckley (Cornell) and Steve Zinder (Cornell), who then completed their term. The final 2 summers were overseen by 2 new co-Directors, Jared R. Leadbetter (Caltech) and Dianne Newman (Caltech). The 6 funded summer iterations of the course included the incorporation of new themes such as single cell approaches applied to natural microbial communities (cell separation and sorting, genome amplification from single cells, and the use of Nano-SIMS tomore » examine assimilation of carbon and nitrogen from isotopically labeled substrates into single cells), genetics and genomics on bacteria freshly isolated during the course of the programs, quantitative systems biology, and modern quantitative light microscopy.« less

Prophylactic stretching does not reduce cramp susceptibility.

PubMed

Miller, Kevin C; Harsen, James D; Long, Blaine C

2018-03-01

Some clinicians advocate stretching to prevent muscle cramps. It is unknown whether static or proprioceptive neuromuscular facilitation (PNF) stretching increases cramp threshold frequency (TF c ), a quantitative measure of cramp susceptibility. Fifteen individuals completed this randomized, counterbalanced, cross-over study. We measured passive hallux range of motion (ROM) and then performed 3 minutes of either static stretching, PNF stretching (hold-relax-with agonist contraction), or no stretching. ROM was reassessed and TF c was measured. PNF stretching increased hallux extension (pre-PNF 81 ± 11°, post-PNF 90 ± 10°; P < 0.05) but not hallux flexion (pre-PNF 40 ± 7°, post-PNF 40 ± 7°; P > 0.05). Static stretching increased hallux extension (pre-static 80 ± 11°, post-static 88 ± 9°; P < 0.05) but not hallux flexion (pre-static 38 ± 9°, post-static 39 ± 8°; P > 0.05). No ROM changes occurred with no stretching (P > 0.05). TF c was unaffected by stretching (no stretching 18 ± 7 Hz, PNF 16 ± 4 Hz, static 16 ± 5 Hz; P = 0.37). Static and PNF stretching increased hallux extension, but neither increased TF c . Acute stretching may not prevent muscle cramping. Muscle Nerve 57: 473-477, 2018. © 2017 Wiley Periodicals, Inc.

Quantitative phylogenetic assessment of microbial communities in diverse environments.

PubMed

von Mering, C; Hugenholtz, P; Raes, J; Tringe, S G; Doerks, T; Jensen, L J; Ward, N; Bork, P

2007-02-23

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.

Quantitative Microbial Risk Assessment Tutorial: Navigate the SDMPB and Identify an 8-digit HUC of Interest

EPA Science Inventory

This tutorial reviews some of the screens, icons, and basic functions of the SDMProjectBuilder (SDMPB) that allow a user to identify a watershed of interest that can be used to choose a pour point or 12-digit HUC (HUC-12) for a microbial assessment. It demonstrates how to identif...

High-throughput screening to identify selective inhibitors of microbial sulfate reduction (and beyond)

NASA Astrophysics Data System (ADS)

Carlson, H. K.; Coates, J. D.; Deutschbauer, A. M.

2015-12-01

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive and corrosive. Current strategies to selectively inhibit sulfidogenesis are based on non-specific biocide treatments, bio-competitive exclusion by alternative electron acceptors or sulfate-analogs which are competitive inhibitors or futile/alternative substrates of the sulfate reduction pathway. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to target SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Once inhibitor selectivity is defined, high-throughput characterization of microbial community structure across compound gradients and identification of fitness determinants using isolate bar-coded transposon mutant libraries can give insights into the genetic mechanisms whereby compounds structure microbial communities. The high-throughput (HT) approach we present can be readily applied to target SRM in diverse environments and more broadly, could be used to identify and quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant for engineering environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

A combined static-dynamic single-dose imaging protocol to compare quantitative dynamic SPECT with static conventional SPECT.

PubMed

Sciammarella, Maria; Shrestha, Uttam M; Seo, Youngho; Gullberg, Grant T; Botvinick, Elias H

2017-08-03

SPECT myocardial perfusion imaging (MPI) is a clinical mainstay that is typically performed with static imaging protocols and visually or semi-quantitatively assessed for perfusion defects based upon the relative intensity of myocardial regions. Dynamic cardiac SPECT presents a new imaging technique based on time-varying information of radiotracer distribution, which permits the evaluation of regional myocardial blood flow (MBF) and coronary flow reserve (CFR). In this work, a preliminary feasibility study was conducted in a small patient sample designed to implement a unique combined static-dynamic single-dose one-day visit imaging protocol to compare quantitative dynamic SPECT with static conventional SPECT for improving the diagnosis of coronary artery disease (CAD). Fifteen patients (11 males, four females, mean age 71 ± 9 years) were enrolled for a combined dynamic and static SPECT (Infinia Hawkeye 4, GE Healthcare) imaging protocol with a single dose of 99m Tc-tetrofosmin administered at rest and a single dose administered at stress in a one-day visit. Out of 15 patients, eleven had selective coronary angiography (SCA), 8 within 6 months and the rest within 24 months of SPECT imaging, without intervening symptoms or interventions. The extent and severity of perfusion defects in each myocardial region was graded visually. Dynamically acquired data were also used to estimate the MBF and CFR. Both visually graded images and estimated CFR were tested against SCA as a reference to evaluate the validity of the methods. Overall, conventional static SPECT was normal in ten patients and abnormal in five patients, dynamic SPECT was normal in 12 patients and abnormal in three patients, and CFR from dynamic SPECT was normal in nine patients and abnormal in six patients. Among those 11 patients with SCA, conventional SPECT was normal in 5, 3 with documented CAD on SCA with an overall accuracy of 64%, sensitivity of 40% and specificity of 83%. Dynamic SPECT image analysis also produced a similar accuracy, sensitivity, and specificity. CFR was normal in 6, each with CAD on SCA with an overall accuracy of 91%, sensitivity of 80%, and specificity of 100%. The mean CFR was significantly lower for SCA detected abnormal than for normal patients (3.86±1.06 vs 1.94±0. 0.67, P < 0.001). The visually assessed image findings in static and dynamic SPECT are subjective, and may not reflect direct physiologic measures of coronary lesion based on SCA. The CFR measured with dynamic SPECT is fully objective, with better sensitivity and specificity, available only with the data generated from the dynamic SPECT method.

Quantitative inhibition of soil C and N cycling by ectomycorrhizal fungi under field condition

NASA Astrophysics Data System (ADS)

Averill, C.; Hawkes, C.

2014-12-01

Ectomycorrhizal (ECM) ecosystems store more carbon than non-ectomycorrhizal ecosystems at global scale. Recent theoretical and empirical work suggests the presence of ECM fungi allows plants to compete directly with decomposers for soil nitrogen (N) via exo-enzyme synthesis. Experimental ECM exclusion often results in a release from competition of saprotrophic decomposers, allowing for increased C-degrading enzyme production, increased microbial biomass, and eventually declines in soil C stocks. Our knowledge of this phenomenon is limited, however, to the presence or absence of ECM fungi. It remains unknown if competitive repression of saprotrophic microbes and soil C cycling by ECM fungi varies with ECM abundance. This is particularly relevant to global change experiments when manipulations alter plant C allocation to ECM symbionts. To test if variation in ECM abundance alters the competitive inhibition of saprotrophic soil microbes (quantitative inhibition) we established experimental ECM exclusion treatments along an ECM abundance gradient. We dug trenches to experimentally exclude ECM fungi, allowing us to test for competitive release of soil saprotrophs from competition. To control for disturbance we placed in-growth bags both inside and outside of trenches. Consistent with the quantitative inhibition hypothesis, sites with more ECM fungi had significantly less microbial biomass per unit soil C and lower rates of N mineralization. Consistent with a release from competition, C-degrading enzyme activities were higher and gross proteolytic rates were lower per unit microbial biomass inside compared to outside trenches. We interpret this to reflect increased microbial investment in C-acquisition and decreased investment in N-acquisition in the absence of ECM fungi. Furthermore, the increase in C-degrading enzymes per unit microbial biomass was significantly greater in sites with the most abundant ECM fungi. Based on these results, ECM-saprotroph competition does appear to slow soil C cycling and the effect is quantitative. Soil C cycling is at least partly controlled by interactions between ECM fungi and soil saprotrophs. Environmental change that alters ECM abundance may thus alter soil C stocks by ameliorating or exacerbating plant-decomposer competition for nitrogen.

Effect of static magnetic field on electricity production and wastewater treatment in microbial fuel cells.

PubMed

Tao, Qinqin; Zhou, Shaoqi

2014-12-01

The effect of a magnetic field (MF) on electricity production and wastewater treatment in two-chamber microbial fuel cells (MFCs) has been investigated. Electricity production capacity could be improved by the application of a low-intensity static MF. When a MF of 50 mT was applied to MFCs, the maximum voltage, total phosphorus (TP) removal efficiency, and chemical oxygen demand (COD) removal efficiency increased from 523 ± 2 to 553 ± 2 mV, ∼93 to ∼96 %, and ∼80 to >90 %, respectively, while the start-up time and coulombic efficiency decreased from 16 to 10 days and ∼50 to ∼43 %, respectively. The MF effects were immediate, reversible, and not long lasting, and negative effects on electricity generation and COD removal seemed to occur after the MF was removed. The start-up and voltage output were less affected by the MF direction. Nitrogen compounds in magnetic MFCs were nitrified more thoroughly; furthermore, a higher proportion of electrochemically inactive microorganisms were found in magnetic systems. TP was effectively removed by the co-effects of microbe absorption and chemical precipitation. Chemical precipitates were analyzed by a scanning electron microscope capable of energy-dispersive spectroscopy (SEM-EDS) to be a mixture of phosphate, carbonate, and hydroxyl compounds.

Microbes a Tool for the Remediation of Organotin Pollution Determined by Static Headspace Gas Chromatography-Mass Spectrometry.

PubMed

Finnegan, Christopher; Ryan, David; Enright, Anne-Marie; Garcia-Cabellos, Guiomar

2018-03-10

Tributyltin (TBT) is one of the most toxic anthropogenic compounds introduced into the marine environment. Despite its global ban in 2008, TBT is still a problem of great concern due to its high affinity for particulate matter, providing a direct and potentially persistent route of entry into benthic sediments. Bioremediation strategies may constitute an alternative approach to conventional physicochemical methods, benefiting from the microorganism's potential to metabolize anthropogenic compounds. In this work, a simple, precise and accurate static headspace gas chromatography method was developed to investigate the ability of TBT degrading microbes in sedimentary microcosms over a period of 120 days. The proposed method was validated for linearity, repeatability, accuracy, specificity, limit of detection and limit of quantification. The method was subsequently successfully applied for the detection and quantification of TBT and degradation compounds in sediment samples on day 0, 30, 60, 90 and 120 of the experiment employing the principles of green chemistry. On day 120 the concentration of TBT remaining in the microcosms ranged between 91.91 ng/g wet wt for the least effective microbial inoculant to 52.73 ng/g wet wt for the most effective microbial inoculant from a starting concentration of 100 ng/g wet wt.

Effect of mixing during fermentation in yogurt manufacturing.

PubMed

Aguirre-Ezkauriatza, E J; Galarza-González, M G; Uribe-Bujanda, A I; Ríos-Licea, M; López-Pacheco, F; Hernández-Brenes, C M; Alvarez, M M

2008-12-01

In traditional yogurt manufacturing, the yogurt is not agitated during fermentation. However, stirring could be beneficial, particularly for improving heat and mass transport across the fermentation tank. In this contribution, we studied the effect of low-speed agitation during fermentation on process time, acidity profile, and microbial dynamics during yogurt fermentation in 2 laboratory-scale fermenters (3 and 5 L) with different heat-transfer characteristics. Lactobacillus bulgaricus and Streptococcus thermophilus were used as fermenting bacteria. Curves of pH, lactic acid concentration, lactose concentration, and bacterial population profiles during fermentation are presented for static and low-agitation conditions during fermentation. At low-inoculum conditions, agitation reduced the processing time by shortening the lag phase. However, mixing did not modify the duration or the shape of the pH profiles during the exponential phase. In fermentors with poor heat-transfer characteristics, important differences in microbial dynamics were observed between the agitated and nonagitated fermentation experiments; that is, agitation significantly increased the observable specific growth rate and the final microbial count of L. bulgaricus.

Rapid and potentially portable detection and quantification technologies for foodborne pathogens

USDA-ARS?s Scientific Manuscript database

Introduction Traditional microbial culture methods are able to detect and identify a single specific bacterium, but may require days or weeks and typically do not produce quantitative data. The quest for faster, quantitative results has spurred development of “rapid methods” which usually employ bio...

EVALUATION OF RAPID DNA EXTRACTION PROCEDURES FOR THE QUANTITATIVE DETECTION OF FUNGAL CELLS USING REAL TIME PCR ANALYSIS

EPA Science Inventory

The ease and rapidity of quantitative DNA sequence detection by real-time PCR instruments promises to make their use increasingly common for the microbial analysis many different types of environmental samples. To fully exploit the capabilities of these instruments, correspondin...

Quantitative Microbial Risk Assessment Tutorial - Navigate the SDMPB and Identify an 8-digit HUC of Interest - Updated 2017

EPA Science Inventory

This tutorial reviews some of the screens, icons, and basic functions of the SDMProjectBuilder (SDMPB) that allow a user to identify an 8-digit HUC (HUC-8) of interest from which a pour point or 12-digit HUC (HUC-12) can be chosen for a microbial assessment. It demonstrates how t...

Systematic expansion in the order parameter for replica theory of the dynamical glass transition.

PubMed

Jacquin, Hugo; Zamponi, Francesco

2013-03-28

It has been shown recently that predictions from mode-coupling theory for the glass transition of hard-spheres become increasingly bad when dimensionality increases, whereas replica theory predicts a correct scaling. Nevertheless if one focuses on the regime around the dynamical transition in three dimensions, mode-coupling results are far more convincing than replica theory predictions. It seems thus necessary to reconcile the two theoretic approaches in order to obtain a theory that interpolates between low-dimensional, mode-coupling results, and "mean-field" results from replica theory. Even though quantitative results for the dynamical transition issued from replica theory are not accurate in low dimensions, two different approximation schemes--small cage expansion and replicated hyper-netted-chain (RHNC)--provide the correct qualitative picture for the transition, namely, a discontinuous jump of a static order parameter from zero to a finite value. The purpose of this work is to develop a systematic expansion around the RHNC result in powers of the static order parameter, and to calculate the first correction in this expansion. Interestingly, this correction involves the static three-body correlations of the liquid. More importantly, we separately demonstrate that higher order terms in the expansion are quantitatively relevant at the transition, and that the usual mode-coupling kernel, involving two-body direct correlation functions of the liquid, cannot be recovered from static computations.

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology.

PubMed

Smith, Cindy J; Osborn, A Mark

2009-01-01

Quantitative PCR (Q-PCR or real-time PCR) approaches are now widely applied in microbial ecology to quantify the abundance and expression of taxonomic and functional gene markers within the environment. Q-PCR-based analyses combine 'traditional' end-point detection PCR with fluorescent detection technologies to record the accumulation of amplicons in 'real time' during each cycle of the PCR amplification. By detection of amplicons during the early exponential phase of the PCR, this enables the quantification of gene (or transcript) numbers when these are proportional to the starting template concentration. When Q-PCR is coupled with a preceding reverse transcription reaction, it can be used to quantify gene expression (RT-Q-PCR). This review firstly addresses the theoretical and practical implementation of Q-PCR and RT-Q-PCR protocols in microbial ecology, highlighting key experimental considerations. Secondly, we review the applications of (RT)-Q-PCR analyses in environmental microbiology and evaluate the contribution and advances gained from such approaches. Finally, we conclude by offering future perspectives on the application of (RT)-Q-PCR in furthering understanding in microbial ecology, in particular, when coupled with other molecular approaches and more traditional investigations of environmental systems.

Construction and Characterization of a Cellulolytic Consortium Enriched from the Hindgut of Holotrichia parallela Larvae.

PubMed

Sheng, Ping; Huang, Jiangli; Zhang, Zhihong; Wang, Dongsheng; Tian, Xiaojuan; Ding, Jiannan

2016-09-30

Degradation of rice straw by cooperative microbial activities is at present the most attractive alternative to fuels and provides a basis for biomass conversion. The use of microbial consortia in the biodegradation of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, and so on. In this study, a cellulolytic microbial consortium was enriched from the hindgut of Holotrichia parallela larvae via continuous subcultivation (20 subcultures in total) under static conditions. The degradation ratio for rice straw was about 83.1% after three days of cultivation, indicating its strong cellulolytic activity. The diversity analysis results showed that the bacterial diversity and richness decreased during the consortium enrichment process, and the consortium enrichment process could lead to a significant enrichment of phyla Proteobacteria and Spirochaetes, classes Clostridia, Epsilonproteobacteria, and Betaproteobacteria, and genera Arcobacter , Treponema , Comamonas , and Clostridium . Some of these are well known as typical cellulolytic and hemicellulolytic microorganisms. Our results revealed that the microbial consortium identified herein is a potential candidate for use in the degradation of waste lignocellulosic biomass and further highlights the hindgut of the larvae as a reservoir of extensive and specific cellulolytic and hemicellulolytic microbes.

Effect of static scatterers in laser speckle contrast imaging: an experimental study on correlation and contrast.

PubMed

Vaz, Pedro G; Humeau-Heurtier, Anne; Figueiras, Edite; Correia, Carlos; Cardoso, João

2017-12-29

Laser speckle contrast imaging (LSCI) is a non-invasive microvascular blood flow assessment technique with good temporal and spatial resolution. Most LSCI systems, including commercial devices, can perform only qualitative blood flow evaluation, which is a major limitation of this technique. There are several factors that prevent the utilization of LSCI as a quantitative technique. Among these factors, we can highlight the effect of static scatterers. The goal of this work was to study the influence of differences in static and dynamic scatterer concentration on laser speckle correlation and contrast. In order to achieve this, a laser speckle prototype was developed and tested using an optical phantom with various concentrations of static and dynamic scatterers. It was found that the laser speckle correlation could be used to estimate the relative concentration of static/dynamic scatterers within a sample. Moreover, the speckle correlation proved to be independent of the dynamic scatterer velocity, which is a fundamental characteristic to be used in contrast correction.

Effect of static scatterers in laser speckle contrast imaging: an experimental study on correlation and contrast

NASA Astrophysics Data System (ADS)

Vaz, Pedro G.; Humeau-Heurtier, Anne; Figueiras, Edite; Correia, Carlos; Cardoso, João

2018-01-01

Laser speckle contrast imaging (LSCI) is a non-invasive microvascular blood flow assessment technique with good temporal and spatial resolution. Most LSCI systems, including commercial devices, can perform only qualitative blood flow evaluation, which is a major limitation of this technique. There are several factors that prevent the utilization of LSCI as a quantitative technique. Among these factors, we can highlight the effect of static scatterers. The goal of this work was to study the influence of differences in static and dynamic scatterer concentration on laser speckle correlation and contrast. In order to achieve this, a laser speckle prototype was developed and tested using an optical phantom with various concentrations of static and dynamic scatterers. It was found that the laser speckle correlation could be used to estimate the relative concentration of static/dynamic scatterers within a sample. Moreover, the speckle correlation proved to be independent of the dynamic scatterer velocity, which is a fundamental characteristic to be used in contrast correction.

T cell resistance to activation by dendritic cells requires long-term culture in simulated microgravity

NASA Astrophysics Data System (ADS)

Bradley, Jillian H.; Stein, Rachel; Randolph, Brad; Molina, Emily; Arnold, Jennifer P.; Gregg, Randal K.

2017-11-01

Immune impairment mediated by microgravity threatens the success of space exploration requiring long-duration spaceflight. The cells of most concern, T lymphocytes, coordinate the host response against microbial and cancerous challenges leading to elimination and long-term protection. T cells are activated upon recognition of specific microbial peptides bound on the surface of antigen presenting cells, such as dendritic cells (DC). Subsequently, this engagement results in T cell proliferation and differentiation into effector T cells driven by autocrine interleukin-2 (IL-2) and other cytokines. Finally, the effector T cells acquire the weaponry needed to destroy microbial invaders and tumors. Studies conducted on T cells during spaceflight, or using Earth-based culture systems, have shown reduced production of cytokines, proliferation and effector functions as compared to controls. This may account for the cases of viral reactivation events and opportunistic infections associated with astronauts of numerous missions. This work has largely been based upon the outcome of T cell activation by stimulatory factors that target select T cell signaling pathways rather than the complex, signaling events related to the natural process of antigen presentation by DC. This study tested the response of an ovalbumin peptide-specific T cell line, OT-II TCH, to activation by DC when the T cells were cultured 24-120 h in a simulated microgravity (SMG) environment generated by a rotary cell culture system. Following 72 h culture of T cells in SMG (SMG-T) or control static (Static-T) conditions, IL-2 production by the T cells was reduced in SMG-T cells compared to Static-T cells upon stimulation by phorbol 12-myristate 13-acetate (PMA) and ionomycin. However, when the SMG-T cells were stimulated with DC and peptide, IL-2 was significantly increased compared to Static-T cells. Such enhanced IL-2 production by SMG-T cells peaked at 72 h SMG culture time and decreased thereafter. When activation of SMG-T cells occurred in SMG, the T cells produced less IL-2 than control T cell cultures upon incubation with PMA and ionomycin. Short-term (24 h) SMG culture and activation of T cells by DC resulted in enhanced IL-2 production compared to Static-T cells, however, when culture was extended to 120 h, SMG-T cells secreted significantly less IL-2 than Static-T cells. SMG-T cell IL-2 doubled upon stimulation of the DC prior to addition to the T cell culture but remained less than control. SMG-T cell resistance to activation appeared comparable to the phenomenon of T cell exhaustion observed in patients with chronic diseases or persistent tumors. That is, long-term culture of T cells in SMG resulted in increased expression of the inhibitory receptor, CTLA-4. Blockade of CTLA-4 interaction with DC ligands resulted in improved T cell IL-2 production. Overall, this is the first study to determine the efficacy of DC in activating peptide-specific T cells. Furthermore, the findings suggests that countermeasures to restore T cell responsiveness in astronauts during long-term spaceflight or those living in microgravity environments should target possible inhibitory pathways that arise on activated T cells following stimulation.

T cell resistance to activation by dendritic cells requires long-term culture in simulated microgravity.

PubMed

Bradley, Jillian H; Stein, Rachel; Randolph, Brad; Molina, Emily; Arnold, Jennifer P; Gregg, Randal K

2017-11-01

Immune impairment mediated by microgravity threatens the success of space exploration requiring long-duration spaceflight. The cells of most concern, T lymphocytes, coordinate the host response against microbial and cancerous challenges leading to elimination and long-term protection. T cells are activated upon recognition of specific microbial peptides bound on the surface of antigen presenting cells, such as dendritic cells (DC). Subsequently, this engagement results in T cell proliferation and differentiation into effector T cells driven by autocrine interleukin-2 (IL-2) and other cytokines. Finally, the effector T cells acquire the weaponry needed to destroy microbial invaders and tumors. Studies conducted on T cells during spaceflight, or using Earth-based culture systems, have shown reduced production of cytokines, proliferation and effector functions as compared to controls. This may account for the cases of viral reactivation events and opportunistic infections associated with astronauts of numerous missions. This work has largely been based upon the outcome of T cell activation by stimulatory factors that target select T cell signaling pathways rather than the complex, signaling events related to the natural process of antigen presentation by DC. This study tested the response of an ovalbumin peptide-specific T cell line, OT-II TCH, to activation by DC when the T cells were cultured 24-120 h in a simulated microgravity (SMG) environment generated by a rotary cell culture system. Following 72 h culture of T cells in SMG (SMG-T) or control static (Static-T) conditions, IL-2 production by the T cells was reduced in SMG-T cells compared to Static-T cells upon stimulation by phorbol 12-myristate 13-acetate (PMA) and ionomycin. However, when the SMG-T cells were stimulated with DC and peptide, IL-2 was significantly increased compared to Static-T cells. Such enhanced IL-2 production by SMG-T cells peaked at 72 h SMG culture time and decreased thereafter. When activation of SMG-T cells occurred in SMG, the T cells produced less IL-2 than control T cell cultures upon incubation with PMA and ionomycin. Short-term (24 h) SMG culture and activation of T cells by DC resulted in enhanced IL-2 production compared to Static-T cells, however, when culture was extended to 120 h, SMG-T cells secreted significantly less IL-2 than Static-T cells. SMG-T cell IL-2 doubled upon stimulation of the DC prior to addition to the T cell culture but remained less than control. SMG-T cell resistance to activation appeared comparable to the phenomenon of T cell exhaustion observed in patients with chronic diseases or persistent tumors. That is, long-term culture of T cells in SMG resulted in increased expression of the inhibitory receptor, CTLA-4. Blockade of CTLA-4 interaction with DC ligands resulted in improved T cell IL-2 production. Overall, this is the first study to determine the efficacy of DC in activating peptide-specific T cells. Furthermore, the findings suggests that countermeasures to restore T cell responsiveness in astronauts during long-term spaceflight or those living in microgravity environments should target possible inhibitory pathways that arise on activated T cells following stimulation. Copyright © 2017 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.

PubMed

Cassler, M; Peterson, C L; Ledger, A; Pomponi, S A; Wright, A E; Winegar, R; McCarthy, P J; Lopez, J V

2008-04-01

In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.

Quantitative analysis of transverse bacterial migration induced by chemotaxis in a packed column with structured physical heterogeneity.

PubMed

Wang, Meng; Ford, Roseanne M

2010-01-15

A two-dimensional mathematical model was developed to simulate transport phenomena of chemotactic bacteria in a sand-packed column designed with structured physical heterogeneity in the presence of a localized chemical source. In contrast to mathematical models in previous research work, in which bacteria were typically treated as immobile colloids, this model incorporated a convective-like chemotaxis term to represent chemotactic migration. Consistency between experimental observation and model prediction supported the assertions that (1) dispersion-induced microbial transfer between adjacent conductive zones occurred at the interface and had little influence on bacterial transport in the bulk flow of the permeable layers and (2) the enhanced transverse bacterial migration in chemotactic experiments relative to nonchemotactic controls was mainly due to directed migration toward the chemical source zone. On the basis of parameter sensitivity analysis, chemotactic parameters determined in bulk aqueous fluid were adequate to predict the microbial transport in our intermediate-scale porous media system. Additionally, the analysis of adsorption coefficient values supported the observation of a previous study that microbial deposition to the surface of porous media might be decreased under the effect of chemoattractant gradients. By quantitatively describing bacterial transport and distribution in a heterogeneous system, this mathematical model serves to advance our understanding of chemotaxis and motility effects in granular media systems and provides insights for modeling microbial transport in in situ microbial processes.

Combined use of microbial consortia isolated from different agricultural soils and cyclodextrin as a bioremediation technique for herbicide contaminated soils.

PubMed

Villaverde, J; Rubio-Bellido, M; Lara-Moreno, A; Merchan, F; Morillo, E

2018-02-01

The phenylurea herbicide diuron is persistent in soil, water and groundwater and is considered to be a highly toxic molecule. The principal product of its biodegradation, 3,4-dichloroaniline, exhibits greater toxicity than diuron and is persistent in the environment. Five diuron degrading microbial consortia (C1C5), isolated from different agricultural soils, were investigated for diuron mineralization activity. The C2 consortium was able to mineralize 81.6% of the diuron in solution, while consortium C3 was only able to mineralize 22.9%. Isolated consortia were also tested in soil slurries and in all cases, except consortium C4, DT 50 (the time required for the diuron concentration to decline to half of its initial value) was drastically reduced, from 700 days (non-inoculated control) to 546, 351, and 171 days for the consortia C5, C2, and C1, respectively. In order to test the effectiveness of the isolated consortium C1 in a more realistic scenario, soil diuron mineralization assays were performed under static conditions (40% of the soil water-holding capacity). A significant enhancement of diuron mineralization was observed after C1 inoculation, with 23.2% of the herbicide being mineralized in comparison to 13.1% for the control experiment. Hydroxypropyl-β-cyclodextrin, a biodegradable organic enhancer of pollutant bioavailability, used in combination with C1 bioaugmentation in static conditions, resulted in a significant decrease in the DT 50 (214 days; 881 days, control experiment). To the best of our knowledge, this is the first report of the use of soil-isolated microbial consortia in combination with cyclodextrins proposed as a bioremediation technique for pesticide contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering Ecosystems and Synthetic Ecologies#

PubMed Central

Mee, Michael T; Wang, Harris H

2012-01-01

Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here, we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology. PMID:22722235

Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei▿

PubMed Central

Bowers, Robert M.; Lauber, Christian L.; Wiedinmyer, Christine; Hamady, Micah; Hallar, Anna G.; Fall, Ray; Knight, Rob; Fierer, Noah

2009-01-01

Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 105 to 6.6 × 106 cells m−3 of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria. PMID:19502432

Combined static-dynamic compaction of metal powder and ceramic materials

NASA Astrophysics Data System (ADS)

Mironovs, V.; Korjakins, A.; Tatarinov, A.; Barone, E.; Glushchenkov, V.

2017-10-01

Combined static-dynamic compaction of powder material presents advantages for achievement of a higher degree of powder compaction for in dry conditions. One of possible realizations is the use of pulsed electromagnetic compaction (MPC) applied in addition to the static pre-compaction carried out by a hydraulic press. Experimental MPC equipment was used for compaction powders of SiC and Al-B with W fibers at different stages of grinding. The degree of compaction was evaluated by shock plate’s displacement at different levels and regimes of dynamic loading. The paper demonstrates feasibility of the method for compaction of the selected ceramic and metal powders and presents some quantitative data for practices.

Comparison of local exchange potentials of electron-N2 scattering

NASA Astrophysics Data System (ADS)

Rumble, J. R., Jr.; Truhlar, D. G.

1980-05-01

Vibrationally and electronically elastic electron scattering by N2 at 2-30 eV impact energy is considered. Static, static-exchange, and static-exchange-plus-polarization potentials, Cade-Sales-Wahl and INDO/1s wave functions, and semiclassical exchange and Hara free-electron-gas exchange potentials are examined. It is shown that the semiclassical exchange approximation is too attractive at low energy for N2. It is also shown quantitatively by consideration of partial and total integral cross sections how the effects of approximations to exchange become smaller as the incident energy is increased until the differences are about 8% for the total integral cross section at 30 eV.

Quantitative myocardial perfusion from static cardiac and dynamic arterial CT

NASA Astrophysics Data System (ADS)

Bindschadler, Michael; Branch, Kelley R.; Alessio, Adam M.

2018-05-01

Quantitative myocardial blood flow (MBF) estimation by dynamic contrast enhanced cardiac computed tomography (CT) requires multi-frame acquisition of contrast transit through the blood pool and myocardium to inform the arterial input and tissue response functions. Both the input and the tissue response functions for the entire myocardium are sampled with each acquisition. However, the long breath holds and frequent sampling can result in significant motion artifacts and relatively high radiation dose. To address these limitations, we propose and evaluate a new static cardiac and dynamic arterial (SCDA) quantitative MBF approach where (1) the input function is well sampled using either prediction from pre-scan timing bolus data or measured from dynamic thin slice ‘bolus tracking’ acquisitions, and (2) the whole-heart tissue response data is limited to one contrast enhanced CT acquisition. A perfusion model uses the dynamic arterial input function to generate a family of possible myocardial contrast enhancement curves corresponding to a range of MBF values. Combined with the timing of the single whole-heart acquisition, these curves generate a lookup table relating myocardial contrast enhancement to quantitative MBF. We tested the SCDA approach in 28 patients that underwent a full dynamic CT protocol both at rest and vasodilator stress conditions. Using measured input function plus single (enhanced CT only) or plus double (enhanced and contrast free baseline CT’s) myocardial acquisitions yielded MBF estimates with root mean square (RMS) error of 1.2 ml/min/g and 0.35 ml/min/g, and radiation dose reductions of 90% and 83%, respectively. The prediction of the input function based on timing bolus data and the static acquisition had an RMS error compared to the measured input function of 26.0% which led to MBF estimation errors greater than threefold higher than using the measured input function. SCDA presents a new, simplified approach for quantitative perfusion imaging with an acquisition strategy offering substantial radiation dose and computational complexity savings over dynamic CT.

Advances in Quantitative Proteomics of Microbes and Microbial Communities

NASA Astrophysics Data System (ADS)

Waldbauer, J.; Zhang, L.; Rizzo, A. I.

2015-12-01

Quantitative measurements of gene expression are key to developing a mechanistic, predictive understanding of how microbial metabolism drives many biogeochemical fluxes and responds to environmental change. High-throughput RNA-sequencing can afford a wealth of information about transcript-level expression patterns, but it is becoming clear that expression dynamics are often very different at the protein level where biochemistry actually occurs. These divergent dynamics between levels of biological organization necessitate quantitative proteomic measurements to address many biogeochemical questions. The protein-level expression changes that underlie shifts in the magnitude, or even the direction, of metabolic and biogeochemical fluxes can be quite subtle and test the limits of current quantitative proteomics techniques. Here we describe methodologies for high-precision, whole-proteome quantification that are applicable to both model organisms of biogeochemical interest that may not be genetically tractable, and to complex community samples from natural environments. Employing chemical derivatization of peptides with multiple isotopically-coded tags, this strategy is rapid and inexpensive, can be implemented on a wide range of mass spectrometric instrumentation, and is relatively insensitive to chromatographic variability. We demonstrate the utility of this quantitative proteomics approach in application to both isolates and natural communities of sulfur-metabolizing and photosynthetic microbes.

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification†

PubMed Central

Wu, Liyou; Liu, Xueduan; Schadt, Christopher W.; Zhou, Jizhong

2006-01-01

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment. PMID:16820490

The effect of interactions between a bacterial strain isolated from drinking water and a pathogen surrogate on biofilms formation diverged under static vs flow conditions.

PubMed

Dai, D; Raskin, L; Xi, C

2017-12-01

Interactions with water bacteria affect the incorporation of pathogens into biofilms and thus pathogen control in drinking water systems. This study was to examine the impact of static vs flow conditions on interactions between a pathogen and a water bacterium on pathogen biofilm formation under laboratory settings. A pathogen surrogate Escherichia coli and a drinking water isolate Stenotrophomonas maltophilia was selected for this study. Biofilm growth was examined under two distinct conditions, in flow cells with continuous medium supply vs in static microtitre plates with batch culture. E. coli biofilm was greatly stimulated (c. 2-1000 times faster) with the presence of S. maltophilia in flow cells, but surprisingly inhibited (c. 65-95% less biomass) in microtitre plates. These divergent effects were explained through various aspects including surface attachment, cellular growth, extracellular signals and autoaggregation. Interactions with the same water bacterium resulted in different effects on E. coli biofilm formation when culture conditions changed from static to flow. This study highlights the complexity of species interactions on biofilm formation and suggests that environmental conditions such as the flow regime can be taken into consideration for the management of microbial contamination in drinking water systems. © 2017 The Society for Applied Microbiology.

Is DOM driver of the microbial carrying capacity in pristine porous groundwater ecosystems? - lab-scale experiments in 2D sediment flow-through microcosms

NASA Astrophysics Data System (ADS)

Hofmann, Roland; Griebler, Christian

2017-04-01

Groundwater ecosystems are an essential resource for drinking water and at the same time constitute fascinating habitats subject to increasing (anthropogenic) disturbances. In our research, we look for ways to qualitatively and quantitatively access, and predict the resistance and resilience (potential) of groundwater ecosystems in consequence of selected disturbances. As a central goal we hope to identify and quantify the underlying biological and ecological key drivers of the microbial Carrying Capacity (mCC) - an ecological concept established in macro-ecology - we assume directly connected to the ecosystem's productivity and the resistance and resilience of aquifers. We further hypothesize, that the ecosystems' mCC is a result of available energy and constitutes a promising proxy for the potential of groundwater ecosystems to withstand impacts and recover from it. In a first approach we studied the dynamics of the microbial standing stock (biomass) and growth (productivity) productivity of a natural groundwater microbial community in parallel 2-D sediment flow-through systems. Selected zones of the model aquifers were disturbed by elevated DOM concentrations. Both the 'mobile' (free floating) and 'sessile' (sediment attached) microbial components were followed over time in terms of biomass, growth, and specific activities (ATP, carbon use efficiency) and taxonomic composition. Sediment regions supplied with elevated concentrations of natural DOM showed increased biomass, activities and taxonomic richness with the sediment community, while differences in the mobile microbial were marginal. Specifically, the carbon use efficiency was significantly increased in the DOM amended sediment zones. In contrast, the microbial community that received the mainly refractory natural background DOM was able to metabolize polymers more efficiently in substrate use tests (ECOLOG), seen as an adaptation to the energy-poor subsurface. Quasi-stationary conditions were reached in the model aquifers only after several weeks. The quantitative link between microbial productivity and mCC is currently evaluated.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

The applicability of TaqMan-based quantitative real-time PCR assays for detecting and enumeratIng Cryptosporidium spp. oocysts in the environment

EPA Science Inventory

Molecular detection methods such as PCR have been extensively used to type Cryptosporidium oocysts detected in the environment. More recently, studies have developed quantitative real-time PCR assays for detection and quantification of microbial contaminants in water as well as ...

Consumers' behavior in quantitative microbial risk assessment for pathogens in raw milk: Incorporation of the likelihood of consumption as a function of storage time and temperature.

PubMed

Crotta, Matteo; Paterlini, Franco; Rizzi, Rita; Guitian, Javier

2016-02-01

Foodborne disease as a result of raw milk consumption is an increasing concern in Western countries. Quantitative microbial risk assessment models have been used to estimate the risk of illness due to different pathogens in raw milk. In these models, the duration and temperature of storage before consumption have a critical influence in the final outcome of the simulations and are usually described and modeled as independent distributions in the consumer phase module. We hypothesize that this assumption can result in the computation, during simulations, of extreme scenarios that ultimately lead to an overestimation of the risk. In this study, a sensorial analysis was conducted to replicate consumers' behavior. The results of the analysis were used to establish, by means of a logistic model, the relationship between time-temperature combinations and the probability that a serving of raw milk is actually consumed. To assess our hypothesis, 2 recently published quantitative microbial risk assessment models quantifying the risks of listeriosis and salmonellosis related to the consumption of raw milk were implemented. First, the default settings described in the publications were kept; second, the likelihood of consumption as a function of the length and temperature of storage was included. When results were compared, the density of computed extreme scenarios decreased significantly in the modified model; consequently, the probability of illness and the expected number of cases per year also decreased. Reductions of 11.6 and 12.7% in the proportion of computed scenarios in which a contaminated milk serving was consumed were observed for the first and the second study, respectively. Our results confirm that overlooking the time-temperature dependency may yield to an important overestimation of the risk. Furthermore, we provide estimates of this dependency that could easily be implemented in future quantitative microbial risk assessment models of raw milk pathogens. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Allometric scaling of microbial fuel cells and stacks: The lifeform case for scale-up

NASA Astrophysics Data System (ADS)

Greenman, John; Ieropoulos, Ioannis A.

2017-07-01

This case study reports for the first time on the comparison between allometric scaling of lifeforms and scale-up of microbial fuel cell entities; enlarging individual units in volume, footprint and electrode surface area but also multiplying a static size/footprint and electrode surface area to scale-up by stacking. A study published in 2010 by DeLong et al. showed for the first time that Kleiber's law does not apply uniformly to all lifeforms, and that in fact growth rate for prokaryotes is superlinear, for protists is linear and for metazoa is sublinear. The current study, which is utilising data from previous experiments, is showing for the first time that for individual MFC units, which are enlarged, growth rate/power is sublinear, whereas for stacks this is superlinear.

Effect of a prolonged stay in a locked environment on the microbial flora in dogs

NASA Technical Reports Server (NTRS)

Balish, E.; Shih, C.-N.; Yale, C. E.; Mandel, A. D.

1974-01-01

Ten purebred Beagle dogs (all males) were used to determine the effect of a prolonged stay in a locked environment (i.e., no exogenous microbial contamination) on the microbial flora. At monthly intervals the microbial profile (feces, nose, and throat) of each dog was assessed. After 12 months it was found there was no drastic alteration or simplification of the microbial profile of isolated or control dogs. Although isolated dogs had slightly higher levels of anaerobic bacteria and somewhat lower levels of enterococci, the major groups of anaerobic, aerobic, and facultative bacteria remained qualitatively and quantitatively similar for the 12-month study period. Although they were only minor components of the fecal flora, Candida albicans and Shigella sonnei were consistently isolated in larger numbers from the dogs in the locked environment.

Development of Cellular Absorptive Tracers (CATs) for a Quantitative Characterization of Microbial Mass in Flow Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saripalli, Prasad; Brown, Christopher F.; Lindberg, Michael J.

We report on a new Cellular Absorptive Tracers (CATs) method, for a simple, non-destructive characterization of bacterial mass in flow systems. Results show that adsorption of a CAT molecule into the cellular mass results in its retardation during flow, which is a good, quantitative measure of the biomass quantity and distribution. No such methods are currently available for a quantitative characterization of cell mass.

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery

PubMed Central

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery. PMID:26925051

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery.

PubMed

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery.

[A novel quantitative approach to study dynamic anaerobic process at micro scale].

PubMed

Zhang, Zhong-Liang; Wu, Jing; Jiang, Jian-Kai; Jiang, Jie; Li, Huai-Zhi

2012-11-01

Anaerobic digestion is attracting more and more interests because of its advantages such as low cost and recovery of clean energy etc. In order to overcome the drawbacks of the existed methods to study the dynamic anaerobic process, a novel microscopical quantitative approach at the granule level was developed combining both the microdevice and the quantitative image analysis techniques. This experiment displayed the process and characteristics of the gas production at static state for the first time and the results indicated that the method was of satisfactory repeatability. The gas production process at static state could be divided into three stages including rapid linear increasing stage, decelerated increasing stage and slow linear increasing stage. The rapid linear increasing stage was long and the biogas rate was high under high initial organic loading rate. The results showed that it was feasible to make the anaerobic process to be carried out in the microdevice; furthermore this novel method was reliable and could clearly display the dynamic process of the anaerobic reaction at the micro scale. The results are helpful to understand the anaerobic process.

Challenging the in-vivo assessment of biomechanical properties of the uterine cervix: A critical analysis of ultrasound based quasi-static procedures.

PubMed

Maurer, M M; Badir, S; Pensalfini, M; Bajka, M; Abitabile, P; Zimmermann, R; Mazza, E

2015-06-25

Measuring the stiffness of the uterine cervix might be useful in the prediction of preterm delivery, a still unsolved health issue of global dimensions. Recently, a number of clinical studies have addressed this topic, proposing quantitative methods for the assessment of the mechanical properties of the cervix. Quasi-static elastography, maximum compressibility using ultrasound and aspiration tests have been applied for this purpose. The results obtained with the different methods seem to provide contradictory information about the physiologic development of cervical stiffness during pregnancy. Simulations and experiments were performed in order to rationalize the findings obtained with ultrasound based, quasi-static procedures. The experimental and computational results clearly illustrate that standardization of quasi-static elastography leads to repeatable strain values, but for different loading forces. Since force cannot be controlled, this current approach does not allow the distinction between a globally soft and stiff cervix. It is further shown that introducing a reference elastomer into the elastography measurement might overcome the problem of force standardization, but a careful mechanical analysis is required to obtain reliable stiffness values for cervical tissue. In contrast, the maximum compressibility procedure leads to a repeatable, semi-quantitative assessment of cervical consistency, due to the nonlinear nature of the mechanical behavior of cervical tissue. The evolution of cervical stiffness in pregnancy obtained with this procedure is in line with data from aspiration tests. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nuclear physics: Macroscopic aspects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiatecki, W.J.

1993-12-01

A systematic macroscopic, leptodermous approach to nuclear statics and dynamics is described, based formally on the assumptions {h_bar} {yields} 0 and b/R << 1, where b is the surface diffuseness and R the nuclear radius. The resulting static model of shell-corrected nuclear binding energies and deformabilities is accurate to better than 1 part in a thousand and yields a firm determination of the principal properties of the nuclear fluid. As regards dynamics, the above approach suggests that nuclear shape evolutions will often be dominated by dissipation, but quantitative comparisons with experimental data are more difficult than in the case ofmore » statics. In its simplest liquid drop version the model exhibits interesting formal connections to the classic astronomical problem of rotating gravitating masses.« less

From Position-Specific Labeling to Environmental Fluxomics: Elucidating Biogeochemical Cycles from the Metabolic Perspective (BG Division Outstanding ECS Award Lecture)

NASA Astrophysics Data System (ADS)

Dippold, Michaela; Apostel, Carolin; Dijkstra, Paul; Kuzyakov, Yakov

2017-04-01

Understanding soil and sedimentary organic matter (SOM) dynamics is one of the most important challenges in biogeoscience. To disentangle the fluxes and transformations of C in soils a detailed knowledge on the biochemical pathways and its controlling factors is required. Biogeochemists' view on the C transformation of microorganisms in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the microbial anabolism. Biochemists, however, thoroughly identified in the past decades the individual reactions of glycolysis, pentose-phosphate pathway and citric acid cycle underlying the microbial catabolism. At various points within that metabolic network the anabolic fluxes feeding biomass formation branch off. Recent studies on metabolic flux tracing by position-specific isotope labeling allowed tracing these C transformations in soils in situ, an approach which is qunatitatively complemented by metabolic flux modeling. This approach has reached new impact by the cutting-edge combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites which allows 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. Thus, the combination of position-specific labeling, compound-specific isotope incorporation in biomarkers and quantitative metabolic flux modelling provide the toolbox for quantitative soil fluxomics. Our studies combining position-specific labeled glucose with amino sugar 13C analysis showed that up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in citric acid cycle. Thus, oxidizing catabolic pathways and anabolic pathways, i.e. building-up new cellular compounds, occurred in soils simultaneously, a combination unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. Coupling these results with the position-specific fingerprint of microbial biomarkers revealed that microbial groups show deviating adaptation strategies and that they react on environmental changes by activation or deactivation of specific metabolic pathways such as anaplerotic fluxes. To understand how microorganisms catalyze the biogeochemical fluxes in soil a profound understanding of their metabolic adaptation strategies such as recycling or switching between pathways is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the underlying microbial processes.

High-Throughput Screening To Identify Potent and Specific Inhibitors of Microbial Sulfate Reduction.

PubMed

Carlson, Hans K; Mullan, Mark R; Mosqueda, Lorraine A; Chen, Steven; Arkin, Michelle R; Coates, John D

2017-06-20

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive, and corrosive. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to identify potent and selective inhibitors of SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Zinc pyrithione is the most potent inhibitor of sulfidogenesis that we identified, and is several orders of magnitude more potent than commonly used industrial biocides. Both zinc and copper pyrithione are also moderately selective against SRM. The high-throughput (HT) approach we present can be readily adapted to target SRM in diverse environments and similar strategies could be used to quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant to efforts to engineer environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Human-Associated Fecal Quantitative Polymerase Chain ReactionMeasurements and Simulated Risk of Gastrointestinal Illness in Recreational Waters Contaminated with Raw Sewage

EPA Science Inventory

We used quantitative microbial risk assessment (QMRA) to estimate the risk of gastrointestinal (GI) illness associated with swimming in recreational waters containing different concentrations of human-associated fecal qPCR markers from raw sewage– HF183 and HumM2. The volume/volu...

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Statistical Physics Approaches to Microbial Ecology

NASA Astrophysics Data System (ADS)

Mehta, Pankaj

The unprecedented ability to quantitatively measure and probe complex microbial communities has renewed interest in identifying the fundamental ecological principles governing community ecology in microbial ecosystems. Here, we present work from our group and others showing how ideas from statistical physics can help us uncover these ecological principles. Two major lessons emerge from this work. First, large, ecosystems with many species often display new, emergent ecological behaviors that are absent in small ecosystems with just a few species. To paraphrase Nobel laureate Phil Anderson, ''More is Different'', especially in community ecology. Second, the lack of trophic layer separation in microbial ecology fundamentally distinguishes microbial ecology from classical paradigms of community ecology and leads to qualitative different rules for community assembly in microbes. I illustrate these ideas using both theoretical modeling and novel new experiments on large microbial ecosystems performed by our collaborators (Joshua Goldford and Alvaro Sanchez). Work supported by Simons Investigator in MMLS and NIH R35 R35 GM119461.

Microbiota of little penguins and short-tailed shearwaters during development

PubMed Central

Arnould, John P. Y.; Allnutt, Theo R.; Crowley, Tamsyn; Krause, Lutz; Reynolds, John; Dann, Peter; Smith, Stuart C.

2017-01-01

The establishment and early colonisation of the gastrointestinal (GI) tract has been recognised as a crucial stage in chick development, with pioneering microbial species responsible for influencing the development of the GI tract and influencing host health, fitness and disease status throughout life. Development of the microbiota in long lived seabirds is poorly understood. This study characterised the microbial composition of little penguin and short-tailed shearwater chicks throughout development, using Quantitative Real Time PCR (qPCR) and 16S rRNA sequencing. The results indicated that microbial development differed between the two seabird species with the short-tailed shearwater microbiota being relatively stable throughout development whilst significant fluctuations in the microbial composition and an upward trend in the abundance of Firmicutes and Bacteroidetes were observed in the little penguin. When the microbial composition of adults and chicks was compared, both species showed low similarity in microbial composition, indicating that the adult microbiota may have a negligible influence over the chick’s microbiota. PMID:28806408

Microbial secondary succession in a chronosequence of chalk grasslands.

PubMed

Kuramae, Eiko E; Gamper, Hannes A; Yergeau, Etienne; Piceno, Yvette M; Brodie, Eoin L; Desantis, Todd Z; Andersen, Gary L; van Veen, Johannes A; Kowalchuk, George A

2010-05-01

Although secondary succession has been studied extensively, we have little knowledge of the succession of soil-borne microbial communities. In this study, we therefore examined the structures of the microbial communities across two separate chronosequences of chalk grasslands in Limburg, the Netherlands, which are at different stages of secondary succession after being abandoned for between 17 and >66 years. Arable fields were also included in the investigation as non-abandoned references. Changes in the soil-borne microbial communities, as determined by phylogenetic microarray and quantitative PCR methodologies, were correlated with the prevailing environmental conditions related to vegetation and soil biochemistry. We observed clear patterns of microbial secondary succession related to soil age, pH and phosphate status, as exemplified by the overrepresentation of Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and alpha-, delta- and epsilon-Proteobacteria at late successional stages. Moreover, effects of secondary succession versus changes in soil pH could be resolved, with pH significantly altering the trajectory of microbial succession.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gentry, T.; Schadt, C.; Zhou, J.

Microarray technology has the unparalleled potential tosimultaneously determine the dynamics and/or activities of most, if notall, of the microbial populations in complex environments such as soilsand sediments. Researchers have developed several types of arrays thatcharacterize the microbial populations in these samples based on theirphylogenetic relatedness or functional genomic content. Several recentstudies have used these microarrays to investigate ecological issues;however, most have only analyzed a limited number of samples withrelatively few experiments utilizing the full high-throughput potentialof microarray analysis. This is due in part to the unique analyticalchallenges that these samples present with regard to sensitivity,specificity, quantitation, and data analysis. Thismore » review discussesspecific applications of microarrays to microbial ecology research alongwith some of the latest studies addressing the difficulties encounteredduring analysis of complex microbial communities within environmentalsamples. With continued development, microarray technology may ultimatelyachieve its potential for comprehensive, high-throughput characterizationof microbial populations in near real-time.« less

Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

PubMed Central

Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

2012-01-01

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

PubMed

Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

2012-12-01

Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

Sulfur isotopic constraints from a single enzyme on the cellular to global sulfur cycles

NASA Astrophysics Data System (ADS)

Sim, M. S.; Adkins, J. F.; Sessions, A. L.; Orphan, V. J.; McGlynn, S.

2017-12-01

Since first reported more than a half century ago, sulfur isotope fractionation between sulfate and sulfide has been used as a diagnostic indicator of microbial sulfate reduction, giving added dimensions to the microbial ecological and geochemical studies of the sulfur cycle. A wide range of fractionation has attracted particular attention because it may serve as a potential indicator of environmental or physiological variables such as substrate concentrations or specific respiration rates. In theory, the magnitude of isotope fractionation depends upon the sulfur isotope effect imparted by the involved enzymes and the relative rate of each enzymatic reaction. The former defines the possible range of fractionation quantitatively, while the latter responds to environmental stimuli, providing an underlying rationale for the varying fractionations. The experimental efforts so far have concentrated largely on the latter, the factors affecting the size of fractionation. Recently, however, the direct assessment of intracellular processes emerges as a promising means for the quantitative analysis of microbial sulfur isotope fractionation as a function of environmental or physiological variables. Here, we experimentally determined for the first time the sulfur isotope fractionation during APS reduction, the first reductive step in the dissimilatory sulfate reduction pathway, using the enzyme purified from Desulfovibrio vulgaris Miyazaki. APS reductase carried out the one-step, two-electron reduction of APS to sulfite, without the production of other metabolic intermediates. Nearly identical isotope effects were obtained at two different temperatures, while the rate of APS reduction more than quadrupled with a temperature increase from 20 to 32°C. When placed in context of the linear network model for microbial sulfur isotope fractionation, our finding could provide a new, semi-quantitative constraint on the sulfur cycle at levels from cellular to global.

Quantitative microbial risk assessment for Escherichia coli O157:H7, Salmonella enterica, and Listeria monocytogenes in leafy green vegetables consumed at salad bars, based on modeling supply chain logistics.

PubMed

Tromp, S O; Rijgersberg, H; Franz, E

2010-10-01

Quantitative microbial risk assessments do not usually account for the planning and ordering mechanisms (logistics) of a food supply chain. These mechanisms and consumer demand determine the storage and delay times of products. The aim of this study was to quantitatively assess the difference between simulating supply chain logistics (MOD) and assuming fixed storage times (FIX) in microbial risk estimation for the supply chain of fresh-cut leafy green vegetables destined for working-canteen salad bars. The results of the FIX model were previously published (E. Franz, S. O. Tromp, H. Rijgersberg, and H. J. van der Fels-Klerx, J. Food Prot. 73:274-285, 2010). Pathogen growth was modeled using stochastic discrete-event simulation of the applied logistics concept. The public health effects were assessed by conducting an exposure assessment and risk characterization. The relative growths of Escherichia coli O157 (17%) and Salmonella enterica (15%) were identical in the MOD and FIX models. In contrast, the relative growth of Listeria monocytogenes was considerably higher in the MOD model (1,156%) than in the FIX model (194%). The probability of L. monocytogenes infection in The Netherlands was higher in the MOD model (5.18×10(-8)) than in the FIX model (1.23×10(-8)). The risk of listeriosis-induced fetal mortality in the perinatal population increased from 1.24×10(-4) (FIX) to 1.66×10(-4) (MOD). Modeling the probabilistic nature of supply chain logistics is of additional value for microbial risk assessments regarding psychrotrophic pathogens in food products for which time and temperature are the postharvest preventive measures in guaranteeing food safety.

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

PubMed Central

Staley, Christopher; Gordon, Katrina V.; Schoen, Mary E.

2012-01-01

Before new, rapid quantitative PCR (qPCR) methods for assessment of recreational water quality and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant source has been diluted in environmental waters is needed. This study determined the limits of detection and quantification of the human-associated Bacteroides sp. (HF183) and human polyomavirus (HPyV) qPCR methods for sewage diluted in buffer and in five ambient, Florida water types (estuarine, marine, tannic, lake, and river). HF183 was quantifiable in sewage diluted up to 10−6 in 500-ml ambient-water samples, but HPyVs were not quantifiable in dilutions of >10−4. Specificity, which was assessed using fecal composites from dogs, birds, and cattle, was 100% for HPyVs and 81% for HF183. Quantitative microbial risk assessment (QMRA) estimated the possible norovirus levels in sewage and the human health risk at various sewage dilutions. When juxtaposed with the MST marker detection limits, the QMRA analysis revealed that HF183 was detectable when the modeled risk of gastrointestinal (GI) illness was at or below the benchmark of 10 illnesses per 1,000 exposures, but the HPyV method was generally not sensitive enough to detect potential health risks at the 0.01 threshold for frequency of illness. The tradeoff between sensitivity and specificity in the MST methods indicates that HF183 data should be interpreted judiciously, preferably in conjunction with a more host-specific marker, and that better methods of concentrating HPyVs from environmental waters are needed if this method is to be useful in a watershed management or monitoring context. PMID:22885746

Revealing and analyzing networks of environmental systems

NASA Astrophysics Data System (ADS)

Eveillard, D.; Bittner, L.; Chaffron, S.; Guidi, L.; Raes, J.; Karsenti, E.; Bowler, C.; Gorsky, G.

2015-12-01

Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete. Within this seminar, we will illustrate two complementary approaches that aim to overcome these points in different manners. First, we will present a network analysis that focus on the biological carbon pump in the global ocean. The biological carbon pump is the process by which photosynthesis transforms CO2 to organic carbon sinking to the deep-ocean as particles where it is sequestered. While the intensity of the pump correlate to plankton community composition, the underlying ecosystem structure and interactions driving this process remain largely uncharacterized Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve understanding of these drivers. We show that specific plankton communities correlate with carbon export and highlight unexpected and overlooked taxa such as Radiolaria, alveolate parasites and bacterial pathogens, as well as Synechococcus and their phages, as key players in the biological pump. Additionally, we show that the abundances of just a few bacterial and viral genes predict most of the global ocean carbon export's variability. Together these findings help elucidate ecosystem drivers of the biological carbon pump and present a case study for scaling from genes-to-ecosystems. Second, we will show preliminary results on a probabilistic modeling that predicts microbial community structure across observed physicochemical data, from a putative network and partial quantitative knowledge. This modeling shows that, despite distinct quantitative environmental perturbations, the constraints on community structure could remain stable.

Relationships between microstructure and mechanical properties of Ti-5Al-5Mo-5V-3Cr-1Zr alloy

NASA Astrophysics Data System (ADS)

Li, Z. Y.; Wu, G. Q.; Huang, Z.

2018-03-01

Through a statistical, quantitative analysis on microstructure of Ti-5Al-5Mo-5V-3Cr-1Zr (Ti55531) alloy, the relationships between microstructure and mechanical properties and heat treatment temperatures were investigated. The results show that in Widmanstätten structure, the size of β grain is greatly increased with increasing annealing temperature. Static toughness is related to grain boundary alpha phase discontinuity, the tensile strength is related to acicular alpha phase interface length and acicular alpha phase proportion. In duplex microstructure, the tensile strength is related to the equiaxed alpha proportion. Elongation, static toughness and crack forming work are related to the equiaxed alpha proportion and negatively related to secondary phase proportion. The microstructure can be described quantitatively and the mechanical properties can be predicted by analysis of microstructure.

Towards quantitative mass spectrometry-based metabolomics in microbial and mammalian systems.

PubMed

Kapoore, Rahul Vijay; Vaidyanathan, Seetharaman

2016-10-28

Metabolome analyses are a suite of analytical approaches that enable us to capture changes in the metabolome (small molecular weight components, typically less than 1500 Da) in biological systems. Mass spectrometry (MS) has been widely used for this purpose. The key challenge here is to be able to capture changes in a reproducible and reliant manner that is representative of the events that take place in vivo Typically, the analysis is carried out in vitro, by isolating the system and extracting the metabolome. MS-based approaches enable us to capture metabolomic changes with high sensitivity and resolution. When developing the technique for different biological systems, there are similarities in challenges and differences that are specific to the system under investigation. Here, we review some of the challenges in capturing quantitative changes in the metabolome with MS based approaches, primarily in microbial and mammalian systems.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Author(s).

Respiration and enzymatic activities as indicators of stabilization of sewage sludge composting.

PubMed

Nikaeen, Mahnaz; Nafez, Amir Hossein; Bina, Bijan; Nabavi, BiBi Fatemeh; Hassanzadeh, Akbar

2015-05-01

The objective of this work was to study the evolution of physico-chemical and microbial parameters in the composting process of sewage sludge (SS) with pruning wastes (PW) in order to compare these parameters with respect to their applicability in the evaluation of organic matter (OM) stabilization. To evaluate the composting process and organic matter stability, different microbial activities were compared during composting of anaerobically digested SS with two volumetric ratios, 1:1 and 3:1 of PW:SS and two aeration techniques including aerated static piles (ASP) and turned windrows (TW). Dehydrogenase activity, fluorescein diacetate hydrolysis, and specific oxygen uptake rate (SOUR) were used as microbial activity indices. These indices were compared with traditional parameters, including temperature, pH, moisture content, organic matter, and C/N ratio. The results showed that the TW method and 3:1 (PW:SS) proportion was superior to the ASP method and 1:1 proportion, since the former accelerate the composting process by catalyzing the OM stabilization. Enzymatic activities and SOUR, which reflect microbial activity, correlated well with temperature fluctuations. Based on these results it appears that SOUR and the enzymatic activities are useful parameters to monitor the stabilization of SS compost. Copyright © 2015 Elsevier Ltd. All rights reserved.

Colonizing the embryonic zebrafish gut with anaerobic bacteria derived from the human gastrointestinal tract.

PubMed

Toh, Michael C; Goodyear, Mara; Daigneault, Michelle; Allen-Vercoe, Emma; Van Raay, Terence J

2013-06-01

The zebrafish has become increasingly popular for microbiological research. It has been used as an infection model for a variety of pathogens, and is also emerging as a tool for studying interactions between a host and its resident microbial communities. The mouse microbiota has been transplanted into the zebrafish gut, but to our knowledge, there has been no attempt to introduce a bacterial community derived from the human gut. We explored two methods for colonizing the developing gut of 5-day-old germ-free zebrafish larvae with a defined anaerobic microbial community derived from a single human fecal sample. Both environmental exposure (static immersion) and direct microinjection into the gut resulted in the establishment of two species-Lactobacillus paracasei and Eubacterium limosum-from a community of 30 strains consisting of 22 anaerobic species. Of particular interest is E. limosum, which, as a strict anaerobe, represents a group of bacteria which until now have not been shown to colonize the developing zebrafish gut. Our success here indicates that further investigation of zebrafish as a tool for studying human gut microbial communities is warranted.

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

PubMed Central

Kim, Minsu; Or, Dani

2016-01-01

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils. PMID:26807803

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning. PMID:28961933

Respiratory trace feature analysis for the prediction of respiratory-gated PET quantification.

PubMed

Wang, Shouyi; Bowen, Stephen R; Chaovalitwongse, W Art; Sandison, George A; Grabowski, Thomas J; Kinahan, Paul E

2014-02-21

The benefits of respiratory gating in quantitative PET/CT vary tremendously between individual patients. Respiratory pattern is among many patient-specific characteristics that are thought to play an important role in gating-induced imaging improvements. However, the quantitative relationship between patient-specific characteristics of respiratory pattern and improvements in quantitative accuracy from respiratory-gated PET/CT has not been well established. If such a relationship could be estimated, then patient-specific respiratory patterns could be used to prospectively select appropriate motion compensation during image acquisition on a per-patient basis. This study was undertaken to develop a novel statistical model that predicts quantitative changes in PET/CT imaging due to respiratory gating. Free-breathing static FDG-PET images without gating and respiratory-gated FDG-PET images were collected from 22 lung and liver cancer patients on a PET/CT scanner. PET imaging quality was quantified with peak standardized uptake value (SUV(peak)) over lesions of interest. Relative differences in SUV(peak) between static and gated PET images were calculated to indicate quantitative imaging changes due to gating. A comprehensive multidimensional extraction of the morphological and statistical characteristics of respiratory patterns was conducted, resulting in 16 features that characterize representative patterns of a single respiratory trace. The six most informative features were subsequently extracted using a stepwise feature selection approach. The multiple-regression model was trained and tested based on a leave-one-subject-out cross-validation. The predicted quantitative improvements in PET imaging achieved an accuracy higher than 90% using a criterion with a dynamic error-tolerance range for SUV(peak) values. The results of this study suggest that our prediction framework could be applied to determine which patients would likely benefit from respiratory motion compensation when clinicians quantitatively assess PET/CT for therapy target definition and response assessment.

Respiratory trace feature analysis for the prediction of respiratory-gated PET quantification

NASA Astrophysics Data System (ADS)

Wang, Shouyi; Bowen, Stephen R.; Chaovalitwongse, W. Art; Sandison, George A.; Grabowski, Thomas J.; Kinahan, Paul E.

2014-02-01

The benefits of respiratory gating in quantitative PET/CT vary tremendously between individual patients. Respiratory pattern is among many patient-specific characteristics that are thought to play an important role in gating-induced imaging improvements. However, the quantitative relationship between patient-specific characteristics of respiratory pattern and improvements in quantitative accuracy from respiratory-gated PET/CT has not been well established. If such a relationship could be estimated, then patient-specific respiratory patterns could be used to prospectively select appropriate motion compensation during image acquisition on a per-patient basis. This study was undertaken to develop a novel statistical model that predicts quantitative changes in PET/CT imaging due to respiratory gating. Free-breathing static FDG-PET images without gating and respiratory-gated FDG-PET images were collected from 22 lung and liver cancer patients on a PET/CT scanner. PET imaging quality was quantified with peak standardized uptake value (SUVpeak) over lesions of interest. Relative differences in SUVpeak between static and gated PET images were calculated to indicate quantitative imaging changes due to gating. A comprehensive multidimensional extraction of the morphological and statistical characteristics of respiratory patterns was conducted, resulting in 16 features that characterize representative patterns of a single respiratory trace. The six most informative features were subsequently extracted using a stepwise feature selection approach. The multiple-regression model was trained and tested based on a leave-one-subject-out cross-validation. The predicted quantitative improvements in PET imaging achieved an accuracy higher than 90% using a criterion with a dynamic error-tolerance range for SUVpeak values. The results of this study suggest that our prediction framework could be applied to determine which patients would likely benefit from respiratory motion compensation when clinicians quantitatively assess PET/CT for therapy target definition and response assessment.

Pulsed high voltage electric discharge disinfection of microbially contaminated liquids.

PubMed

Anpilov, A M; Barkhudarov, E M; Christofi, N; Kop'ev, V A; Kossyi, I A; Taktakishvili, M I; Zadiraka, Y

2002-01-01

To examine the use of a novel multielectrode slipping surface discharge (SSD) treatment system, capable of pulsed plasma discharge directly in water, in killing micro-organisms. Potable water containing Escherichia coli and somatic coliphages was treated with pulsed electric discharges generated by the SSD. The SSD system was highly efficient in the microbial disinfection of water with a low energy utilization (eta approximately 10-4 kW h l-1). The SSD treatment was effective in the destruction of E. coli and its coliphages through the generation of u.v. radiation, ozone and free radicals. The non-thermal treatment method can be used for the eradication of micro-organisms in a range of contaminated liquids, including milk, negating the use of pasteurization. The method utilizes multipoint electric discharges capable of treating large volumes of liquid under static and flowing regimes.

Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors

PubMed Central

Shuryak, Igor; Dadachova, Ekaterina

2016-01-01

Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental conditions (e.g. fluctuations of temperature and/or nutrient levels) coincide with radioactive contamination; (2) an organism’s radioresistance and bioremediation efficiency in rich laboratory media may be insufficient to carry out radionuclide bioremediation in the field—robustness against multiple stressors is needed. PMID:26808049

Longitudinal relationships among posturography and gait measures in multiple sclerosis.

PubMed

Fritz, Nora E; Newsome, Scott D; Eloyan, Ani; Marasigan, Rhul Evans R; Calabresi, Peter A; Zackowski, Kathleen M

2015-05-19

Gait and balance dysfunction frequently occurs early in the multiple sclerosis (MS) disease course. Hence, we sought to determine the longitudinal relationships among quantitative measures of gait and balance in individuals with MS. Fifty-seven ambulatory individuals with MS (28 relapsing-remitting, 29 progressive) were evaluated using posturography, quantitative sensorimotor and gait measures, and overall MS disability with the Expanded Disability Status Scale at each session. Our cohort's age was 45.8 ± 10.4 years (mean ± SD), follow-up time 32.8 ± 15.4 months, median Expanded Disability Status Scale score 3.5, and 56% were women. Poorer performance on balance measures was related to slower walking velocity. Two posturography measures, the anterior-posterior sway and sway during static eyes open, feet apart conditions, were significant contributors to walk velocity over time (approximate R(2) = 0.95), such that poorer performance on the posturography measures was related to slower walking velocity. Similarly, the anterior-posterior sway and sway during static eyes closed, feet together conditions were also significant contributors to the Timed 25-Foot Walk performance over time (approximate R(2) = 0.83). This longitudinal cohort study establishes a strong relationship between clinical gait measures and posturography. The data show that increases in static posturography and reductions in dynamic posturography are associated with a decline in walk velocity and Timed 25-Foot Walk performance over time. Furthermore, longitudinal balance measures predict future walking performance. Quantitative walking and balance measures are important additions to clinical testing to explore longitudinal change and understand fall risk in this progressive disease population. © 2015 American Academy of Neurology.

Rapid System to Quantitatively Characterize the Airborne Microbial Community

NASA Technical Reports Server (NTRS)

Macnaughton, Sarah J.

1998-01-01

Bioaerosols have been linked to a wide range of different allergies and respiratory illnesses. Currently, microorganism culture is the most commonly used method for exposure assessment. Such culture techniques, however, generally fail to detect between 90-99% of the actual viable biomass. Consequently, an unbiased technique for detecting airborne microorganisms is essential. In this Phase II proposal, a portable air sampling device his been developed for the collection of airborne microbial biomass from indoor (and outdoor) environments. Methods were evaluated for extracting and identifying lipids that provide information on indoor air microbial biomass, and automation of these procedures was investigated. Also, techniques to automate the extraction of DNA were explored.

Biogeochemical Cycle of Methanol in Anoxic Deep-Sea Sediments

PubMed Central

Yanagawa, Katsunori; Tani, Atsushi; Yamamoto, Naoya; Hachikubo, Akihiro; Kano, Akihiro; Matsumoto, Ryo; Suzuki, Yohey

2016-01-01

The biological flux and lifetime of methanol in anoxic marine sediments are largely unknown. We herein reported, for the first time, quantitative methanol removal rates in subsurface sediments. Anaerobic incubation experiments with radiotracers showed high rates of microbial methanol consumption. Notably, methanol oxidation to CO2 surpassed methanol assimilation and methanogenesis from CO2/H2 and methanol. Nevertheless, a significant decrease in methanol was not observed after the incubation, and this was attributed to the microbial production of methanol in parallel with its consumption. These results suggest that microbial reactions play an important role in the sources and sinks of methanol in subseafloor sediments. PMID:27301420

Quantitative Analysis of Cancer Cell Migration in Gradients Of EGF, HGF, and SDF-alpha Using a Microfluidic Chemotaxis Device

DTIC Science & Technology

2005-01-01

Quantitative Analysis of Cancer Cell Migration in Gradients of EGF, HGF, and SDF-alpha Using a Microfluidic Chemotaxis Device The University of California...allowing for parallel analysis . Additionally, simple methods of localizing gels into microdevices are demonstrated. The device was characterized by...To overcome some of these drawbacks, several approaches have utilized free diffusion to produce gradients in static environ - ments.5-9 However

Peter St. John | NREL

Science.gov Websites

for microbial strain design to optimize the production of value-added chemicals from lignin using Pseudomonas putida. Featured Publications "A quantitative model for the prediction of sooting tendency

Drift in ocean currents impacts intergenerational microbial exposure to temperature.

PubMed

Doblin, Martina A; van Sebille, Erik

2016-05-17

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.

Subsonic Static and Dynamic Aerodynamics of Blunt Entry Vehicles

NASA Technical Reports Server (NTRS)

Mitcheltree, Robert A.; Fremaux, Charles M.; Yates, Leslie A.

1999-01-01

The incompressible subsonic aerodynamics of four entry-vehicle shapes with variable c.g. locations are examined in the Langley 20-Foot Vertical Spin Tunnel. The shapes examined are spherically-blunted cones with half-cone angles of 30, 45, and 60 deg. The nose bluntness varies between 0.25 and 0.5 times the base diameter. The Reynolds number based on model diameter for these tests is near 500,000. Quantitative data on attitude and location are collected using a video-based data acquisition system and reduced with a six deg-of-freedom inverse method. All of the shapes examined suffered from strong dynamic instabilities which could produced limit cycles with sufficient amplitudes to overcome static stability of the configuration. Increasing cone half-angle or nose bluntness increases drag but decreases static and dynamic stability.

Lattice QCD static potentials of the meson-meson and tetraquark systems computed with both quenched and full QCD

NASA Astrophysics Data System (ADS)

Bicudo, P.; Cardoso, M.; Oliveira, O.; Silva, P. J.

2017-10-01

We revisit the static potential for the Q Q Q ¯Q ¯ system using SU(3) lattice simulations, studying both the color singlets' ground state and first excited state. We consider geometries where the two static quarks and the two antiquarks are at the corners of rectangles of different sizes. We analyze the transition between a tetraquark system and a two-meson system with a two by two correlator matrix. We compare the potentials computed with quenched QCD and with dynamical quarks. We also compare our simulations with the results of previous studies and analyze quantitatively fits of our results with Ansätze inspired in the string flip-flop model and in its possible color excitations.

Focusing on Environmental Biofilms With Variable-Pressure Scanning Electron Microscopy

NASA Astrophysics Data System (ADS)

Joubert, L.; Wolfaardt, G. M.; Du Plessis, K.

2006-12-01

Since the term biofilm has been coined almost 30 years ago, visualization has formed an integral part of investigations on microbial attachment. Electron microscopic (EM) biofilm studies, however, have been limited by the hydrated extracellular matrix which loses structural integrity with conventional preparative techniques, and under required high-vacuum conditions, resulting in a loss of information on spatial relationships and distribution of biofilm microbes. Recent advances in EM technology enable the application of Variable Pressure Scanning Electron Microscopy (VP SEM) to biofilms, allowing low vacuum and hydrated chamber atmosphere during visualization. Environmental biofilm samples can be viewed in situ, unfixed and fully hydrated, with application of gold-sputter-coating only, to increase image resolution. As the impact of microbial biofilms can be both hazardous and beneficial to man and his environment, recognition of biofilms as a natural form of microbial existence is needed to fully assess the potential role of microbial communities on technology. The integration of multiple techniques to elucidate biofilm processes has become imperative for unraveling complex phenotypic adaptations of this microbial lifestyle. We applied VP SEM as integrative technique with traditional and novel analytical techniques to (1)localize lignocellulosic microbial consortia applied for producing alternative bio-energy sources in the mining wastewater industry, (2) characterize and visualize wetland microbial communities in the treatment of winery wastewater, and (3)determine the impact of recombinant technology on yeast biofilm behavior. Visualization of microbial attachment to a lignocellulose substrate, and degradation of exposed plant tissue, gave insight into fiber degradation and volatile fatty acid production for biological sulphate removal from mining wastewater. Also, the 3D-architecture of complex biofilms developing in constructed wetlands was correlated with molecular fingerprints of wetland communities using tRFLP (Terminal Restriction Fragment Length Polymorphism) - and gave evidence of temporal and spatial variation in a wetland system, to potentially be applied as management tool in wastewater treatment. Visualization of differences in biofilm development by wild and recombinant yeast strains furthermore supported real-time quantitative data of biofilm development by Cryptococcus laurentii and Saccharomyces yeast strains. In all cases VP SEM allowed a more holistic interpretation of biofilm processes than afforded by quantitative empirical data only.

FEASIBILITY STUDY FOR IDENTIFICATION OF STATIC AND DYNAMIC EXPOSURE USING CCD IMAGING TECHNIQUE FOR Caso4:Dy TL DOSEMETERS.

PubMed

Srivastava, Kshama; Soin, Seepika; Sapra, B K; Ratna, P; Datta, D

2017-11-01

The occupational exposure incurred by the radiation workers due to the external radiation is estimated using personal dosemeter placed on the human body during the monitoring period. In certain situations, it is required to determine whether the dosemeter alone was exposed accidentally/intentionally in radiation field (static exposure) or was exposed while being worn by a worker moving in his workplace (dynamic exposure). The present thermoluminscent (TL) based personnel monitoring systems are not capable of distinguishing between the above stated (static and dynamic) exposure conditions. The feasibility of a new methodology developed using the charge coupled device based imaging technique for identification of the static/dynamic exposure of CaSO4:Dy based TL detectors for low energy photons has been investigated. The techniques for the qualitative and the quantitative assessments of the exposure conditions are presented in this paper. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Bacterial survival following shock compression in the GigaPascal range

NASA Astrophysics Data System (ADS)

Hazael, Rachael; Fitzmaurice, Brianna C.; Foglia, Fabrizia; Appleby-Thomas, Gareth J.; McMillan, Paul F.

2017-09-01

The possibility that life can exist within previously unconsidered habitats is causing us to expand our understanding of potential planetary biospheres. Significant populations of living organisms have been identified at depths extending up to several km below the Earth's surface; whereas laboratory experiments have shown that microbial species can survive following exposure to GigaPascal (GPa) pressures. Understanding the degree to which simple organisms such as microbes survive such extreme pressurization under static compression conditions is being actively investigated. The survival of bacteria under dynamic shock compression is also of interest. Such studies are being partly driven to test the hypothesis of potential transport of biological organisms between planetary systems. Shock compression is also of interest for the potential modification and sterilization of foodstuffs and agricultural products. Here we report the survival of Shewanella oneidensis bacteria exposed to dynamic (shock) compression. The samples examined included: (a) a "wild type" (WT) strain and (b) a "pressure adapted" (PA) population obtained by culturing survivors from static compression experiments to 750 MPa. Following exposure to peak shock pressures of 1.5 and 2.5 GPa the proportion of survivors was established as the number of colony forming units (CFU) present after recovery to ambient conditions. The data were compared with previous results in which the same bacterial samples were exposed to static pressurization to the same pressures, for 15 minutes each. The results indicate that shock compression leads to survival of a significantly greater proportion of both WT and PA organisms. The significantly shorter duration of the pressure pulse during the shock experiments (2-3 μs) likely contributes to the increased survival of the microbial species. One reason for this can involve the crossover from deformable to rigid solid-like mechanical relaxational behavior that occurs for bacterial cell walls on the order of seconds in the time-dependent strain rate.

The long-term reliability of static and dynamic quantitative sensory testing in healthy individuals.

PubMed

Marcuzzi, Anna; Wrigley, Paul J; Dean, Catherine M; Adams, Roger; Hush, Julia M

2017-07-01

Quantitative sensory tests (QSTs) have been increasingly used to investigate alterations in somatosensory function in a wide range of painful conditions. The interpretation of these findings is based on the assumption that the measures are stable and reproducible. To date, reliability of QST has been investigated for short test-retest intervals. The aim of this study was to investigate the long-term reliability of a multimodal QST assessment in healthy people, with testing conducted on 3 occasions over 4 months. Forty-two healthy people were enrolled in the study. Static and dynamic tests were performed, including cold and heat pain threshold (CPT, HPT), mechanical wind-up [wind-up ratio (WUR)], pressure pain threshold (PPT), 2-point discrimination (TPD), and conditioned pain modulation (CPM). Systematic bias, relative reliability and agreement were analysed using repeated measure analysis of variance, intraclass correlation coefficients (ICCs3,1) and SE of the measurement (SEM), respectively. Static QST (CPT, HPT, PPT, and TPD) showed good-to-excellent reliability (ICCs: 0.68-0.90). Dynamic QST (WUR and CPM) showed poor-to-good reliability (ICCs: 0.35-0.61). A significant linear decrease over time was observed for mechanical QST at the back (PPT and TPD) and for CPM (P < 0.01). Static QST were stable over a period of 4 months; however, a small systematic decrease over time has been observed for mechanical QST. Dynamic QST showed considerable variability over time; in particular, CPM using PPT as the test stimulus did not show adequate reliability, suggesting that this test paradigm may be less useful for monitoring individuals over time.

Environmental and Microbial Features Affecting Denitrification and Anammox Hotspots in an Estuarine Ecosystem

NASA Astrophysics Data System (ADS)

Lisa, J.; Song, B.; Lefcheck, J. S.; Tobias, C. R.

2016-02-01

Biogeochemical hotspots are characterized as a few sites that exhibit extremely high reaction rates relative to surrounding area, and often account for a high percentage of the overall reaction rates in an ecosystem. Criteria for quantitatively identifying these sites have not been well established. Further, the underlying mechanisms of hotspots have been described in terms of environmental conditions, with little attention paid to the microbial community. The objectives of this study were to establish quantitative criteria to identify denitrification and anammox hotspots, and determine the underlying microbial and environmental factors responsible for elevated N2 production. We used 15N isotope pairing incubation experiments to measure denitrification and anammox rates in the New River Estuary, NC. Quantitative PCR assays of nitrous oxide reductase (nosZ Clades I and II) and hydrazine oxidoreductase (hzo) genes were conducted to estimate denitrifier and anammox abundance. Structural Equation Modeling (SEM) was used to elucidate complex causal relationships between environmental and biological variables. Denitrification hotspots, quantitatively defined as statistical outliers, accounted for 35.6% total denitrification while comprising only 7.3% of the sites. Anammox hotspots,10.6% of the sites, accounted for 60.9% of total anammox. SEM revealed increased sediment organics at lower salinities supported higher functional gene abundance, which in turn resulted in higher N2 production. Surprisingly, denitrification rates were significantly and positively correlated with nosZ Clade II gene abundance, after accounting for the non-significant contributions of the naturally more abundant nosZ Clade I, and other environmental covariates. This is the first time that a quantitative definition of biogeochemical hotspots was put forth and used to determine the importance of anammox and denitrification hotspots in estuarine nitrogen removal capacity. Despite the low area coverage, denitrification and anammox hotspots are major nitrogen removal components and may play a significant role in mitigating eutrophication.

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Goyal, Akshit; Maslov, Sergei

2018-04-01

Microbial ecosystems are remarkably diverse, stable, and usually consist of a mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real ecosystem data, specifically species abundance and prevalence distributions. Resource competition and metabolic commensalism drive the stochastic ecosystem assembly in our model. We demonstrate that even when supplied with just one resource, ecosystems can exhibit high diversity, increasing stability, and partial reproducibility between samples.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

PubMed

Marine, Rachel; McCarren, Coleen; Vorrasane, Vansay; Nasko, Dan; Crowgey, Erin; Polson, Shawn W; Wommack, K Eric

2014-01-30

Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested. Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes. MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

A Universally Applicable and Rapid Method for Measuring the Growth of Streptomyces and Other Filamentous Microorganisms by Methylene Blue Adsorption-Desorption

PubMed Central

Fischer, Marco

2013-01-01

Quantitative assessment of growth of filamentous microorganisms, such as streptomycetes, is generally restricted to determination of dry weight. Here, we describe a straightforward methylene blue-based sorption assay to monitor microbial growth quantitatively, simply, and rapidly. The assay is equally applicable to unicellular and filamentous bacterial and eukaryotic microorganisms. PMID:23666340

Environmental and microbial factors influencing methane and nitrous oxide fluxes in Mediterranean cork oak woodlands: trees make a difference.

PubMed

Shvaleva, Alla; Siljanen, Henri M P; Correia, Alexandra; Costa E Silva, Filipe; Lamprecht, Richard E; Lobo-do-Vale, Raquel; Bicho, Catarina; Fangueiro, David; Anderson, Margaret; Pereira, João S; Chaves, Maria M; Cruz, Cristina; Martikainen, Pertti J

2015-01-01

Cork oak woodlands (montado) are agroforestry systems distributed all over the Mediterranean basin with a very important social, economic and ecological value. A generalized cork oak decline has been occurring in the last decades jeopardizing its future sustainability. It is unknown how loss of tree cover affects microbial processes that are consuming greenhouse gases in the montado ecosystem. The study was conducted under two different conditions in the natural understory of a cork oak woodland in center Portugal: under tree canopy (UC) and open areas without trees (OA). Fluxes of methane and nitrous oxide were measured with a static chamber technique. In order to quantify methanotrophs and bacteria capable of nitrous oxide consumption, we used quantitative real-time PCR targeting the pmoA and nosZ genes encoding the subunit of particulate methane mono-oxygenase and catalytic subunit of the nitrous oxide reductase, respectively. A significant seasonal effect was found on CH4 and N2O fluxes and pmoA and nosZ gene abundance. Tree cover had no effect on methane fluxes; conversely, whereas the UC plots were net emitters of nitrous oxide, the loss of tree cover resulted in a shift in the emission pattern such that the OA plots were a net sink for nitrous oxide. In a seasonal time scale, the UC had higher gene abundance of Type I methanotrophs. Methane flux correlated negatively with abundance of Type I methanotrophs in the UC plots. Nitrous oxide flux correlated negatively with nosZ gene abundance at the OA plots in contrast to that at the UC plots. In the UC soil, soil organic matter had a positive effect on soil extracellular enzyme activities, which correlated positively with the N2O flux. Our results demonstrated that tree cover affects soil properties, key enzyme activities and abundance of microorganisms and, consequently net CH4 and N2O exchange.

Hydrogen Biogeochemistry in Anaerobic and Photosynthetic Ecosystems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The simple biochemistry of molecular hydrogen is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, a great majority of microbial redox processes involve hydrogen as a reactant, product or potential by-product. Accordingly, the energetics (thermodynamics) of each of these processes is affected by variations in local H2 concentrations. It has long been established that this effect is important in governing microbe-microbe interactions and there are multiple demonstrations that "interspecies hydrogen transfer" can alter the products of, inhibit/stimulate, or even reverse microbial metabolic reactions. In anoxic sediments, H2 concentrations themselves are thought to be controlled by the thermodynamics of the predominant H2-consuming microbial process. In sediments from Cape Lookout Bight, this relationship quantitatively describes the co-variation of H2 concentrations with temperature (for methanogens and sulfate reducers) and with sulfate concentration (for sulfate reducers). The quantitative aspect is import= for two reasons: 1) it permits the modeling of H2-sensitive biogeochemistry, such as anaerobic methane oxidation or pathways of organic matter remineralization, as a function of environmental controls; 2) for such a relationship to be observed requires that intracellular biochemistry and bioenergetics are being directly expressed in a component of the extracellular medium. H2 could therefore be utilized a non-invasive probe of cellular energetic function in intact microbial ecosystems. Based on the latter principle we have measured down-core profiles of H2 and other relevant physico-chemical parameters in order to calculate the metabolic energy yields (DG) that support microbial metabolism in Cape Lookout Bight sediments. Methanogens in this system apparently function with energy yields significantly smaller than the minimum requirements suggested by pure culture studies. Our recent work has extended the study of hydrogen to cyanobacterial mat communities. The large amounts of reducing power generated during photosynthetic activity carry the potential to contribute a swamping term to the H2 economy of the anaerobic microbial populations within the mat - and thereby to alter the population structure and biogeochemical function of the mat as a whole. In hypersaline microbial mats, we observe a distinct diel cycle in H2 production and a substantial corresponding flux. On an early Earth dominated by microbial mats, this transmission of photosynthetic reducing power may have carried important implications for both biospheric and atmospheric evolution.

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents

PubMed Central

2013-01-01

Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods. PMID:23755882

A 3D inversion for all-space magnetotelluric data with static shift correction

NASA Astrophysics Data System (ADS)

Zhang, Kun

2017-04-01

Base on the previous studies on the static shift correction and 3D inversion algorithms, we improve the NLCG 3D inversion method and propose a new static shift correction method which work in the inversion. The static shift correction method is based on the 3D theory and real data. The static shift can be detected by the quantitative analysis of apparent parameters (apparent resistivity and impedance phase) of MT in high frequency range, and completed correction with inversion. The method is an automatic processing technology of computer with 0 cost, and avoids the additional field work and indoor processing with good results. The 3D inversion algorithm is improved (Zhang et al., 2013) base on the NLCG method of Newman & Alumbaugh (2000) and Rodi & Mackie (2001). For the algorithm, we added the parallel structure, improved the computational efficiency, reduced the memory of computer and added the topographic and marine factors. So the 3D inversion could work in general PC with high efficiency and accuracy. And all the MT data of surface stations, seabed stations and underground stations can be used in the inversion algorithm.

Local Viscoelastic Properties of Live Cells Investigated Using Dynamic and Quasi-Static Atomic Force Microscopy Methods

PubMed Central

Cartagena, Alexander; Raman, Arvind

2014-01-01

The measurement of viscoelasticity of cells in physiological environments with high spatio-temporal resolution is a key goal in cell mechanobiology. Traditionally only the elastic properties have been measured from quasi-static force-distance curves using the atomic force microscope (AFM). Recently, dynamic AFM-based methods have been proposed to map the local in vitro viscoelastic properties of living cells with nanoscale resolution. However, the differences in viscoelastic properties estimated from such dynamic and traditional quasi-static techniques are poorly understood. In this work we quantitatively reconstruct the local force and dissipation gradients (viscoelasticity) on live fibroblast cells in buffer solutions using Lorentz force excited cantilevers and present a careful comparison between mechanical properties (local stiffness and damping) extracted using dynamic and quasi-static force spectroscopy methods. The results highlight the dependence of measured viscoelastic properties on both the frequency at which the chosen technique operates as well as the interactions with subcellular components beyond certain indentation depth, both of which are responsible for differences between the viscoelasticity property maps acquired using the dynamic AFM method against the quasi-static measurements. PMID:24606928

Dynamic 68Ga-DOTATOC PET/CT and static image in NET patients. Correlation of parameters during PRRT.

PubMed

Van Binnebeek, Sofie; Koole, Michel; Terwinghe, Christelle; Baete, Kristof; Vanbilloen, Bert; Haustermans, Karine; Clement, Paul M; Bogaerts, Kris; Verbruggen, Alfons; Nackaerts, Kris; Van Cutsem, Eric; Verslype, Chris; Mottaghy, Felix M; Deroose, Christophe M

2016-06-28

To investigate the relationship between the dynamic parameters (Ki) and static image-derived parameters of 68Ga-DOTATOC-PET, to determine which static parameter best reflects underlying somatostatin-receptor-expression (SSR) levels on neuroendocrine tumours (NETs). 20 patients with metastasized NETs underwent a dynamic and static 68Ga-DOTATOC-PET before PRRT and at 7 and 40 weeks after the first administration of 90Y-DOTATOC (in total 4 cycles were planned); 175 lesions were defined and analyzed on the dynamic as well as static scans. Quantitative analysis was performed using the software PMOD. One to five target lesions per patient were chosen and delineated manually on the baseline dynamic scan and further, on the corresponding static 68Ga-DOTATOC-PET and the dynamic and static 68Ga-DOTATOC-PET at the other time-points; SUVmax and SUVmean of the lesions was assessed on the other six scans. The input function was retrieved from the abdominal aorta on the images. Further on, Ki was calculated using the Patlak-Plot. At last, 5 reference regions for normalization of SUVtumour were delineated on the static scans resulting in 5 ratios (SUVratio). SUVmax and SUVmean of the tumoural lesions on the dynamic 68Ga-DOTATOC-PET had a very strong correlation with the corresponding parameters in the static scan (R²: 0.94 and 0.95 respectively). SUVmax, SUVmean and Ki of the lesions showed a good linear correlation; the SUVratios correlated poorly with Ki. A significantly better correlation was noticed between Ki and SUVtumour(max and mean) (p < 0.0001). As the dynamic parameter Ki correlates best with the absolute SUVtumour, SUVtumour best reflects underlying SSR-levels in NETs.

A Study of the Use of Contact Loading to Simulate Low Velocity Impact

NASA Technical Reports Server (NTRS)

Highsmith, Alton L.

1997-01-01

Although numerous studies on the impact response of laminated composites have been conducted, there is as yet no agreement within the composites community on what parameter or parameters are adequate for quantifying the severity of an impact event. One of the more interesting approaches that has been proposed uses the maximum contact force during impact to "quantify" the severity of the impact event, provided that the impact velocity is sufficiently low. A significant advantage of this approach, should it prove to be reliable, is that quasi-static contact loading could be used to simulate low velocity impact. In principle, a single specimen, loaded quasi-statically to successively increasing contact loads could be used to map the entire spectrum of damage as a function of maximum contact force. The present study had as its objective assessing whether or not the maximum contact force during impact is a suitable parameter for characterizing an impact. The response of [+/-60/0(sub 4)/+/-60/0(sub 2)](sub s) laminates fabricated from Fiberite T300/934 graphite epoxy and subjected to quasi-static contact loading and to low velocity impact was studied. Three quasi-static contact load levels - 525 lb., 600 lb., and 675 lb. - were selected. Three impact energy levels - 1.14 ft.-lb., 2.0 ft.-lb., and 2.60 ft.-lb. - were chosen in an effort to produce impact events in which the maximum contact forces during the impact events were 525 lb., 600 lb., and 625 lb., respectively. Damage development was documented using dye-penetrant enhanced x-ray radiography. A digital image processing technique was used to obtain quantitative information about the damage zone. Although it was intended that the impact load levels produce maximum contact forces equal to those used in the quasi-static contact experiments, larger contact forces were developed during impact loading. In spite of this, the damage zones developed in impacted specimens were smaller than the damage zones developed in specimens subjected to the corresponding quasi-static contact loading. The impacted specimens may have a greater tendency to develop fiber fracture, but, at present, a quantitative assessment of fiber fracture is not available. In addressing whether or not contact force is an adequate metric for describing the severity of an impact event, the results of this study suggest that it is not. In cases where the quasi-static load level and the maximum contact force during impact were comparable, the quasi-statically loaded specimens consistently developed larger damage zones. It should be noted, however, that using quasi-static damage data to forecast the behavior of impacted material may give conservative estimates of the residual strength of impacted composites.

Ecology, Microbial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopka, Allan

2009-05-15

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Microbial examination of anaerobic sludge adaptation to animal slurry.

PubMed

Moset, V; Cerisuelo, A; Ferrer, P; Jimenez, A; Bertolini, E; Cambra-López, M

2014-01-01

The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-Diversity

NASA Technical Reports Server (NTRS)

Ramirez, Gustavo A; Vaishampayan, Parag A.

2011-01-01

Alpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.

Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells.

PubMed

Ren, Z; Steinberg, L M; Regan, J M

2008-01-01

Converting biodegradable materials into electricity, microbial fuel cells (MFCs) present a promising technology for renewable energy production in specific applications. Unlike typical soluble substrates that have been used as electron donors in MFC studies, cellulose is unique because it requires a microbial consortium that can metabolize both an insoluble electron donor (cellulose) and electron acceptor (electrode). In this study, electricity generation and the microbial ecology of cellulose-fed MFCs were analyzed using a defined co-culture of Clostridium cellulolyticum and Geobacter sulfurreducens. Fluorescent in situ hybridization and quantitative PCR showed that when particulate MN301 cellulose was used as sole substrate, most Clostridium cells were found adhered to cellulose particles in suspension, while most Geobacter cells were attached to the electrode. By comparison, both bacteria resided in suspension and biofilm samples when soluble carboxymethyl cellulose was used. This distinct function-related distribution of the bacteria suggests an opportunity to optimize reactor operation by settling cellulose and decanting supernatant to extend cellulose hydrolysis and improve cellulose-electricity conversion. (c) IWA Publishing 2008.

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

PubMed Central

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

2012-01-01

Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production. PMID:22955886

Toward Accurate and Quantitative Comparative Metagenomics

PubMed Central

Nayfach, Stephen; Pollard, Katherine S.

2016-01-01

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

Toward Accurate and Quantitative Comparative Metagenomics.

PubMed

Nayfach, Stephen; Pollard, Katherine S

2016-08-25

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

Methods for quantitative and qualitative evaluation of vaginal microflora during menstruation.

PubMed Central

Onderdonk, A B; Zamarchi, G R; Walsh, J A; Mellor, R D; Muñoz, A; Kass, E H

1986-01-01

The quantitative and qualitative changes in the bacterial flora of the vagina during menstruation have received inadequate study. Similarly, the effect of vaginal tampons on the microbial flora as well as the relationship between the microbial flora of the vagina and that of the tampon has not been adequately evaluated. The purposes of the present study were (i) to develop quantitative methods for studying the vaginal flora and the flora of tampons obtained during menstruation and (ii) to determine whether there were differences between the microflora of the tampon and that of the vaginal vault. Tampon and swab samples were obtained at various times from eight young healthy volunteers for 8 to 10 menstrual cycles. Samples consisted of swabs from women wearing menstrual pads compared with swab and tampon samples taken at various times during the menstrual cycle. Samples were analyzed for total facultative and anaerobic bacterial counts, and the six dominant bacterial species in each culture were identified. Statistical evaluation of the results indicates that total bacterial counts decreased during menstruation and that swab and tampon samples yielded similar total counts per unit weight of sample. The numbers of bacteria in tampons tended to be lower than in swabs taken at the same time. Overall, during menstruation, the concentrations of lactobacilli declined, but otherwise there was little difference among the species found during menstruation compared with those found in intermenstrual samples. Cotton tampons had little discernible effect on the microbial flora. PMID:3954346

Measurement of the neutral composition of the lower thermosphere above Fort Churchill by rocket-borne mass spectrometer.

NASA Technical Reports Server (NTRS)

Hickman, D. R.; Nier, A. O.

1972-01-01

Measurement of the neutral atmospheric composition above Fort Churchill, Canada (59 N, 94 W), by mass spectrometers in two rocket flights at 0835 CST on Feb. 4 and 6, 1969. A quantitative measure for the extent of agreement with static diffusive equilibrium is introduced, and substantial agreement with profiles predicted when static diffusive equilibrium was assumed is found for all constituents including helium. A sensitive search for atomic nitrogen yielded upper limits of a few per cent for one flight and of 0.2% for the other.

Effect of nonideal square-law detection on static calibration in noise-injection radiometers

NASA Technical Reports Server (NTRS)

Hearn, C. P.

1984-01-01

The effect of nonideal square-law detection on the static calibration for a class of Dicke radiometers is examined. It is shown that fourth-order curvature in the detection characteristic adds a nonlinear term to the linear calibration relationship normally ascribed to noise-injection, balanced Dicke radiometers. The minimum error, based on an optimum straight-line fit to the calibration curve, is derived in terms of the power series coefficients describing the input-output characteristics of the detector. These coefficients can be determined by simple measurements, and detection nonlinearity is, therefore, quantitatively related to radiometric measurement error.

Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes.

PubMed

Hoshino, Tatsuhiko; Inagaki, Fumio

2017-01-01

Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA. To address this issue, we applied stochastic labeling approach with random-tag sequences and developed a NGS-based quantification protocol, which enables simultaneous sequencing and quantification of the targeted DNA. This quantitative sequencing (qSeq) is initiated from single-primer extension (SPE) using a primer with random tag adjacent to the 5' end of target-specific sequence. During SPE, each DNA molecule is stochastically labeled with the random tag. Subsequently, first-round PCR is conducted, specifically targeting the SPE product, followed by second-round PCR to index for NGS. The number of random tags is only determined during the SPE step and is therefore not affected by the two rounds of PCR that may introduce amplification biases. In the case of 16S rRNA genes, after NGS sequencing and taxonomic classification, the absolute number of target phylotypes 16S rRNA gene can be estimated by Poisson statistics by counting random tags incorporated at the end of sequence. To test the feasibility of this approach, the 16S rRNA gene of Sulfolobus tokodaii was subjected to qSeq, which resulted in accurate quantification of 5.0 × 103 to 5.0 × 104 copies of the 16S rRNA gene. Furthermore, qSeq was applied to mock microbial communities and environmental samples, and the results were comparable to those obtained using digital PCR and relative abundance based on a standard sequence library. We demonstrated that the qSeq protocol proposed here is advantageous for providing less-biased absolute copy numbers of each target DNA with NGS sequencing at one time. By this new experiment scheme in microbial ecology, microbial community compositions can be explored in more quantitative manner, thus expanding our knowledge of microbial ecosystems in natural environments.

Method for analyzing microbial communities

DOEpatents

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.

Analysis of Volatile Markers for Virgin Olive Oil Aroma Defects by SPME-GC/FID: Possible Sources of Incorrect Data.

PubMed

Oliver-Pozo, Celia; Aparicio-Ruiz, Ramón; Romero, Inmaculada; García-González, Diego L

2015-12-09

The need to explain virgin olive oil (VOO) aroma descriptors by means of volatiles has raised interest in applying analytical techniques for trapping and quantitating volatiles. Static headspace sampling with solid phase microextraction (SPME) as trapping material is one of the most applied solutions for analyzing volatiles. The use of an internal standard and the determination of the response factors of the main volatiles seem to guarantee the correct determination of volatile concentrations in VOOs by SPME-GC/FID. This paper, however, shows that the competition phenomena between volatiles in their adsorption to the SPME fiber, inherent in static headspace sampling, may affect the quantitation. These phenomena are more noticeable in the particular case of highly odorant matrices, such as rancid and vinegary VOOs with high intensity of defect. The competition phenomena can modify the measurement sensitivity, which can be observed in volatile quantitation as well as in the recording of internal standard areas in different matrices. This paper analyzes the bias of the peak areas and concentrations of those volatiles that are markers for each sensory defect of VOOs (rancid, vinegary, musty, and fusty) when the intensity and complexity of aroma are increased. Of the 17 volatile markers studied in this work, 10 presented some anomalies in the quantitation in highly odorant matrices due the competition phenomena. However, quantitation was not affected in the concentration ranges at which each volatile marker is typically found in the defective oils they were characteristic of, validating their use as markers.

Novel Sensor for the In Situ Measurement of Uranium Fluxes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hatfield, Kirk

2015-02-10

The goal of this project was to develop a sensor that incorporates the field-tested concepts of the passive flux meter to provide direct in situ measures of flux for uranium and groundwater in porous media. Measurable contaminant fluxes [J] are essentially the product of concentration [C] and groundwater flux or specific discharge [q ]. The sensor measures [J] and [q] by changes in contaminant and tracer amounts respectively on a sorbent. By using measurement rather than inference from static parameters, the sensor can directly advance conceptual and computational models for field scale simulations. The sensor was deployed in conjunction withmore » DOE in obtaining field-scale quantification of subsurface processes affecting uranium transport (e.g., advection) and transformation (e.g., uranium attenuation) at the Rifle IFRC Site in Rifle, Colorado. Project results have expanded our current understanding of how field-scale spatial variations in fluxes of uranium, groundwater and salient electron donor/acceptors are coupled to spatial variations in measured microbial biomass/community composition, effective field-scale uranium mass balances, attenuation, and stability. The coupling between uranium, various nutrients and micro flora can be used to estimate field-scale rates of uranium attenuation and field-scale transitions in microbial communities. This research focuses on uranium (VI), but the sensor principles and design are applicable to field-scale fate and transport of other radionuclides. Laboratory studies focused on sorbent selection and calibration, along with sensor development and validation under controlled conditions. Field studies were conducted at the Rifle IFRC Site in Rifle, Colorado. These studies were closely coordinated with existing SBR (formerly ERSP) projects to complement data collection. Small field tests were conducted during the first two years that focused on evaluating field-scale deployment procedures and validating sensor performance under controlled field conditions. In the third and fourth year a suite of larger field studies were conducted. For these studies, the uranium flux sensor was used with uranium speciation measurements and molecular-biological tools to characterize microbial community and active biomass at synonymous wells distributed in a large grid. These field efforts quantified spatial changes in uranium flux and field-scale rates of uranium attenuation (ambient and stimulated), uranium stability, and quantitatively assessed how fluxes and effective reaction rates were coupled to spatial variations in microbial community and active biomass. Analyses of data from these field experiments were used to generate estimates of Monod kinetic parameters that are ‘effective’ in nature and optimal for modeling uranium fate and transport at the field-scale. This project provided the opportunity to develop the first sensor that provides direct measures of both uranium (VI) and groundwater flux. A multidisciplinary team was assembled to include two geochemists, a microbiologist, and two quantitative contaminant hydrologists. Now that the project is complete, the sensor can be deployed at DOE sites to evaluate field-scale uranium attenuation, source behavior, the efficacy of remediation, and off-site risk. Because the sensor requires no power, it can be deployed at remote sites for periods of days to months. The fundamental science derived from this project can be used to advance the development of predictive models for various transport and attenuation processes in aquifers. Proper development of these models is critical for long-term stewardship of contaminated sites in the context of predicting uranium source behavior, remediation performance, and off-site risk.« less

Use of 16S rRNA sequencing and quantitative PCR to correlate venous leg ulcer bacterial bioburden dynamics with wound expansion, antibiotic therapy, and healing

PubMed Central

Sprockett, Daniel D.; Ammons, Christine G.; Tuttle, Marie S.

2016-01-01

Clinical diagnosis of infection in chronic wounds is currently limited to subjective clinical signs and culture-based methods that underestimate the complexity of wound microbial bioburden as revealed by DNA-based microbial identification methods. Here, we use 16S rRNA next generation sequencing and quantitative polymerase chain reaction to characterize weekly changes in bacterial load, community structure, and diversity associated with a chronic venous leg ulcer over the 15-week course of treatment and healing. Our DNA-based methods and detailed sampling scheme reveal that the bacterial bioburden of the wound is unexpectedly dynamic, including changes in the bacterial load and community structure that correlate with wound expansion, antibiotic therapy, and healing. We demonstrate that these multidimensional changes in bacterial bioburden can be summarized using swabs taken prior to debridement, and therefore, can be more easily collected serially than debridement or biopsy samples. Overall, this case illustrates the importance of detailed clinical indicators and longitudinal sampling to determine the pathogenic significance of chronic wound microbial dynamics and guide best use of antimicrobials for improvement of healing outcomes. PMID:25902876

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community.

PubMed

Mayali, Xavier; Weber, Peter K

2018-05-01

To quantitatively link microbial identity with biogeochemical function, we carried out 14 simultaneous stable isotope probing experiments with organic and inorganic C and N substrates to measure the isotope incorporation by over one hundred co-occurring eukaryotic and prokaryotic populations in a coastal community. We found that nitrate was the most commonly incorporated substrate, and that light-driven carbon fixation was carried out by some bacterial taxa from the Flavobacteriales and OM60 (NOR5) clade, in addition to photoautotrophic phytoplankton. We found that organisms that incorporated starch, maltose, glucose, lactose and bicarbonate were phylogenetically clustered, suggesting that specific bacterial lineages specialized in the incorporation of these substrates. The data further revealed that coastal microorganisms spanned a range of resource utilization strategies from generalists to specialists and demonstrated a high level of substrate partitioning, with two thirds of taxa exhibiting unique substrate incorporation patterns and the remaining third shared by no more than three OTUs each. Specialists exhibited more extreme incorporation levels (high or low), whereas generalists displayed more intermediate activity levels. These results shed valuable insights into the bottom-up ecological strategies enabling the persistence of high microbial diversity in aquatic ecosystems.

Measurement and Prediction of the Thermomechanical Response of Shape Memory Alloy Hybrid Composite Beams

NASA Technical Reports Server (NTRS)

Davis, Brian; Turner, Travis L.; Seelecke, Stefan

2008-01-01

An experimental and numerical investigation into the static and dynamic responses of shape memory alloy hybrid composite (SMAHC) beams is performed to provide quantitative validation of a recently commercialized numerical analysis/design tool for SMAHC structures. The SMAHC beam specimens consist of a composite matrix with embedded pre-strained SMA actuators, which act against the mechanical boundaries of the structure when thermally activated to adaptively stiffen the structure. Numerical results are produced from the numerical model as implemented into the commercial finite element code ABAQUS. A rigorous experimental investigation is undertaken to acquire high fidelity measurements including infrared thermography and projection moire interferometry for full-field temperature and displacement measurements, respectively. High fidelity numerical results are also obtained from the numerical model and include measured parameters, such as geometric imperfection and thermal load. Excellent agreement is achieved between the predicted and measured results of the static and dynamic thermomechanical response, thereby providing quantitative validation of the numerical tool.

QTest: Quantitative Testing of Theories of Binary Choice.

PubMed

Regenwetter, Michel; Davis-Stober, Clintin P; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

2014-01-01

The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of "Random Cumulative Prospect Theory." A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences.

Microbial Metabolic Roles in Bedrock Degradation and the Genesis of Biomineral and Biopattern Biosignatures in Caves and Mines

NASA Astrophysics Data System (ADS)

Boston, P. J.

2016-12-01

In subsurface environments like natural or anthropogenic caves (aka mines), microorganisms facilitate considerable bedrock degradation under a variety of circumstances. Mobilization of materials from these processes frequently produces distinctive biominerals, identifiable biotextures, and unique biopatterns. Microbial activities can even determine the form of speleothems (secondary mineral cave decorations), thus providing highly conspicuous macroscopic biosignatures. It is critical to understand microbial-mineral interactions, recognizing that while the lithology controls important aspects of the environment, in turn, the geochemistry is greatly affected by the biology. Microbial communities can contribute to the actual formation of cavities (speleogenesis), and subsequent enlargement of caves and vugs and the mineral deposits that enrich many subterranean spaces. A major challenge is to quantify such influences. Genetic analysis is revealing a vast but highly partitioned biodiversity in the overall rock fracture habitat of Earth's crust especially in caves and mines where the three phases of matter (solid rock, fluids, and gases) typically interact producing high niche richness. Lessons learned from the microbial/geochemical systems that we have studied include: 1) significant similarities in metabolic functions between different geochemical systems, 2) ubiquity of metal oxidation for energy, 3) ubiquity of biofilms, some highly mineralized, 4) highly interdependent, multi-species communities that can only transform materials in consortia, 5) complex ecological succession including characteristic pioneer species, 6) often very slow growth rates in culture, 7) prevalence of very small cell sizes, ( 100 - 500 nm diam.), 8) mineral reprecipitation of mobilized materials, often dependent on the presence of live microbial communities to produce initial amorphous compounds followed by gradual crystallization, and 9) resultant in situ self-fossilization. Microbial metabolism occurs against a complex backdrop of hydrology, geochemistry, and geological structures of subsurface environments. These are not static but change in response to both short term and much longer geological time scales thus presenting significant challenges in interpretation.

Drift in ocean currents impacts intergenerational microbial exposure to temperature

PubMed Central

Doblin, Martina A.; van Sebille, Erik

2016-01-01

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034–1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming. PMID:27140608

Assessment of microbial products in the biosorption process of Cu(II) onto aerobic granular sludge: Extracellular polymeric substances contribution and soluble microbial products release.

PubMed

Huang, Linxian; Li, Meilin; Si, Guangchao; Wei, Jinglin; Ngo, Huu Hao; Guo, Wenshan; Xu, Weiying; Du, Bin; Wei, Qin; Wei, Dong

2018-05-18

In the present study, the responses of microbial products in the biosorption process of Cu(II) onto aerobic granular sludge were evaluated by using batch and spectroscopic approaches. Batch experimental data showed that extracellular polymeric substances (EPSs) contributed to Cu(II) removal from an aqueous solution, especially when treating low metal concentrations, whereas soluble microbial products (SMPs) were released under the metal stress during biosorption process. A three-dimensional excitation-emission matrix (3D-EEM) identified four main fluorescence peaks in the EPS, i.e., tryptophan protein-like, aromatic protein-like, humic-like and fulvic acid-like substances, and their fluorescence intensities decreased gradually in the presence of Cu(II) during the sorption process. Particularly, tryptophan protein-like substances quenched the Cu(II) binding to a much higher extent through a static quenching process with less than one class of binding sites. According to the synchronous fluorescence spectra, the whole fluorescence intensity of released SMP samples expressed an increased trend with different degrees along with contact time. Two-dimensional correlation spectroscopy (2D-COS) suggested that the fulvic-like fluorescence fraction might be more susceptible to metal exposure than other fractions. The result of molecular weight distribution demonstrated that the SMPs released from the biosorption process differed significantly according to contact time. The result obtained could provide new insights into the responses of microbial products from aerobic granular sludge with heavy metal treatment. Copyright © 2018. Published by Elsevier Inc.

Multifunctional sample preparation kit and on-chip quantitative nucleic acid sequence-based amplification tests for microbial detection.

PubMed

Zhao, Xinyan; Dong, Tao

2012-10-16

This study reports a quantitative nucleic acid sequence-based amplification (Q-NASBA) microfluidic platform composed of a membrane-based sampling module, a sample preparation cassette, and a 24-channel Q-NASBA chip for environmental investigations on aquatic microorganisms. This low-cost and highly efficient sampling module, having seamless connection with the subsequent steps of sample preparation and quantitative detection, is designed for the collection of microbial communities from aquatic environments. Eight kinds of commercial membrane filters are relevantly analyzed using Saccharomyces cerevisiae, Escherichia coli, and Staphylococcus aureus as model microorganisms. After the microorganisms are concentrated on the membrane filters, the retentate can be easily conserved in a transport medium (TM) buffer and sent to a remote laboratory. A Q-NASBA-oriented sample preparation cassette is originally designed to extract DNA/RNA molecules directly from the captured cells on the membranes. Sequentially, the extract is analyzed within Q-NASBA chips that are compatible with common microplate readers in laboratories. Particularly, a novel analytical algorithmic method is developed for simple but robust on-chip Q-NASBA assays. The reported multifunctional microfluidic system could detect a few microorganisms quantitatively and simultaneously. Further research should be conducted to simplify and standardize ecological investigations on aquatic environments.

Microbiology of Explanted Suture Segments from Infected and Noninfected Surgical Patients

PubMed Central

Krepel, Candace J.; Marks, Richard M.; Rossi, Peter J.; Sanger, James; Goldblatt, Matthew; Graham, Mary Beth; Rothenburger, Stephen; Collier, John; Seabrook, Gary R.

2013-01-01

Sutures under selective host/environmental factors can potentiate postoperative surgical site infection (SSI). The present investigation characterized microbial recovery and biofilm formation from explanted absorbable (AB) and nonabsorbable (NAB) sutures from infected and noninfected sites. AB and NAB sutures were harvested from noninfected (70.9%) and infected (29.1%) sites in 158 patients. At explantation, devices were sonicated and processed for qualitative/quantitative bacteriology; selective sutures were processed for scanning electron microscopy (SEM). Bacteria were recovered from 85 (53.8%) explanted sites; 39 sites were noninfected, and 46 were infected. Suture recovery ranged from 11.1 to 574.6 days postinsertion. A significant difference in mean microbial recovery between noninfected (1.2 isolates) and infected (2.7 isolates) devices (P < 0.05) was noted. Staphylococcus epidermidis, Staphylococcus aureus, coagulase-negative staphylococci (CNS), Peptostreptococcus spp., Bacteroides fragilis, Escherichia coli, Enterococcus spp., Pseudomonas aeruginosa, and Serratia spp. were recovered from infected devices, while commensal skin flora was recovered from noninfected devices. No significant difference in quantitative microbial recovery between infected monofilament and multifilament sutures was noted. Biofilm was present in 100% and 66.6% of infected and noninfected devices, respectively (P < 0.042). We conclude that both monofilament and braided sutures provide a hospitable surface for microbial adherence: (i) a significant difference in microbial recovery from infected and noninfected sutures was noted, (ii) infected sutures harbored a mixed flora, including multidrug-resistant health care-associated pathogens, and (iii) a significant difference in the presence or absence of a biofilm in infected versus noninfected explanted devices was noted. Further studies to document the benefit of focused risk reduction strategies to minimize suture contamination and biofilm formation postimplantation are warranted. PMID:23175247

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

PubMed Central

Turner, Stephanie; Mikutta, Robert; Meyer-Stüve, Sandra; Guggenberger, Georg; Schaarschmidt, Frank; Lazar, Cassandre S.; Dohrmann, Reiner; Schippers, Axel

2017-01-01

Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils. PMID:28579976

Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Oubre, Cherie M.; Birmele, Michele N.; Castro, Victoria A.; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.; Jones, Kathy U.; Singhal, Adesh; Johnston, Angela S.; Roman, Monserrate C.; Ozbolt, Tamra A.;

[Analysis of Microbial Community in the Membrane Bio-Reactor (MBR) Rural Sewage Treatment System].

PubMed

Kong, Xiao; Cui, Bing-jian; Jin, De-cai; Wu, Shang-hua; Yang, Bo; Deng, Ye; Zhuang, Guo-qiang; Zhuang, Xu-liang

2015-09-01

Uncontrolled release and arbitrary irrigation reuse of rural wastewater may lead to water pollution, and the microbial pathogens could threaten the safety of freshwater resources and public health. To understand the microbial community structure of rural wastewater and provide the theory for microbial risk assessment of wastewater irrigation, microbial community diversities in the Membrane Bio-Reactor (MBR) process for rural wastewater treatment was studied by terminal restriction fragment length polymorphism (T-RFLP) and 16S rDNA gene clone library. Meanwhile, changes of Arcobacter spp. and total bacteria before and after treatment were detected through real-time quantitative PCR. The clone library results showed that there were 73 positive clones included Proteobacteria (91. 80%), Firmicutes (2. 70%), Bacteroidetes (1. 40%), and uncultured bacteria (4. 10%) in the untreated wastewater. The typical pathogenic genus Arcobacter belonging to e-Proteobacteria was the dominant component of the library, accounting for 68. 5% of all clones. The main groups and their abundance in different treatments were significantly distinct. The highest values of species abundance (S), Shannon-Wiener (H) and Evenness (E) were observed in the adjusting tank, which were 43. 0, 3. 56 and 0. 95, respectively. The real-time quantitative PCR results showed that the copy number of Arcobacter spp. was (1. 09 ± 0. 064 0) x 10(11) copies.L-1 in the untreated sewage, which was consistent with the result of 16S rDNA gene clone library. Compared to untreated wastewater, bacterial copy number in the treated effluent decreased 100 to 1 000 times, respectively, suggesting that MBR treatment system could remove the microbial quantity in such scale. In the recycled water, the physicochemical parameters and indicator bacteria met the water quality standard of farmland irrigation. However, further research is needed to estimate the potential health risks caused by residual pathogenic microorganisms in future.

Considerations for estimating microbial environmental data concentrations collected from a field setting

PubMed Central

Silvestri, Erin E; Yund, Cynthia; Taft, Sarah; Bowling, Charlena Yoder; Chappie, Daniel; Garrahan, Kevin; Brady-Roberts, Eletha; Stone, Harry; Nichols, Tonya L

2017-01-01

In the event of an indoor release of an environmentally persistent microbial pathogen such as Bacillus anthracis, the potential for human exposure will be considered when remedial decisions are made. Microbial site characterization and clearance sampling data collected in the field might be used to estimate exposure. However, there are many challenges associated with estimating environmental concentrations of B. anthracis or other spore-forming organisms after such an event before being able to estimate exposure. These challenges include: (1) collecting environmental field samples that are adequate for the intended purpose, (2) conducting laboratory analyses and selecting the reporting format needed for the laboratory data, and (3) analyzing and interpreting the data using appropriate statistical techniques. This paper summarizes some key challenges faced in collecting, analyzing, and interpreting microbial field data from a contaminated site. Although the paper was written with considerations for B. anthracis contamination, it may also be applicable to other bacterial agents. It explores the implications and limitations of using field data for determining environmental concentrations both before and after decontamination. Several findings were of interest. First, to date, the only validated surface/sampling device combinations are swabs and sponge-sticks on stainless steel surfaces, thus limiting availability of quantitative analytical results which could be used for statistical analysis. Second, agreement needs to be reached with the analytical laboratory on the definition of the countable range and on reporting of data below the limit of quantitation. Finally, the distribution of the microbial field data and statistical methods needed for a particular data set could vary depending on these data that were collected, and guidance is needed on appropriate statistical software for handling microbial data. Further, research is needed to develop better methods to estimate human exposure from pathogens using environmental data collected from a field setting. PMID:26883476

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

NASA Astrophysics Data System (ADS)

Maslov, Sergei; Sneppen, Kim

2017-01-01

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

Electricity generation by anaerobic bacteria and anoxic sediments from hypersaline soda lakes

USGS Publications Warehouse

Miller, L.G.; Oremland, R.S.

2008-01-01

Anaerobic bacteria and anoxic sediments from soda lakes produced electricity in microbial fuel cells (MFCs). No electricity was generated in the absence of bacterial metabolism. Arsenate respiring bacteria isolated from moderately hypersaline Mono Lake (Bacillus selenitireducens), and salt-saturated Searles Lake, CA (strain SLAS-1) oxidized lactate using arsenate as the electron acceptor. However, these cultures grew equally well without added arsenate using the MFC anode as their electron acceptor, and in the process oxidized lactate more efficiently. The decrease in electricity generation by consumption of added alternative electron acceptors (i.e. arsenate) which competed with the anode for available electrons proved to be a useful indicator of microbial activity and hence life in the fuel cells. Shaken sediment slurries from these two lakes also generated electricity, with or without added lactate. Hydrogen added to sediment slurries was consumed but did not stimulate electricity production. Finally, electricity was generated in statically incubated "intact" sediment cores from these lakes. More power was produced in sediment from Mono Lake than from Searles Lake, however microbial fuel cells could detect low levels of metabolism operating under moderate and extreme conditions of salt stress. ?? 2008 US Government.

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

PubMed Central

Maslov, Sergei; Sneppen, Kim

2017-01-01

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

Measures of static postural control moderate the association of strength and power with functional dynamic balance.

PubMed

Forte, Roberta; Boreham, Colin A G; De Vito, Giuseppe; Ditroilo, Massimiliano; Pesce, Caterina

2014-12-01

Age-related reductions in strength and power are considered to negatively impact balance control, but the existence of a direct association is still an issue of debate. This is possibly due to the fact that balance assessment is complex, reflects different underlying physiologic mechanisms and involves quantitative measurements of postural sway or timing of performance during balance tasks. The present study evaluated the moderator effect of static postural control on the association of power and strength with dynamic balance tasks. Fifty-seven healthy 65-75 year old individuals performed tests of dynamic functional balance (walking speed under different conditions) and of strength, power and static postural control. Dynamic balance performance (walking speed) was associated with lower limb strength and power, as well as postural control under conditions requiring postural adjustments (narrow surface walking r(2) = 0.31, p < 0.001). An interaction effect between strength and static postural control was found with narrow surface walking and talking while walking (change of β 0.980, p < 0.001 in strength for 1 SD improvements in static postural control for narrow walking, and [Formula: see text] -0.730, p < 0.01 in talking while walking). These results indicate that good static postural control facilitates the utilisation of lower limb strength to better perform complex, dynamic functional balance tasks. Practical implications for assessment and training are discussed.

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information

PubMed Central

Edsgärd, Daniel; Iglesias, Maria Jesus; Reilly, Sarah-Jayne; Hamsten, Anders; Tornvall, Per; Odeberg, Jacob; Emanuelsson, Olof

2016-01-01

Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively. PMID:26887787

Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.

PubMed

Hawley, Alyse K; Kheirandish, Sam; Mueller, Andreas; Leung, Hilary T C; Norbeck, Angela D; Brewer, Heather M; Pasa-Tolic, Ljiljana; Hallam, Steven J

2013-01-01

Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics. © 2013 Elsevier Inc. All rights reserved.

Smoking cessation alters subgingival microbial recolonization.

PubMed

Fullmer, S C; Preshaw, P M; Heasman, P A; Kumar, P S

2009-06-01

Smoking cessation improves the clinical manifestations of periodontitis; however, its effect on the subgingival biofilm, the primary etiological agent of periodontitis, is unclear. The purpose of this study was to investigate, longitudinally, if smoking cessation altered the composition of the subgingival microbial community, by means of a quantitative, cultivation-independent assay for bacterial profiling. Subgingival plaque was collected at baseline, and 3, 6, and 12 months post-treatment from smokers who received root planing and smoking cessation counseling. The plaque was analyzed by terminal restriction fragment length polymorphism (t-RFLP). Microbial profiles differed significantly between smokers and quitters at 6 and 12 months following smoking cessation. The microbial community in smokers was similar to baseline, while quitters demonstrated significantly divergent profiles. Changes in bacterial levels contributed to this shift. These findings reveal a critical role for smoking cessation in altering the subgingival biofilm and suggest a mechanism for improved periodontal health associated with smoking cessation.

Respiration-to-DNA ratio reflects physiological state of microorganisms in root-free and rhizosphere soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, E.; Blagodatsky, S.; Kuzyakov, Y.

2009-04-01

The double-stranded DNA (dsDNA) content in soil can serve as a measure of microbial biomass under near steady-state conditions and quantitatively reflect the exponential microbial growth initiated by substrate addition. The yield of respired CO2 per microbial biomass unit (expressed as DNA content) could be a valuable physiological indicator reflecting state of soil microbial community. Therefore, investigations combining both analyses of DNA content and respiration of soil microorganisms under steady-state and during periods of rapid growth are needed. We studied the relationship between CO2 evolution and microbial dsDNA content in native and glucose-amended samples of root-free and rhizosphere soil under Beta vulgaris (Cambisol, loamy sand from the field experiment of the Institute of Agroecology FAL, Braunschweig, Germany). Quantity of dsDNA was determined by direct DNA isolation from soil with mechanic and enzymatic disruption of microbial cell walls with following spectrofluorimetric detection with PicoGreen (Blagodatskaya et al., 2003). Microbial biomass and the kinetic parameters of microbial growth were estimated by dynamics of the CO2 emission from soil amended with glucose and nutrients (Blagodatsky et al., 2000). The CO2 production rate was measured hourly at 22оС using an automated infrared-gas analyzer system. The overall increase in microbial biomass, DNA content, maximal specific growth rate and therefore, in the fraction of microorganisms with r-strategy were observed in rhizosphere as compared to bulk soil. The rhizosphere effect for microbial respiration, biomass and specific growth rate was more pronounced for plots with half-rate of N fertilizer compared to full N addition. The DNA content was significantly lower in bulk compared to rhizosphere soil both before and during microbial growth initiated by glucose amendment. Addition of glucose to the soil strongly increased the amount of CO2 respired per DNA unit. Without substrate addition the VCO2-to-total DNA ratios were lower than 0.1 µg CO2-C µg-1 total DNA h-1 whereas during exponential microbial growth these values increased consistently and exceeded 1 µg CO2-C µg-1 DNA h-1. Thus, the VCO2-to-total DNA ratio strongly changes along with the physiological state of soil microorganisms and can be used as valuable physiological parameter. In growing microorganisms the quantity of CO2 evolved per unit of newly formed DNA was identical in rhizosphere and root free soil and averaged for 13.5 ± 1.1 µg CO2-C µg-1 newly formed DNA. The CO2 yield per unit of newly formed DNA allows the estimation of microbial growth efficiency and validation of specific growth rates obtained during kinetic analysis of respiration curves. The study was supported by European Commission (Marie Curie IIF program, project MICROSOM) and by Alexander von Humboldt Foundation. References: Blagodatskaya EV, Blagodatskii SA, Anderson TH. 2003. Quantitative Isolation of Microbial DNA from Different Types of Soils of Natural and Agricultural Ecosystems. Microbiology 72(6):744-749. Blagodatsky SA, Heinemeyer O, Richter J. 2000. Estimating the active and total soil microbial biomass by kinetic respiration analysis. Biology and Fertility of Soils 32(1):73-81.

Quantitative prediction of repaglinide-rifampicin complex drug interactions using dynamic and static mechanistic models: delineating differential CYP3A4 induction and OATP1B1 inhibition potential of rifampicin.

PubMed

Varma, Manthena V S; Lin, Jian; Bi, Yi-An; Rotter, Charles J; Fahmi, Odette A; Lam, Justine L; El-Kattan, Ayman F; Goosen, Theunis C; Lai, Yurong

2013-05-01

Repaglinide is mainly metabolized by cytochrome P450 enzymes CYP2C8 and CYP3A4, and it is also a substrate to a hepatic uptake transporter, organic anion transporting polypeptide (OATP)1B1. The purpose of this study is to predict the dosing time-dependent pharmacokinetic interactions of repaglinide with rifampicin, using mechanistic models. In vitro hepatic transport of repaglinide, characterized using sandwich-cultured human hepatocytes, and intrinsic metabolic parameters were used to build a dynamic whole-body physiologically-based pharmacokinetic (PBPK) model. The PBPK model adequately described repaglinide plasma concentration-time profiles and successfully predicted area under the plasma concentration-time curve ratios of repaglinide (within ± 25% error), dosed (staggered 0-24 hours) after rifampicin treatment when primarily considering induction of CYP3A4 and reversible inhibition of OATP1B1 by rifampicin. Further, a static mechanistic "extended net-effect" model incorporating transport and metabolic disposition parameters of repaglinide and interaction potency of rifampicin was devised. Predictions based on the static model are similar to those observed in the clinic (average error ∼19%) and to those based on the PBPK model. Both the models suggested that the combined effect of increased gut extraction and decreased hepatic uptake caused minimal repaglinide systemic exposure change when repaglinide is dosed simultaneously or 1 hour after the rifampicin dose. On the other hand, isolated induction effect as a result of temporal separation of the two drugs translated to an approximate 5-fold reduction in repaglinide systemic exposure. In conclusion, both dynamic and static mechanistic models are instrumental in delineating the quantitative contribution of transport and metabolism in the dosing time-dependent repaglinide-rifampicin interactions.

Quantitative SIMS Imaging of Agar-Based Microbial Communities.

PubMed

Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

2018-05-01

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Effect of bioaugmentation and biostimulation on sulfate-reducing column startup captured by functional gene profiling.

PubMed

Pereyra, Luciana P; Hiibel, Sage R; Perrault, Elizabeth M; Reardon, Kenneth F; Pruden, Amy

2012-10-01

Sulfate-reducing permeable reactive zones (SR-PRZs) depend upon a complex microbial community to utilize a lignocellulosic substrate and produce sulfides, which remediate mine drainage by binding heavy metals. To gain insight into the impact of the microbial community composition on the startup time and pseudo-steady-state performance, functional genes corresponding to cellulose-degrading (CD), fermentative, sulfate-reducing, and methanogenic microorganisms were characterized in columns simulating SR-PRZs using quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). Duplicate columns were bioaugmented with sulfate-reducing or CD bacteria or biostimulated with ethanol or carboxymethyl cellulose and compared with baseline dairy manure inoculum and uninoculated controls. Sulfate removal began after ~ 15 days for all columns and pseudo-steady state was achieved by Day 30. Despite similar performance, DGGE profiles of 16S rRNA gene and functional genes at pseudo-steady state were distinct among the column treatments, suggesting the potential to control ultimate microbial community composition via bioaugmentation and biostimulation. qPCR revealed enrichment of functional genes in all columns between the initial and pseudo-steady-state time points. This is the first functional gene-based study of CD, fermentative and sulfate-reducing bacteria and methanogenic archaea in a lignocellulose-based environment and provides new qualitative and quantitative insight into startup of a complex microbial system. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Knowledge Management for the Analysis of Complex Experimentation.

ERIC Educational Resources Information Center

Maule, R.; Schacher, G.; Gallup, S.

2002-01-01

Describes a knowledge management system that was developed to help provide structure for dynamic and static data and to aid in the analysis of complex experimentation. Topics include quantitative and qualitative data; mining operations using artificial intelligence techniques; information architecture of the system; and transforming data into…

Accuracy of the NDI Wave Speech Research System

ERIC Educational Resources Information Center

Berry, Jeffrey J.

2011-01-01

Purpose: This work provides a quantitative assessment of the positional tracking accuracy of the NDI Wave Speech Research System. Method: Three experiments were completed: (a) static rigid-body tracking across different locations in the electromagnetic field volume, (b) dynamic rigid-body tracking across different locations within the…

Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

PubMed

Kerepesi, Csaba; Grolmusz, Vince

2016-05-01

DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet--a webserver implementation of AMPHORA2--, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under-performers: they counted quite reliably each short read to their respective taxon, producing the typical genome length bias. The benchmark dataset is available at http://pitgroup.org/static/3RandomGenome-100kavg150bps.fna.

Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic

PubMed Central

Frank-Fahle, Béatrice A.; Yergeau, Étienne; Greer, Charles W.; Lantuit, Hugues; Wagner, Dirk

2014-01-01

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic. PMID:24416279

Cheese Microbial Risk Assessments — A Review

PubMed Central

Choi, Kyoung-Hee; Lee, Heeyoung; Lee, Soomin; Kim, Sejeong; Yoon, Yohan

2016-01-01

Cheese is generally considered a safe and nutritious food, but foodborne illnesses linked to cheese consumption have occurred in many countries. Several microbial risk assessments related to Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli infections, causing cheese-related foodborne illnesses, have been conducted. Although the assessments of microbial risk in soft and low moisture cheeses such as semi-hard and hard cheeses have been accomplished, it has been more focused on the correlations between pathogenic bacteria and soft cheese, because cheese-associated foodborne illnesses have been attributed to the consumption of soft cheeses. As a part of this microbial risk assessment, predictive models have been developed to describe the relationship between several factors (pH, Aw, starter culture, and time) and the fates of foodborne pathogens in cheese. Predictions from these studies have been used for microbial risk assessment as a part of exposure assessment. These microbial risk assessments have identified that risk increased in cheese with high moisture content, especially for raw milk cheese, but the risk can be reduced by preharvest and postharvest preventions. For accurate quantitative microbial risk assessment, more data including interventions such as curd cooking conditions (temperature and time) and ripening period should be available for predictive models developed with cheese, cheese consumption amounts and cheese intake frequency data as well as more dose-response models. PMID:26950859

New directions in coral reef microbial ecology.

PubMed

Garren, Melissa; Azam, Farooq

2012-04-01

Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Microbial assessment of cabin air quality on commercial airliners

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Stuecker, Tara; Bearman, Gregory; Venkateswaran, Kasthuri

2005-01-01

The microbial burdens of 69 cabin air samples collected from commercial airliners were assessed via conventional culture-dependent, and molecular-based microbial enumeration assays. Cabin air samples from each of four separate flights aboard two different carriers were collected via air-impingement. Microbial enumeration techniques targeting DNA, ATP, and endotoxin were employed to estimate total microbial burden. The total viable microbial population ranged from 0 to 3.6 x10 4 cells per 100 liters of air, as assessed by the ATP-assay. When these same samples were plated on R2A minimal medium, anywhere from 2% to 80% of these viable populations were cultivable. Five of the 29 samples examined exhibited higher cultivable counts than ATP derived viable counts, perhaps a consequence of the dormant nature (and thus lower concentration of intracellular ATP) of cells inhabiting these air cabin samples. Ribosomal RNA gene sequence analysis showed these samples to consist of a moderately diverse group of bacteria, including human pathogens. Enumeration of ribosomal genes via quantitative-PCR indicated that population densities ranged from 5 x 10 1 ' to IO 7 cells per 100 liters of air. Each of the aforementioned strategies for assessing overall microbial burden has its strengths and weaknesses; this publication serves as a testament to the power of their use in concert.

Quantitative analysis of microbial biomass yield in aerobic bioreactor.

PubMed

Watanabe, Osamu; Isoda, Satoru

2013-12-01

We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

3D Biomimetic Magnetic Structures for Static Magnetic Field Stimulation of Osteogenesis.

PubMed

Paun, Irina Alexandra; Popescu, Roxana Cristina; Calin, Bogdan Stefanita; Mustaciosu, Cosmin Catalin; Dinescu, Maria; Luculescu, Catalin Romeo

2018-02-07

We designed, fabricated and optimized 3D biomimetic magnetic structures that stimulate the osteogenesis in static magnetic fields. The structures were fabricated by direct laser writing via two-photon polymerization of IP-L780 photopolymer and were based on ellipsoidal, hexagonal units organized in a multilayered architecture. The magnetic activity of the structures was assured by coating with a thin layer of collagen-chitosan-hydroxyapatite-magnetic nanoparticles composite. In vitro experiments using MG-63 osteoblast-like cells for 3D structures with gradients of pore size helped us to find an optimum pore size between 20-40 µm. Starting from optimized 3D structures, we evaluated both qualitatively and quantitatively the effects of static magnetic fields of up to 250 mT on cell proliferation and differentiation, by ALP (alkaline phosphatase) production, Alizarin Red and osteocalcin secretion measurements. We demonstrated that the synergic effect of 3D structure optimization and static magnetic stimulation enhances the bone regeneration by a factor greater than 2 as compared with the same structure in the absence of a magnetic field.

3D Biomimetic Magnetic Structures for Static Magnetic Field Stimulation of Osteogenesis

PubMed Central

Paun, Irina Alexandra; Popescu, Roxana Cristina; Calin, Bogdan Stefanita; Mustaciosu, Cosmin Catalin; Dinescu, Maria; Luculescu, Catalin Romeo

2018-01-01

We designed, fabricated and optimized 3D biomimetic magnetic structures that stimulate the osteogenesis in static magnetic fields. The structures were fabricated by direct laser writing via two-photon polymerization of IP-L780 photopolymer and were based on ellipsoidal, hexagonal units organized in a multilayered architecture. The magnetic activity of the structures was assured by coating with a thin layer of collagen-chitosan-hydroxyapatite-magnetic nanoparticles composite. In vitro experiments using MG-63 osteoblast-like cells for 3D structures with gradients of pore size helped us to find an optimum pore size between 20–40 µm. Starting from optimized 3D structures, we evaluated both qualitatively and quantitatively the effects of static magnetic fields of up to 250 mT on cell proliferation and differentiation, by ALP (alkaline phosphatase) production, Alizarin Red and osteocalcin secretion measurements. We demonstrated that the synergic effect of 3D structure optimization and static magnetic stimulation enhances the bone regeneration by a factor greater than 2 as compared with the same structure in the absence of a magnetic field. PMID:29414875

Characterisation of microbial biocoenosis in vertical subsurface flow constructed wetlands.

PubMed

Tietz, Alexandra; Kirschner, Alexander; Langergraber, Günter; Sleytr, Kirsten; Haberl, Raimund

2007-07-15

In this study a quantitative description of the microbial biocoenosis in subsurface vertical flow constructed wetlands fed with municipal wastewater was carried out. Three different methods (substrate induced respiration, ATP measurement and fumigation-extraction) were applied to measure the microbial biomass at different depths of planted and unplanted systems. Additionally, bacterial biomass was determined by epifluorescence microscopy and productivity was measured via (14)C leucine incorporation into bacterial biomass. All methods showed that >50% of microbial biomass and bacterial activity could be found in the first cm and about 95% in the first 10 cm of the filter layer. Bacterial biomass in the first 10 cm of the filter body accounted only for 16-19% of the total microbial biomass. Whether fungi or methodical uncertainties are mainly responsible for the difference between microbial and bacterial biomass remains to be examined. A comparison between the purification performance of planted and unplanted pilot-scale subsurface vertical flow constructed wetlands (PSCWs) showed no significant difference with the exception of the reduction of enterococci. The microbial biomass in all depths of the filter body was also not different in planted and unplanted systems. Compared with data from soils the microbial biomass in the PSCWs was high, although the specific surface area of the used sandy filter material available for biofilm growth was lower, especially in the beginning of the set-up of the PSCWs, due to missing clay and silt fraction.

Quantitative Microbial Risk Assessment and Infectious Disease Transmission Modeling of Waterborne Enteric Pathogens.

PubMed

Brouwer, Andrew F; Masters, Nina B; Eisenberg, Joseph N S

2018-04-20

Waterborne enteric pathogens remain a global health threat. Increasingly, quantitative microbial risk assessment (QMRA) and infectious disease transmission modeling (IDTM) are used to assess waterborne pathogen risks and evaluate mitigation. These modeling efforts, however, have largely been conducted independently for different purposes and in different settings. In this review, we examine the settings where each modeling strategy is employed. QMRA research has focused on food contamination and recreational water in high-income countries (HICs) and drinking water and wastewater in low- and middle-income countries (LMICs). IDTM research has focused on large outbreaks (predominately LMICs) and vaccine-preventable diseases (LMICs and HICs). Human ecology determines the niches that pathogens exploit, leading researchers to focus on different risk assessment research strategies in different settings. To enhance risk modeling, QMRA and IDTM approaches should be integrated to include dynamics of pathogens in the environment and pathogen transmission through populations.

Endotoxins in Environmental and Clinical Samples Assessed by GC-Tandem MS

NASA Astrophysics Data System (ADS)

Szponar, Bogumila

Bacteria appeared on the Earth millions years before us and human evolution was triggered by the constant presence of pathogenic and symbiotic microorganisms in our surroundings. Interplay occurred between higher organism and microbial consortia residing in the host organs and on the epithelial surfaces; another natural space of bacteria-human interaction is the indoor environment where we spend the majority of our lifetime. Indoor microbial exposure affects our well-being and can result in respiratory symptoms, such as allergies and asthma, since both dead and live microorganisms and their cell constituents, including lipopolysaccharides (LPS, endotoxins), interact with our immune system. Thus, there is a demand for robust tools for qualitative and quantitative determination of the microbial communities that we are exposed to.

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

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.

Bovine mastitis may be associated with the deprivation of gut Lactobacillus.

PubMed

Ma, C; Zhao, J; Xi, X; Ding, J; Wang, H; Zhang, H; Kwok, L Y

2016-02-01

Bovine mastitis is an economical important microbial disease in dairy industry. Some recent human clinical trials have shown that oral probiotics supplementation could effectively control clinical mastitis, suggesting that the mechanism of mastitis protection might be achieved via the host gut microbiota. We aimed to test our hypothesis that bovine mastitis was related to changes in both the mammary and gut microbial profiles. By quantitative PCR, the milk and faecal microbial profiles of cows with low (<3×10 5 cells/ml) and high (>1×10 6 cells/ml) somatic cell count (SCC) were compared. Firstly, we observed drastic differences in both the milk and faecal microbial compositions at genus and Lactobacillus-species levels between the two groups. Secondly, the pattern of faecal microbial community changes of mastitis cows was similar to that of the milk, characterised by a general increase in the mastitis pathogens (Enterococcus, Streptococcus and Staphylococcus) and deprivation of Lactobacillus and its members (L. salivarius, L. sakei, L. ruminis, L. delbrueckii, L. buchneri, and L. acidophilus). Thirdly, only the faecal lactobacilli, but not bifidobacteria correlated with the milk microbial communities and SCC. Our data together hint to a close association between bovine mastitis, the host gut and milk microbiota.

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring

PubMed Central

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-01-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40–60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats. PMID:28072418

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring.

PubMed

Ward, Laura; Taylor, Michael W; Power, Jean F; Scott, Bradley J; McDonald, Ian R; Stott, Matthew B

2017-05-01

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE PAGES

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

2016-08-09

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Quantitation of Fine Displacement in Echography

NASA Astrophysics Data System (ADS)

Masuda, Kohji; Ishihara, Ken; Yoshii, Ken; Furukawa, Toshiyuki; Kumagai, Sadatoshi; Maeda, Hajime; Kodama, Shinzo

1993-05-01

A High-speed Digital Subtraction Echography was developed to visualize the fine displacement of human internal organs. This method indicates differences in position through time series images of high-frame-rate echography. Fine displacement less than ultrasonic wavelength can be observed. This method, however, lacks the ability to quantitatively measure displacement length. The subtraction between two successive images was affected by displacement direction in spite of the displacement length being the same. To solve this problem, convolution of an echogram with Gaussian distribution was used. To express displacement length as brightness quantitatively, normalization using a brightness gradient was applied. The quantitation algorithm was applied to successive B-mode images. Compared to the simply subtracted images, quantitated images express more precisely the motion of organs. Expansion of the carotid artery and fine motion of ventricular walls can be visualized more easily. Displacement length can be quantitated with wavelength. Under more static conditions, this system quantitates displacement length that is much less than wavelength.

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Modeling human perception of orientation in altered gravity

PubMed Central

Clark, Torin K.; Newman, Michael C.; Oman, Charles M.; Merfeld, Daniel M.; Young, Laurence R.

2015-01-01

Altered gravity environments, such as those experienced by astronauts, impact spatial orientation perception, and can lead to spatial disorientation and sensorimotor impairment. To more fully understand and quantify the impact of altered gravity on orientation perception, several mathematical models have been proposed. The utricular shear, tangent, and the idiotropic vector models aim to predict static perception of tilt in hyper-gravity. Predictions from these prior models are compared to the available data, but are found to systematically err from the perceptions experimentally observed. Alternatively, we propose a modified utricular shear model for static tilt perception in hyper-gravity. Previous dynamic models of vestibular function and orientation perception are limited to 1 G. Specifically, they fail to predict the characteristic overestimation of roll tilt observed in hyper-gravity environments. To address this, we have proposed a modification to a previous observer-type canal-otolith interaction model based upon the hypothesis that the central nervous system (CNS) treats otolith stimulation in the utricular plane differently than stimulation out of the utricular plane. Here we evaluate our modified utricular shear and modified observer models in four altered gravity motion paradigms: (a) static roll tilt in hyper-gravity, (b) static pitch tilt in hyper-gravity, (c) static roll tilt in hypo-gravity, and (d) static pitch tilt in hypo-gravity. The modified models match available data in each of the conditions considered. Our static modified utricular shear model and dynamic modified observer model may be used to help quantitatively predict astronaut perception of orientation in altered gravity environments. PMID:25999822

Visualizing risks in cancer communication: A systematic review of computer-supported visual aids.

PubMed

Stellamanns, Jan; Ruetters, Dana; Dahal, Keshav; Schillmoeller, Zita; Huebner, Jutta

2017-08-01

Health websites are becoming important sources for cancer information. Lay users, patients and carers seek support for critical decisions, but they are prone to common biases when quantitative information is presented. Graphical representations of risk data can facilitate comprehension, and interactive visualizations are popular. This review summarizes the evidence on computer-supported graphs that present risk data and their effects on various measures. The systematic literature search was conducted in several databases, including MEDLINE, EMBASE and CINAHL. Only studies with a controlled design were included. Relevant publications were carefully selected and critically appraised by two reviewers. Thirteen studies were included. Ten studies evaluated static graphs and three dynamic formats. Most decision scenarios were hypothetical. Static graphs could improve accuracy, comprehension, and behavioural intention. But the results were heterogeneous and inconsistent among the studies. Dynamic formats were not superior or even impaired performance compared to static formats. Static graphs show promising but inconsistent results, while research on dynamic visualizations is scarce and must be interpreted cautiously due to methodical limitations. Well-designed and context-specific static graphs can support web-based cancer risk communication in particular populations. The application of dynamic formats cannot be recommended and needs further research. Copyright © 2017 Elsevier B.V. All rights reserved.

Static and dynamic light scattering of healthy and malaria-parasite invaded red blood cells

NASA Astrophysics Data System (ADS)

Park, Yongkeun; Diez-Silva, Monica; Fu, Dan; Popescu, Gabriel; Choi, Wonshik; Barman, Ishan; Suresh, Subra; Feld, Michael S.

2010-03-01

We present the light scattering of individual Plasmodium falciparum-parasitized human red blood cells (Pf-RBCs), and demonstrate progressive alterations to the scattering signal arising from the development of malaria-inducing parasites. By selectively imaging the electric fields using quantitative phase microscopy and a Fourier transform light scattering technique, we calculate the light scattering maps of individual Pf-RBCs. We show that the onset and progression of pathological states of the Pf-RBCs can be clearly identified by the static scattering maps. Progressive changes to the biophysical properties of the Pf-RBC membrane are captured from dynamic light scattering.

A statics-dynamics equivalence through the fluctuation–dissipation ratio provides a window into the spin-glass phase from nonequilibrium measurements

PubMed Central

Baity-Jesi, Marco; Calore, Enrico; Cruz, Andres; Fernandez, Luis Antonio; Gil-Narvión, José Miguel; Gordillo-Guerrero, Antonio; Iñiguez, David; Maiorano, Andrea; Marinari, Enzo; Martin-Mayor, Victor; Monforte-Garcia, Jorge; Muñoz Sudupe, Antonio; Navarro, Denis; Parisi, Giorgio; Perez-Gaviro, Sergio; Ricci-Tersenghi, Federico; Ruiz-Lorenzo, Juan Jesus; Schifano, Sebastiano Fabio; Tarancón, Alfonso; Tripiccione, Raffaele; Yllanes, David

2017-01-01

We have performed a very accurate computation of the nonequilibrium fluctuation–dissipation ratio for the 3D Edwards–Anderson Ising spin glass, by means of large-scale simulations on the special-purpose computers Janus and Janus II. This ratio (computed for finite times on very large, effectively infinite, systems) is compared with the equilibrium probability distribution of the spin overlap for finite sizes. Our main result is a quantitative statics-dynamics dictionary, which could allow the experimental exploration of important features of the spin-glass phase without requiring uncontrollable extrapolations to infinite times or system sizes. PMID:28174274

Measurement of residual solvents in a drug substance by a purge-and-trap method.

PubMed

Lakatos, Miklós

2008-08-05

The purge-and-trap (P&T) gas extraction method combined with gas chromatography was studied for its suitability for quantitative residual solvents determination in a water-soluble active pharmaceutical ingredient (API). Some analytical method performance characteristics were investigated, namely, the repeatability, the accuracy and the detection limit of determination. The results show that the P&T technique is--as expected--more sensitive than the static headspace, thus it can be used for the determination of residual solvents pertaining to the ICH Class 1 group. It was found that it could be an alternative sample preparation method besides the static headspace (HS) method.

Evaluation of an interactive, case-based review session in teaching medical microbiology.

PubMed

Blewett, Earl L; Kisamore, Jennifer L

2009-08-27

Oklahoma State University-Center for Health Sciences (OSU-CHS) has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial. Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session. Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session. The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified.

Evaluation of an interactive, case-based review session in teaching medical microbiology

PubMed Central

Blewett, Earl L; Kisamore, Jennifer L

2009-01-01

Background Oklahoma State University-Center for Health Sciences (OSU-CHS) has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial. Methods Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session. Results Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session. Conclusion The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified. PMID:19712473

Application of quantitative microbial risk assessments for estimation of risk management metrics: Clostridium perfringens in ready-to-eat and partially cooked meat and poultry products as an example.

PubMed

Crouch, Edmund A; Labarre, David; Golden, Neal J; Kause, Janell R; Dearfield, Kerry L

2009-10-01

The U.S. Department of Agriculture, Food Safety and Inspection Service is exploring quantitative risk assessment methodologies to incorporate the use of the Codex Alimentarius' newly adopted risk management metrics (e.g., food safety objectives and performance objectives). It is suggested that use of these metrics would more closely tie the results of quantitative microbial risk assessments (QMRAs) to public health outcomes. By estimating the food safety objective (the maximum frequency and/or concentration of a hazard in a food at the time of consumption) and the performance objective (the maximum frequency and/or concentration of a hazard in a food at a specified step in the food chain before the time of consumption), risk managers will have a better understanding of the appropriate level of protection (ALOP) from microbial hazards for public health protection. We here demonstrate a general methodology that allows identification of an ALOP and evaluation of corresponding metrics at appropriate points in the food chain. It requires a two-dimensional probabilistic risk assessment, the example used being the Monte Carlo QMRA for Clostridium perfringens in ready-to eat and partially cooked meat and poultry products, with minor modifications to evaluate and abstract required measures. For demonstration purposes, the QMRA model was applied specifically to hot dogs produced and consumed in the United States. Evaluation of the cumulative uncertainty distribution for illness rate allows a specification of an ALOP that, with defined confidence, corresponds to current industry practices.

Cotton defense induction patterns under spatially, temporally and quantitatively varying herbivory levels

USDA-ARS?s Scientific Manuscript database

The optimal defense theory (ODT) predicts that plants allocate defense compounds to their tissues depending on its value and the likelihood of herbivore attack. Whereas ODT has been confirmed for static damage levels it remains poorly understood if ODT holds true for defense organization of inducibl...

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

PubMed

Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

2017-01-01

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.

Diflerent formulations of microbial respiratory losses and microbial efficiency have pronounced short and long term consequences for soil C dynamics and soil respiration

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Billings, S. A.

2016-12-01

Much of the variability in projections of Earth's future C balance derives from uncertainty in how to formulate and parameterize models of biologically mediated transformations of soil organic C (SOC). Over the past decade, models of belowground decomposition have incorporated more realism, namely microbial biomass and exoenzyme pools, but it remains unclear whether microbially mediated decomposition is accurately formulated. Different models and different assumptions about how microbial efficiency, defined in terms of respiratory losses, varies with temperature exert great influence on SOC and CO2 flux projections for the future. Here, we incorporate a physiologically realistic formulation of CO2 loss from microbes, distinct from extant formulations and logically consistent with microbial C uptake and losses, into belowground dynamics and contrast its projections for SOC pools and CO2 flux from soils to those from the phenomenological formulations of efficiency in current models. We quantitatively describe how short and long term SOC dynamics are influenced by different mathematical formulations of efficiency, and that our lack of knowledge regarding loss rates from SOC and microbial biomass pools, specific respiration rate and maximum substrate uptake rate severely constrains our ability to confidently parameterize microbial SOC modules in Earth System Models. Both steady-state SOC and microbial biomass C pools, as well as transient responses to perturbations, can differ substantially depending on how microbial efficiency is derived. In particular, the discrepancy between SOC stocks for different formulations of efficiency varies from negligible to more than two orders of magnitude, depending on the relative values of respiratory versus non-respiratory losses from microbial biomass. Mass-specific respiration and proportional loss rates from soil microbes emerge as key determinants of the consequences of different formulations of efficiency for C flux in soils.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung.

PubMed

Holman, Beverley F; Cuplov, Vesna; Hutton, Brian F; Groves, Ashley M; Thielemans, Kris

2016-04-21

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant (18)F-FDG and (18)F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

NASA Astrophysics Data System (ADS)

Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

2016-04-01

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

Ecofriendly degradation of sulfonated diazo dye C.I. Reactive Green 19A using Micrococcus glutamicus NCIM-2168.

PubMed

Saratale, R G; Saratale, G D; Chang, J S; Govindwar, S P

2009-09-01

Micrococcus glutamicus NCIM-2168 exhibited complete decolorization and degradation of C.I. Reactive Green 19A (an initial concentration of 50 mg l(-1)) within 42 h at temperature 37 degrees C and pH 8, under static condition. Extent of mineralization was determined with total organic carbon (TOC) and chemical oxygen demand (COD) measurement, showing a satisfactory reduction of TOC (72%) and COD (66%) within 42 h. Enzyme studies shows involvement of oxidoreductive enzymes in decolorization/degradation process. Analytical studies of the extracted metabolites confirmed the significant degradation of Reactive Green 19A into various metabolites. The microbial toxicity and phytotoxicity assay revealed that the degradation of Reactive Green 19A produced nontoxic metabolites. In addition, the M. glutamicus strain was applied to decolorize a mixture of ten reactive dyes showing a 63% decolorization (in terms of decrease in ADMI value) within 72 h, along with 48% and 42% reduction in TOC and COD under static condition.

Ammonia removal via microbial fuel cell (MFC) dynamic reactor

NASA Astrophysics Data System (ADS)

Alabiad, I.; Ali, U. F. M.; Zakarya, I. A.; Ibrahim, N.; Radzi, R. W.; Zulkurnai, N. Z.; Azmi, N. H.

2017-06-01

Landfill leachate is generally known as high-strength wastewater that is difficult to handle and contains dissolved extracts and suspended matter. Microbial fuel cells (MFCs) were designed to treat landfill leachate while continuously producing power (voltage output). Three different anodes were tested in MFC reactors: carbon black, activated carbon, and zinc electrodes. Movements in the MFC reactor during treatment were also a key factor for testing. Results showed a difference in ammonia levels in the three anodes used. The study compared the efficiency of static and dynamic modes of MFC in removing ammonia. Continual leachate movement in the reactor could increase the rate of removal of the ammonia components. The setup provided a viable condition for maximum removal because the reactor movement caused the sludge to disintegrate, which allowed ammonia to separate easily from the parent leachate. Ammonia removal also resulted from the transfer of ammonium through the membrane or from ammonia loss. Constant exchange of ionic content benefited the MFC performance by increasing power production and decreasing internal electrode material resistance. This paper presents the results of the analyses of leachate treatment from the solid waste landfill located in Padang Siding Landfill, Perlis. The performance of ammonia removal was enhanced using different types of electrodes. In both modes, activated carbon performed better than black carbon and zinc. The respective percentages of ammonia removal for activated carbon of dynamic over static were 96.6%, 66.6%, and 92.8% for activated carbon, zinc, and black carbon. The results provide further information on the possibility of using MFCs in landfill leachate treatment systems.

Evolution of microbial dynamics during the maturation phase of the composting of different types of waste.

PubMed

Villar, Iria; Alves, David; Garrido, Josefina; Mato, Salustiano

2016-08-01

During composting, facilities usually exert greater control over the bio-oxidative phase of the process, which uses a specific technology and generally has a fixed duration. After this phase, the material is deposited to mature, with less monitoring during the maturation phase. While there has been considerable study of biological parameters during the thermophilic phase, there is less research on the stabilization and maturation phase. This study evaluates the effects of the type of starting material on the evolution of microbial dynamics during the maturation phase of composting. Three waste types were used: sludge from the fish processing industry, municipal sewage sludge and pig manure, each independently mixed with shredded pine wood as bulking agent. The composting system for each waste type comprised a static reactor with capacity of 600L for the bio-oxidative phase followed by stabilization and maturation phase in triplicate 200L boxes for 112days. Phospholipid fatty acids, enzyme activities and physico-chemical parameters were measured throughout the maturation phase. The evolution of the total microbial biomass, Gram + bacteria, Gram - bacteria, fungi and enzymatic activities (β-glucosidase, cellulase, protease, acid and alkaline phosphatase) depended significantly on the waste type (p<0.001). The predominant microbial community for each waste type remained present throughout the maturation process, indicating that the waste type determines the microorganisms that are able to develop at this stage. While fungi predominated during fish sludge maturation, manure and municipal sludge were characterized by a greater proportion of bacteria. Both the structure of the microbial community and enzymatic activities provided important information for monitoring the composting process. More attention should be paid to the maturation phase in order to optimize composting. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Spatiotemporal microbiota dynamics from quantitative in vitro and in silico models of the gut

NASA Astrophysics Data System (ADS)

Hwa, Terence

The human gut harbors a dynamic microbial community whose composition bears great importance for the health of the host. Here, we investigate how colonic physiology impacts bacterial growth behaviors, which ultimately dictate the gut microbiota composition. Combining measurements of bacterial growth physiology with analysis of published data on human physiology into a quantitative modeling framework, we show how hydrodynamic forces in the colon, in concert with other physiological factors, determine the abundances of the major bacterial phyla in the gut. Our model quantitatively explains the observed variation of microbiota composition among healthy adults, and predicts colonic water absorption (manifested as stool consistency) and nutrient intake to be two key factors determining this composition. The model further reveals that both factors, which have been identified in recent correlative studies, exert their effects through the same mechanism: changes in colonic pH that differentially affect the growth of different bacteria. Our findings show that a predictive and mechanistic understanding of microbial ecology in the human gut is possible, and offer the hope for the rational design of intervention strategies to actively control the microbiota. This work is supported by the Bill and Melinda Gates Foundation.

Quantitative Microbial Risk Assessment of Freshwater Impacted by Animal Fecal Material

EPA Science Inventory

We evaluated the potential for human illness from a hypothetical recreational exposure to freshwater impacted by land-applied, agricultural animal fecal material. The hypothetical exposure scenario included the following characteristics: 1) fresh cattle manure, pig slurry, or ch...

Effects of Nutrient Enrichment on Microbial Communities and Carbon Cycling in Wetland Soils

NASA Astrophysics Data System (ADS)

Hartman, W.; Neubauer, S. C.; Richardson, C. J.

2013-12-01

Soil microbial communities are responsible for catalyzing biogeochemical transformations underlying critical wetland functions, including cycling of carbon (C) and nutrients, and emissions of greenhouse gasses (GHG). Alteration of nutrient availability in wetland soils may commonly occur as the result of anthropogenic impacts including runoff from human land uses in uplands, alteration of hydrology, and atmospheric deposition. However, the impacts of altered nutrient availability on microbial communities and carbon cycling in wetland soils are poorly understood. To assess these impacts, soil microbial communities and carbon cycling were determined in replicate experimental nutrient addition plots (control, +N, +P, +NP) across several wetland types, including pocosin peat bogs (NC), freshwater tidal marshes (GA), and tidal salt marshes (SC). Microbial communities were determined by pyrosequencing (Roche 454) extracted soil DNA, targeting both bacteria (16S rDNA) and fungi (LSU) at a depth of ca. 1000 sequences per plot. Wetland carbon cycling was evaluated using static chambers to determine soil GHG fluxes, and plant inclusion chambers were used to determine ecosystem C cycling. Soil bacterial communities responded to nutrient addition treatments in freshwater and tidal marshes, while fungal communities did not respond to treatments in any of our sites. We also compared microbial communities to continuous biogeochemical variables in soil, and found that bacterial community composition was correlated only with the content and availability of soil phosphorus, while fungi responded to phosphorus stoichiometry and soil pH. Surprisingly, we did not find a significant effect of our nutrient addition treatments on most metrics of carbon cycling. However, we did find that several metrics of soil carbon cycling appeared much more related to soil phosphorus than to nitrogen or soil carbon pools. Finally, while overall microbial community composition was weakly correlated with soil carbon cycling, our work did identify a small number of individual taxonomic groups that were more strongly correlated with soil CO2 flux. These results suggest that a small number of microbial groups may potentially serve as keystone taxa (and functional indicators), which simple community fingerprinting approaches may overlook. Our results also demonstrate strong effects of soil phosphorus availability on both microbial communities and soil carbon cycling, even in wetland types traditionally considered to be nitrogen limited.

Comparative ecology of H2 cycling in sedimentary and phototrophic ecosystems

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Albert, Daniel B.; Alperin, Marc J.; Bebout, Brad M.; Martens, Christopher S.; Des Marais, David J.

2002-01-01

The simple biochemistry of H2 is critical to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. The sensitivity of each of these processes to H2 can be described collectively, through the quantitative language of thermodynamics. A necessary prerequisite is to understand the factors that, in turn, control H2 partial pressures. These factors are assessed for two distinctly different ecosystems. In anoxic sediments from Cape Lookout Bight (North Carolina, USA), H2 partial pressures are strictly maintained at low, steady-state levels by H2-consuming organisms, in a fashion that can be quantitatively predicted by simple thermodynamic calculations. In phototrophic microbial mats from Baja California (Mexico), H2 partial pressures are controlled by the activity of light-sensitive H2-producing organisms, and consequently fluctuate over orders of magnitude on a daily basis. The differences in H2 cycling can subsequently impact any of the H2-sensitive microbial processes in these systems. In one example, methanogenesis in Cape Lookout Bight sediments is completely suppressed through the efficient consumption of H2 by sulfate-reducing bacteria; in contrast, elevated levels of H2 prevail in the producer-controlled phototrophic system, and methanogenesis occurs readily in the presence of 40 mM sulfate.

Occurrence and quantitative microbial risk assessment of Cryptosporidium and Giardia in soil and air samples.

PubMed

Balderrama-Carmona, Ana Paola; Gortáres-Moroyoqui, Pablo; Álvarez-Valencia, Luis Humberto; Castro-Espinoza, Luciano; Mondaca-Fernández, Iram; Balderas-Cortés, José de Jesús; Chaidez-Quiroz, Cristóbal; Meza-Montenegro, María Mercedes

2014-09-01

Cryptosporidium oocysts and Giardia cysts can be transmitted by the fecal-oral route and may cause gastrointestinal parasitic zoonoses. These zoonoses are common in rural zones due to the parasites being harbored in fecally contaminated soil. This study assessed the risk of illness (giardiasis and cryptosporidiosis) from inhaling and/or ingesting soil and/or airborne dust in Potam, Mexico. To assess the risk of infection, Quantitative Microbial Risk Assessment (QMRA) was employed, with the following steps: (1) hazard identification, (2) hazard exposure, (3) dose-response, and (4) risk characterization. Cryptosporidium oocysts and Giardia cysts were observed in 52% and 57%, respectively, of total soil samples (n=21), and in 60% and 80%, respectively, of air samples (n=12). The calculated annual risks were higher than 9.9 × 10(-1) for both parasites in both types of sample. Soil and air inhalation and/or ingestion are important vehicles for these parasites. To our knowledge, the results obtained in the present study represent the first QMRAs for cryptosporidiosis and giardiasis due to soil and air inhalation/ingestion in Mexico. In addition, this is the first evidence of the microbial air quality around these parasites in rural zones. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis.

PubMed

Wen, Chengping; Zheng, Zhijun; Shao, Tiejuan; Liu, Lin; Xie, Zhijun; Le Chatelier, Emmanuelle; He, Zhixing; Zhong, Wendi; Fan, Yongsheng; Zhang, Linshuang; Li, Haichang; Wu, Chunyan; Hu, Changfeng; Xu, Qian; Zhou, Jia; Cai, Shunfeng; Wang, Dawei; Huang, Yun; Breban, Maxime; Qin, Nan; Ehrlich, Stanislav Dusko

2017-07-27

The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers. Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis

PubMed Central

Sulyok, Michael; Liu, Xingzhong; Rao, Mingyong

2016-01-01

Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption. PMID:27337135

Suitability and setup of next-generation sequencing-based method for taxonomic characterization of aquatic microbial biofilm.

PubMed

Bakal, Tomas; Janata, Jiri; Sabova, Lenka; Grabic, Roman; Zlabek, Vladimir; Najmanova, Lucie

2018-06-16

A robust and widely applicable method for sampling of aquatic microbial biofilm and further sample processing is presented. The method is based on next-generation sequencing of V4-V5 variable regions of 16S rRNA gene and further statistical analysis of sequencing data, which could be useful not only to investigate taxonomic composition of biofilm bacterial consortia but also to assess aquatic ecosystem health. Five artificial materials commonly used for biofilm growth (glass, stainless steel, aluminum, polypropylene, polyethylene) were tested to determine the one giving most robust and reproducible results. The effect of used sampler material on total microbial composition was not statistically significant; however, the non-plastic materials (glass, metal) gave more stable outputs without irregularities among sample parallels. The bias of the method is assessed with respect to the employment of a non-quantitative step (PCR amplification) to obtain quantitative results (relative abundance of identified taxa). This aspect is often overlooked in ecological and medical studies. We document that sequencing of a mixture of three merged primary PCR reactions for each sample and further evaluation of median values from three technical replicates for each sample enables to overcome this bias and gives robust and repeatable results well distinguishing among sampling localities and seasons.

SNP-VISTA: An Interactive SNPs Visualization Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shah, Nameeta; Teplitsky, Michael V.; Pennacchio, Len A.

2005-07-05

Recent advances in sequencing technologies promise better diagnostics for many diseases as well as better understanding of evolution of microbial populations. Single Nucleotide Polymorphisms(SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it is possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease and then screen for causative mutations.In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmentalmore » samples makes possible more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at http://genome.lbl.gov/vista/snpvista.« less

Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility.

PubMed

Vigneron, Adrien; Alsop, Eric B; Chambers, Brian; Lomans, Bartholomeus P; Head, Ian M; Tsesmetzis, Nicolas

2016-04-01

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

PubMed

Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

2013-07-01

Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility

PubMed Central

Alsop, Eric B.; Chambers, Brian; Lomans, Bartholomeus P.; Head, Ian M.; Tsesmetzis, Nicolas

2016-01-01

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms. PMID:26896143

New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

PubMed Central

Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

2013-01-01

In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

Formation of Microbial Streamers by Flow-Induced Shear and Their Hydrodynamic Effects

NASA Astrophysics Data System (ADS)

Gong, J.; Olsen, K. A.; Nguyen, T.; Tice, M. M.; 2012; 2013, G. C.

2014-12-01

Microbial streamers are productive elements of surface-attached microbial communities that paradoxically seem to roughen mats under rapid, high shear flows, potentially exposing the mat to greater risk of erosion. They are common features found in modern hot-spring outflow channels, yet their formation mechanisms and effects on mat erosion are poorly understood. We test a hypothesis that streamers are produced by shear-induced viscoelastic deformation, and that streamers grow to heal detached turbulent boundary layers. Laboratory flume experiments were conducted using Particle Image/Tracking Velocimetry (PIV/PTV) to gain quantitative insights into the behavior of flows around small projections constructed from 3D-printed plastics or hydrated EPS gels, as well as artificial streamers. The combined use of fabricated hard and viscoelastic shapes, tracer particles, sheet lasers and high speed cameras allowed visualization of flows and quantitative measurements. Results show that primary and secondary flows (backflow behind projections) combine to produce deformations that drive the elongation of the top and ultimately initiate streamer formation. With insufficient secondary flows, streamers are not able to rise up from the basal mat. This implies that a combination of sufficient topographic relief and flow strength is required for streamers to form. In addition, flow measurements indicate that the presence of artificial streamers made the surface hydraulically smoother, and in effect reducing bed shear at the base. These results suggest a novel set of feedbacks that could reduce net mat erosion in energetic flows, and could help guide the evaluation of biosignatures in sedimentary rocks deposited in the presence of microbial mats.

Energy, ecology and the distribution of microbial life.

PubMed

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Energy, ecology and the distribution of microbial life

PubMed Central

Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

2013-01-01

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

PubMed

Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

2016-11-01

It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

NASA Astrophysics Data System (ADS)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

QTest: Quantitative Testing of Theories of Binary Choice

PubMed Central

Regenwetter, Michel; Davis-Stober, Clintin P.; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

2014-01-01

The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of “Random Cumulative Prospect Theory.” A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences. PMID:24999495

Complicating Canons: A Critical Literacy Challenge to Common Core Assessment

ERIC Educational Resources Information Center

Peel, Anne

2017-01-01

The widespread adoption of the Common Core State Standards in the US has prioritized rigorous reading of complex texts. The emphasis on text complexity has led to instructional and assessment materials that constrain critical literacy practices by emphasizing quantitative features of text, such as sentence length, and a static list of text…

Ericson fluctuations in an open deterministic quantum system: theory meets experiment.

PubMed

Madroñero, Javier; Buchleitner, Andreas

2005-12-31

We provide numerically exact photoexcitation cross sections of rubidium Rydberg states in crossed, static electric, and magnetic fields, in quantitative agreement with recent experimental results. Their spectral backbone underpins a clear transition towards the Ericson regime, associated with a universal, fluctuating behavior of the cross section of strongly coupled, fragmenting quantum systems.

Elementary Students' Reasoning about Angle Constructions

ERIC Educational Resources Information Center

Cullen, Amanda L.; Cullen, Craig J.; O'Hanlon, Wendy A.

2017-01-01

In this report, we discuss the findings from 2 pilot studies investigating the effects of interventions designed to provide students in Grades 3-5 with opportunities to work with dynamic and static models of angles in a dynamic geometry environment. We discuss the effects of the interventions on the children's development of quantitative reasoning…

RELATIONSHIPS OF QUANTITATIVE STRUCTURE-ACTIVITY TO COMPARATIVE TOXICITY OF SELECTED PHENOLS IN THE 'PIMEPHALES PROMELAS' AND 'TETRAHYMENA PYRIFORMIS' TEST SYSTEMS

EPA Science Inventory

The relative toxic response of 27 selected phenols in the 96-hr acute flowthrough Pimephales promelas (fathead minnow) and the 48- to 60-hr chronic static Tetrahymena pyriformis (ciliate protozoan) test systems was evaluated. Log Kow-dependent linear regression analyses revealed ...

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Non-cultural methods of human microflora evaluation for the benefit of crew medical control in confined habitat

NASA Astrophysics Data System (ADS)

Viacheslav, Ilyin; Lana, Moukhamedieva; Georgy, Osipov; Aleksey, Batov; Zoya, Soloviova; Robert, Mardanov; Yana, Panina; Anna, Gegenava

2011-05-01

Current control of human microflora is a great problem not only for the space medicine but also for practical health care. Due to many reasons its realization by classical bacteriological method is difficult in practical application or cannot be done. To evaluate non-cultural methods of microbial control of crews in a confined habitat we evaluated two different methods. The first method is based on digital treatment of microbial visual images, appearing after gram staining of microbial material from natural sample. This way the rate between gram-positive and gram-negative microbe could be gained as well as differentiation of rods and cocci could be attained, which is necessary for primary evaluation of human microbial cenosis in remote confined habitats. The other non-culture method of human microflora evaluation is gas chromatomass spectrometry (gcms) analysis of swabs gathered from different body sites. Gc-ms testing of swabs allows one to validate quantitative and special microflora based on specific lipid markers analysis.

Two fundamentally different classes of microbial genes.

PubMed

Wolf, Yuri I; Makarova, Kira S; Lobkovsky, Alexander E; Koonin, Eugene V

2016-11-07

The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss 1-4 . Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species 5,6 . Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept 7 .

Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure.

PubMed

Coban, Halil; Ertekin, Emine; Ince, Orhan; Turker, Gokhan; Akyol, Çağrı; Ince, Bahar

2016-07-01

The effect of veterinary antibiotics in anaerobic digesters is a concern where methane production efficiency is highly dependent on microbial community structure. In this study, both anaerobic degradation of a common veterinary antibiotic, oxytetracycline (OTC), and its effects on an anaerobic digester microbial community were investigated. Qualitative and quantitative molecular tools were used to monitor changes in microbial community structure during a 60-day batch incubation period of cow manure with the addition of different concentrations of the antibiotic. Molecular data were interpreted by a further redundancy analysis as a multivariate statistics approach. At the end of the experiment, approximately 48, 33, and 17 % of the initially added 50, 100, and 200 mg l(-1) of OTC was still present in the serum bottles which reduced the biogas production via accumulation of some of the volatile fatty acids (VFAs). Biogas production was highly correlated with Methanobacteriales and Methanosarcinales gene copy numbers, and those parameters were negatively affected with oxytetracycline and VFA concentrations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopka, Allan

Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, theymore » interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.« less

Analysis of key microbial community during the start-up of anaerobic ammonium oxidation process with paddy soil as inoculated sludge.

PubMed

Xu, Xianglong; Liu, Guohua; Wang, Yuanyuan; Zhang, Yuankai; Wang, Hao; Qi, Lu; Wang, Hongchen

2018-02-01

A sequencing batch reactor (SBR)-anaerobic ammonium oxidation (anammox) system was started up with the paddy soil as inoculated sludge. The key microbial community structure in the system along with the enrichment time was investigated by using molecular biology methods (e.g., high-throughput 16S rRNA gene sequencing and quantitative PCR). Meanwhile, the influent and effluent water quality was continuously monitored during the whole start-up stage. The results showed that the microbial diversity decreased as the operation time initially and increased afterwards, and the microbial niches in the system were redistributed. The anammox bacterial community structure in the SBR-anammox system shifted during the enrichment, the most dominant anammox bacteria were CandidatusJettenia. The maximum biomass of anammox bacteria achieved 1.68×10 9 copies/g dry sludge during the enrichment period, and the highest removal rate of TN achieved around 75%. Copyright © 2017. Published by Elsevier B.V.

Quantitative, depth-resolved determination of particle motion using multi-exposure, spatial frequency domain laser speckle imaging.

PubMed

Rice, Tyler B; Kwan, Elliott; Hayakawa, Carole K; Durkin, Anthony J; Choi, Bernard; Tromberg, Bruce J

2013-01-01

Laser Speckle Imaging (LSI) is a simple, noninvasive technique for rapid imaging of particle motion in scattering media such as biological tissue. LSI is generally used to derive a qualitative index of relative blood flow due to unknown impact from several variables that affect speckle contrast. These variables may include optical absorption and scattering coefficients, multi-layer dynamics including static, non-ergodic regions, and systematic effects such as laser coherence length. In order to account for these effects and move toward quantitative, depth-resolved LSI, we have developed a method that combines Monte Carlo modeling, multi-exposure speckle imaging (MESI), spatial frequency domain imaging (SFDI), and careful instrument calibration. Monte Carlo models were used to generate total and layer-specific fractional momentum transfer distributions. This information was used to predict speckle contrast as a function of exposure time, spatial frequency, layer thickness, and layer dynamics. To verify with experimental data, controlled phantom experiments with characteristic tissue optical properties were performed using a structured light speckle imaging system. Three main geometries were explored: 1) diffusive dynamic layer beneath a static layer, 2) static layer beneath a diffuse dynamic layer, and 3) directed flow (tube) submerged in a dynamic scattering layer. Data fits were performed using the Monte Carlo model, which accurately reconstructed the type of particle flow (diffusive or directed) in each layer, the layer thickness, and absolute flow speeds to within 15% or better.

Dynamic feature analysis of vector-based images for neuropsychological testing

NASA Astrophysics Data System (ADS)

Smith, Stephen L.; Cervantes, Basilio R.

1998-07-01

The dynamic properties of human motor activities, such as those observed in the course of drawing simple geometric shapes, are considerably more complex and often more informative than the goal to be achieved; in this case a static line drawing. This paper demonstrates how these dynamic properties may be used to provide a means of assessing a patient's visuo-spatial ability -- an important component of neuropsychological testing. The work described here provides a quantitative assessment of visuo-spatial ability, whilst preserving the conventional test environment. Results will be presented for a clinical population of long-term haemodialysis patients and test population comprises three groups of children (1) 7-8 years, (2) 9-10 years and (3) 11-12 years, all of which have no known neurological dysfunction. Ten new dynamic measurements extracted from patient responses in conjunction with one static feature deduced from earlier work describe a patient's visuo-spatial ability in a quantitative manner with sensitivity not previously attainable. The dynamic feature measurements in isolation provide a unique means of tracking a patient's approach to motor activities and could prove useful in monitoring a child' visuo-motor development.

Global microbial carbonate proliferation after the end-Devonian mass extinction: Mainly controlled by demise of skeletal bioconstructors

PubMed Central

Yao, Le; Aretz, Markus; Chen, Jitao; Webb, Gregory E.; Wang, Xiangdong

2016-01-01

Microbial carbonates commonly flourished following mass extinction events. The end-Devonian (Hangenberg) mass extinction event is a first-order mass extinction on the scale of the ‘Big Five’ extinctions. However, to date, it is still unclear whether global microbial carbonate proliferation occurred after the Hangenberg event. The earliest known Carboniferous stromatolites on tidal flats are described from intertidal environments of the lowermost Tournaisian (Qianheishan Formation) in northwestern China. With other early Tournaisian microbe-dominated bioconstructions extensively distributed on shelves, the Qianheishan stromatolites support microbial carbonate proliferation after the Hangenberg extinction. Additional support comes from quantitative analysis of the abundance of microbe-dominated bioconstructions through the Famennian and early Tournaisian, which shows that they were globally distributed (between 40° latitude on both sides of the palaeoequator) and that their abundance increased distinctly in the early Tournaisian compared to the latest Devonian (Strunian). Comparison of variations in the relative abundance of skeleton- versus microbe-dominated bioconstructions across the Hangenberg and ‘Big Five’ extinctions suggests that changes in abundance of skeletal bioconstructors may play a first-order control on microbial carbonate proliferation during extinction transitions but that microbial proliferation is not a general necessary feature after mass extinctions. PMID:28009013

Laser Speckle Imaging of Blood Flow Beneath Static Scattering Media

NASA Astrophysics Data System (ADS)

Regan, Caitlin Anderson

Laser speckle imaging (LSI) is a wide-field optical imaging technique that provides information about the movement of scattering particles in biological samples. LSI is used to create maps of relative blood flow and perfusion in samples such as the skin, brain, teeth, gingiva, and other biological tissues. The presence of static, or non-moving, optical scatterers affects the ability of LSI to provide true quantitative and spatially resolved measurements of blood flow. With in vitro experiments using tissue-simulating phantoms, we determined that temporal analysis of raw speckle image sequences improved the quantitative accuracy of LSI to measure flow beneath a static scattering layer. We then applied the temporal algorithm to assess the potential of LSI to monitor oral health. We designed and tested two generations of miniature LSI devices to measure flow in the pulpal chamber of teeth and in the gingiva. Our preliminary clinical pilot data indicated that speckle contrast may correlate with gingival health. To improve visualization of subsurface blood vessels, we developed a technique called photothermal LSI. We applied a short pulse of laser energy to selectively perturb the motion of red blood cells, increasing the signal from vasculature relative to the surroundings. To study the spectral and depth dependence of laser speckle contrast, we developed a Monte Carlo model of light and momentum transport to simulate speckle contrast. With an increase in the thickness of the overlying static-scattering layer, we observed a quadratic decrease in the quantity of dynamically scattered light collected by the detector. We next applied the model to study multi-exposure speckle imaging (MESI), a method that purportedly improves quantitative accuracy of subsurface blood flow measurements. We unexpectedly determined that MESI faced similar depth limitations as conventional LSI, findings that were supported by in vitro experimental data. Finally, we used the model to study the effects of epidermal melanin absorption on LSI, and demonstrated that speckle contrast is less sensitive to varying melanin content than reflectance. We then proposed a two-wavelength measurement protocol that may enable melanin-independent LSI measurements of blood flow in patients with varying skin types. In conclusion, through in vitro and in silico experiments, we were able to further the understanding of the depth dependent origins of laser speckle contrast as well as the inherent limitations of this technology.

URBAN WATER SYSTEM PATHOGEN ASSESSMENTS: SIGNIFICANCE OF DISTRIBUTION BIOFILMS

EPA Science Inventory

Quantitative microbial risk assessment (QMRA), while not new to science is now providing a fundamental role in framing water guidelines internationally as well as identifying research gaps to be filled. Professor Ashbolt has been instrumental in working QMRA concepts into WHO gui...

URBAN WATER SYSTEM PATHOGEN ASSESSMENT: SIGNIFICANCE OF DISTRIBUTION BIOFILMS

EPA Science Inventory

Quantitative microbial risk assessment (QMRA), while not new to science is now providing a fundamental role in framing water guidelines internationally as well as identifying research gaps to be filled. Professor Ashbolt has been instrumental in working QMRA concepts into WHO gui...

Synthesis of polymer ion-exchange hydrogels under γ - irradiation 60Co

NASA Astrophysics Data System (ADS)

Le, V. M.; Zhevnyak, V. D.; Pak, V. Kh; Ananev, V. A.; Borodin, U. V.

2015-04-01

We have reported earlier about the modification of ion-exchange hydrogel under the influence of gamma radiation. The optimal absorbed dose of irradiation had been choosen for radiation modification of polymer hydrogels by ionits to produce products with a high content of the gel - fractions and sufficient mechanical properties. The dependence of the static exchange capacity of hydrogels on the type of ionit and its fractional composition had been studied. The dependence of the static exchange capacity of the quantitative composition of the ionit in the volume of the hydrogel had been investigated. The ion-exchange medical eye lenses had been made under selected conditions of synthesis. Their sorption properties had been studied.

Dynamic Forces Between Two Deformable Oil Droplets in Water

NASA Astrophysics Data System (ADS)

Dagastine, Raymond R.; Manica, Rogério; Carnie, Steven L.; Chan, D. Y. C.; Stevens, Geoffrey W.; Grieser, Franz

2006-07-01

The understanding of static interactions in colloidal suspensions is well established, whereas dynamic interactions more relevant to biological and other suspended soft-matter systems are less well understood. We present the direct force measurement and quantitative theoretical description for dynamic forces for liquid droplets in another immiscible fluid. Analysis of this system demonstrates the strong link between interfacial deformation, static surface forces, and hydrodynamic drainage, which govern dynamic droplet-droplet interactions over the length scale of nanometers and over the time scales of Brownian collisions. The results and analysis have direct bearing on the control and manipulation of suspended droplets in soft-matter systems ranging from the emulsions in shampoo to cellular interactions.

A High Performance Piezoelectric Sensor for Dynamic Force Monitoring of Landslide.

PubMed

Li, Ming; Cheng, Wei; Chen, Jiangpan; Xie, Ruili; Li, Xiongfei

2017-02-17

Due to the increasing influence of human engineering activities, it is important to monitor the transient disturbance during the evolution process of landslide. For this purpose, a high-performance piezoelectric sensor is presented in this paper. To adapt the high static and dynamic stress environment in slope engineering, two key techniques, namely, the self-structure pressure distribution method (SSPDM) and the capacitive circuit voltage distribution method (CCVDM) are employed in the design of the sensor. The SSPDM can greatly improve the compressive capacity and the CCVDM can quantitatively decrease the high direct response voltage. Then, the calibration experiments are conducted via the independently invented static and transient mechanism since the conventional testing machines cannot match the calibration requirements. The sensitivity coefficient is obtained and the results reveal that the sensor has the characteristics of high compressive capacity, stable sensitivities under different static preload levels and wide-range dynamic measuring linearity. Finally, to reduce the measuring error caused by charge leakage of the piezoelectric element, a low-frequency correction method is proposed and experimental verified. Therefore, with the satisfactory static and dynamic properties and the improving low-frequency measuring reliability, the sensor can complement dynamic monitoring capability of the existing landslide monitoring and forecasting system.

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

PubMed

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 information did not provide quantitative source apportionment for the study catchment. Thus, it could not replace detailed empirical measurement of microbial flux at key catchment outlets to underpin faecal indicator source apportionment. Therefore, the MST techniques reported herein currently may not meet the standards required to be a useful forensic tool, although continued development of the methods and further catchment scale studies could increase confidence in such methods for future application.

Arbuscular Mycorrhizal Fungal Hyphae Alter Soil Bacterial Community and Enhance Polychlorinated Biphenyls Dissipation

PubMed Central

Qin, Hua; Brookes, Philip C.; Xu, Jianming

2016-01-01

We investigated the role of arbuscular mycorrhizal fungal (AMF) hyphae in alternation of soil microbial community and Aroclor 1242 dissipation. A two-compartment rhizobox system with double nylon meshes in the central was employed to exclude the influence of Cucurbita pepo L. root exudates on hyphal compartment soil. To assess the quantitative effect of AMF hyphae on soil microbial community, we separated the hyphal compartment soil into four horizontal layers from the central mesh to outer wall (e.g., L1–L4). Soil total PCBs dissipation rates ranged from 35.67% of L4 layer to 57.39% of L1 layer in AMF inoculated treatment, which were significant higher than the 17.31% of the control (P < 0.05). The dissipation rates of tri-, tetrachlorinated biphenyls as well as the total PCBs were significantly correlated with soil hyphal length (P < 0.01). Real-time quantitative PCR results indicated that the Rhodococcus-like bphC gene was 2–3 orders of magnitude more than that of Pseudomonas-like bphC gene, and was found responded positively to AMF. Phylogenetic analyses of the 16S rDNA sequenced by the Illumina Miseq sequencing platform indicated that AMF hyphae altered bacterial community compositions. The phylum Betaproteobacteria and Actinobacteria were dominated in the soil, while Burkholderiales and Actinomycetales were dominated at the order level. Taxa from the Comamonadaceae responded positively to AMF and trichlorinated biphenyl dissipation, while taxa from the Oxalobacteraceae and Streptomycetaceae responded negatively to AMF and PCB congener dissipation. Our results suggested that the AMF hyphal exudates as well as the hyphae per se did have quantitative effects on shaping soil microbial community, and could modify the PCBs dissipation processes consequently. PMID:27379068

Probabilistic quantitative microbial risk assessment model of norovirus from wastewater irrigated vegetables in Ghana using genome copies and fecal indicator ratio conversion for estimating exposure dose.

PubMed

Owusu-Ansah, Emmanuel de-Graft Johnson; Sampson, Angelina; Amponsah, Samuel K; Abaidoo, Robert C; Dalsgaard, Anders; Hald, Tine

2017-12-01

The need to replace the commonly applied fecal indicator conversions ratio (an assumption of 1:10 -5 virus to fecal indicator organism) in Quantitative Microbial Risk Assessment (QMRA) with models based on quantitative data on the virus of interest has gained prominence due to the different physical and environmental factors that might influence the reliability of using indicator organisms in microbial risk assessment. The challenges facing analytical studies on virus enumeration (genome copies or particles) have contributed to the already existing lack of data in QMRA modelling. This study attempts to fit a QMRA model to genome copies of norovirus data. The model estimates the risk of norovirus infection from the intake of vegetables irrigated with wastewater from different sources. The results were compared to the results of a corresponding model using the fecal indicator conversion ratio to estimate the norovirus count. In all scenarios of using different water sources, the application of the fecal indicator conversion ratio underestimated the norovirus disease burden, measured by the Disability Adjusted Life Years (DALYs), when compared to results using the genome copies norovirus data. In some cases the difference was >2 orders of magnitude. All scenarios using genome copies met the 10 -4 DALY per person per year for consumption of vegetables irrigated with wastewater, although these results are considered to be highly conservative risk estimates. The fecal indicator conversion ratio model of stream-water and drain-water sources of wastewater achieved the 10 -6 DALY per person per year threshold, which tends to indicate an underestimation of health risk when compared to using genome copies for estimating the dose. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative assessment of the microbial risk of leafy greens from farm to consumption: preliminary framework, data, and risk estimates.

PubMed

Danyluk, Michelle D; Schaffner, Donald W

2011-05-01

This project was undertaken to relate what is known about the behavior of Escherichia coli O157:H7 under laboratory conditions and integrate this information to what is known regarding the 2006 E. coli O157:H7 spinach outbreak in the context of a quantitative microbial risk assessment. The risk model explicitly assumes that all contamination arises from exposure in the field. Extracted data, models, and user inputs were entered into an Excel spreadsheet, and the modeling software @RISK was used to perform Monte Carlo simulations. The model predicts that cut leafy greens that are temperature abused will support the growth of E. coli O157:H7, and populations of the organism may increase by as much a 1 log CFU/day under optimal temperature conditions. When the risk model used a starting level of -1 log CFU/g, with 0.1% of incoming servings contaminated, the predicted numbers of cells per serving were within the range of best available estimates of pathogen levels during the outbreak. The model predicts that levels in the field of -1 log CFU/g and 0.1% prevalence could have resulted in an outbreak approximately the size of the 2006 E. coli O157:H7 outbreak. This quantitative microbial risk assessment model represents a preliminary framework that identifies available data and provides initial risk estimates for pathogenic E. coli in leafy greens. Data gaps include retail storage times, correlations between storage time and temperature, determining the importance of E. coli O157:H7 in leafy greens lag time models, and validation of the importance of cross-contamination during the washing process.

Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR.

PubMed

Cui, Qijia; Fang, Tingting; Huang, Yong; Dong, Peiyan; Wang, Hui

2017-07-01

The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present. The most abundant species were Acinetobacter johnsonii, Mycobacterium avium and Aeromonas spp. Quantitative polymerase chain reaction (qPCR) of Escherichia coli (uidA), Aeromonas (aerA), M. avium (16S rRNA), Pseudomonas aeruginosa (oaa) and Salmonella (invA) showed that the aerA genes were the most abundant, occurring in all samples with concentrations of 10 4-6 genome copies/100mL, followed by oaa, invA and M. avium. In total, 34.8% of the samples harbored all genes, indicating the prevalence of these pathogens in this recreational waterbody. Based on the qPCR results, a quantitative microbial risk assessment (QMRA) showed that the annual infection risks of Salmonella, M. avium and P. aeruginosa in five activities were mostly greater than the U.S. EPA risk limit for recreational contacts, and children playing with water may be exposed to the greatest infection risk. Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and qPCR. Copyright © 2016. Published by Elsevier B.V.

Toward Monitoring Parkinson's Through Analysis of Static Handwriting Samples: A Quantitative Analytical Framework.

PubMed

Zhi, Naiqian; Jaeger, Beverly Kris; Gouldstone, Andrew; Sipahi, Rifat; Frank, Samuel

2017-03-01

Detection of changes in micrographia as a manifestation of symptomatic progression or therapeutic response in Parkinson's disease (PD) is challenging as such changes can be subtle. A computerized toolkit based on quantitative analysis of handwriting samples would be valuable as it could supplement and support clinical assessments, help monitor micrographia, and link it to PD. Such a toolkit would be especially useful if it could detect subtle yet relevant changes in handwriting morphology, thus enhancing resolution of the detection procedure. This would be made possible by developing a set of metrics sensitive enough to detect and discern micrographia with specificity. Several metrics that are sensitive to the characteristics of micrographia were developed, with minimal sensitivity to confounding handwriting artifacts. These metrics capture character size-reduction, ink utilization, and pixel density within a writing sample from left to right. They are used here to "score" handwritten signatures of 12 different individuals corresponding to healthy and symptomatic PD conditions, and sample control signatures that had been artificially reduced in size for comparison purposes. Moreover, metric analyses of samples from ten of the 12 individuals for which clinical diagnosis time is known show considerable informative variations when applied to static signature samples obtained before and after diagnosis. In particular, a measure called pixel density variation showed statistically significant differences ( ) between two comparison groups of remote signature recordings: earlier versus recent, based on independent and paired t-test analyses on a total of 40 signature samples. The quantitative framework developed here has the potential to be used in future controlled experiments to study micrographia and links to PD from various aspects, including monitoring and assessment of applied interventions and treatments. The inherent value in this methodology is further enhanced by its reliance solely on static signatures, not requiring dynamic sampling with specialized equipment.

The effect of alum addition on microbial communities in poultry litter.

PubMed

Rothrock, M J; Cook, K L; Warren, J G; Sistani, K

2008-08-01

Alum [Al(2)(SO(4))(3).14H(2)O] is a common poultry litter amendment used to decrease water-soluble phosphorus or reduce ammonia volatilization, or both. Although the physiochemical effects of alum addition have been well researched, little attention has been given to the poultry litter microbial communities. The goal of this study was to use molecular biological methods [denaturing gradient gel electrophoresis (DGGE), community cloning, and quantitative real-time PCR] to characterize general, group-specific and pathogenic microbial communities in alum (10% wt/wt) and non-alum-treated litter. According to quantitative real-time PCR analyses, alum addition to the poultry litter resulted in significant reductions in both Campylobacter jejuni and Escherichia coli concentrations by the end of the first month of the experiment (3 log and 2 log, respectively). The concentrations of Salmonella spp. were below detection (<5 x 10(3) cell.g(-1) of litter) for the entire experiment. The DGGE analyses revealed significant reductions in the Clostridium/Eubacterium and low %GC gram-positive groups in the alum-treated litters by the end of the first month, with no bands detectable for either group after 8 wk of incubation. Conversely, minimal effects of alum addition were observed in the Actinomycetes community. The most significant shift in the microbial community (based on DGGE analyses) occurred in the fungal population, with a large increase in diversity and abundance within 1 mo of alum addition (1 dominant band on d 0 to 9 dominant bands at 4 wk). Specifically, the incidence of Aspergillus spp. increased from 0 to 50% of the sequences in fungal clone libraries (n = 80) over the course of the experiment. This suggests that the addition of alum to poultry litter potentially shifts the microbial populations from bacterially dominated to dominated by fungi. The ramifications of this shift in dominance are still unknown, and future work will be aimed at characterizing these fungi and elucidating their role in the acidified litter environment.

Microbial Monitoring of Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Birmele, Michele

2012-01-01

The International Space Station (ISS) is a closed environment wih rotations of crew and equipment each introducing their own microbial flora making it necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor and time intensive methods to enumerate total bacterial and fungal cells with limited characterization during in-flight testing. Although this culture-based method has been sufficient for monitoring the ISS, future long duration missions will need to perform more comprehensive characterization in-flight, since sample return and ground characterization may not be available. A workshop was held in 2011 at the Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these longterm exploration missions where molecular-based methodologies, such as polymerase chain reaction (PCR), were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for spaceflight environmental monitoring. The goal was to evaluate quantitative/semi-quantitative PCR approaches to space applications for low cost in-flight rapid identification of microorganisms affecting crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity followed by proof-of-concept testing on the highest qualifying candidates with a universally available test organism, Salmonella enterica. The platforms evaluated during proof-of-concept testing included the iCubate 2.0(TradeMark) (iCubate, Huntsville, AL), RAZOR EX (BioFire Diagnostics; Salt Lake City, Utah) and SmartCycler(TradeMark) (Cepheid; Sunnyvale, CA). The analysis identified two potential technologies (iCubate 2.0 and RAZOR EX) that were able to perform sample-to-answer testing with cell sample concentrations between SO to 400 cells. In addition, the commercial systems were evaluated for initial flight safety and readiness, sample concentration needs were reviewed, and a competitive procurement of commercially available platforms was initiated.

Estimating true human and animal host source contribution in quantitative microbial source tracking using the Monte Carlo method.

PubMed

Wang, Dan; Silkie, Sarah S; Nelson, Kara L; Wuertz, Stefan

2010-09-01

Cultivation- and library-independent, quantitative PCR-based methods have become the method of choice in microbial source tracking. However, these qPCR assays are not 100% specific and sensitive for the target sequence in their respective hosts' genome. The factors that can lead to false positive and false negative information in qPCR results are well defined. It is highly desirable to have a way of removing such false information to estimate the true concentration of host-specific genetic markers and help guide the interpretation of environmental monitoring studies. Here we propose a statistical model based on the Law of Total Probability to predict the true concentration of these markers. The distributions of the probabilities of obtaining false information are estimated from representative fecal samples of known origin. Measurement error is derived from the sample precision error of replicated qPCR reactions. Then, the Monte Carlo method is applied to sample from these distributions of probabilities and measurement error. The set of equations given by the Law of Total Probability allows one to calculate the distribution of true concentrations, from which their expected value, confidence interval and other statistical characteristics can be easily evaluated. The output distributions of predicted true concentrations can then be used as input to watershed-wide total maximum daily load determinations, quantitative microbial risk assessment and other environmental models. This model was validated by both statistical simulations and real world samples. It was able to correct the intrinsic false information associated with qPCR assays and output the distribution of true concentrations of Bacteroidales for each animal host group. Model performance was strongly affected by the precision error. It could perform reliably and precisely when the standard deviation of the precision error was small (≤ 0.1). Further improvement on the precision of sample processing and qPCR reaction would greatly improve the performance of the model. This methodology, built upon Bacteroidales assays, is readily transferable to any other microbial source indicator where a universal assay for fecal sources of that indicator exists. Copyright © 2010 Elsevier Ltd. All rights reserved.

Vector analysis of ecoenzyme activities reveal constraints on coupled C, N and P dynamics

EPA Science Inventory

We developed a quantitative method for estimating resource allocation strategies of microbial communities based on the proportional activities of four, key extracellular enzymes, 1,4-ß-glucosidase (BG), leucine amino-peptidase (LAP), 1,4-ß-N-acetylglucosaminidase (NAG...

Quantitative Microbial Risk Assessment of Freshwater Impacted by Animal Fecal Material (proceedings)

EPA Science Inventory

We evaluated the potential for human illness from a hypothetical recreational exposure to freshwater that was impacted by land-applied, agricultural animal fecal material. The scenario included 1) fresh cattle manure, pig slurry, or chicken litter (fecal material) land-applied, a...

Using an Integrated, Multi-disciplinary Framework to Support Quantitative Microbial Risk Assessments

EPA Science Inventory

The Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES) provides the infrastructure to link disparate models and databases seamlessly, giving an assessor the ability to construct an appropriate conceptual site model from a host of modeling choices, so a numbe...

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Final technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edward DeLong

2011-10-07

Our overarching goals in this project were to: Develop and improve high-throughput sequencing methods and analytical approaches for quantitative analyses of microbial gene expression at the Hawaii Ocean Time Series Station and the Bermuda Atlantic Time Series Station; Conduct field analyses following gene expression patterns in picoplankton microbial communities in general, and Prochlorococcus flow sorted from that community, as they respond to different environmental variables (light, macronutrients, dissolved organic carbon), that are predicted to influence activity, productivity, and carbon cycling; Use the expression analyses of flow sorted Prochlorococcus to identify horizontally transferred genes and gene products, in particular those thatmore » are located in genomic islands and likely to confer habitat-specific fitness advantages; Use the microbial community gene expression data that we generate to gain insights, and test hypotheses, about the variability, genomic context, activity and function of as yet uncharacterized gene products, that appear highly expressed in the environment. We achieved the above goals, and even more over the course of the project. This includes a number of novel methodological developments, as well as the standardization of microbial community gene expression analyses in both field surveys, and experimental modalities. The availability of these methods, tools and approaches is changing current practice in microbial community analyses.« less

Microbial composition in microcosms amended with natural and mineral fertilizers under different water regimes

NASA Astrophysics Data System (ADS)

Brad, Traian; Chiriac, Cecilia; Szekeres, Edina; Coman, Cristian; Rudi, Knut; Sandor, Mignon

2017-04-01

Twenty microcosm enclosures containing two types of soil (i.e. a rich Chernozemic and a poorer soil) were fertilized with mineral (NPK-complex) and organic (Gülle, manure and a green fertilizer) materials and placed under dry and wet water regimes. After 10, 20 and 30 days of the experiment, soil samples were analyzed for the structure and composition of microbial communities using next generation sequencing techniques (Illumina) and statistical analysis. The differences between bacteria communities in different soil types, and in different fertilization and hydric treatments were analyzed using quantitative phylogenetic distances and the ANOSIM test. The two types of soil especially selected for the structure of microbial communities, while moisture and the type of fertilizer appeared to have a smaller influence on microbial diversity in microcosms. The alpha-diversity indices (species richness, evenness and phylogenetic diversity) had higher values for the poorer soil compared to the rich Chernozemic soil. For both soil types, the highest bacteria diversity values were obtained after fertilization with manure. The microbial communities in the analyzed soils were complex and dominated by sequences belonging to Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes.

A Comparison of the Quasi-static Mechanical and Nonlinear Viscoelastic Properties of the Human Semitendinosus and Gracilis Tendons

PubMed Central

Abramowitch, Steven D.; Zhang, Xiaoyan; Curran, Molly; Kilger, Robert

2010-01-01

Background Over fifty-percent of anterior cruciate ligament reconstructions are performed using semitendinosus and gracilis tendon autografts. Despite their increased use, there remains little quantitative data on their mechanical behavior. Therefore, the objective of this study was to investigate the quasi-static mechanical and nonlinear viscoelastic properties of human semitendinosus and gracilis tendons, as well as the variation of these properties along their length. Methods Specimens were subjected to a series of uniaxial tensile tests: one-hour static stress-relaxation test, 30-cycle cyclic stress-relaxation test and load to failure test. To describe the nonlinear viscoelastic behavior, the quasi-linear viscoelastic theory was utilized to model data from the static stress relaxation experiment. Findings The constants describing the viscoelastic behavior were similar between the proximal and distal halves of the gracilis tendon. The proximal half of the semitendinosus tendon, however, had a greater viscous response than its distal half, which was also significantly higher than the proximal gracilis tendon. In terms of the quasi-static mechanical properties, the properties were similar between the proximal and distal halves of the semitendinosus tendon. However, the distal gracilis tendon showed a significantly higher tangent modulus and ultimate stress compared to its proximal half, which was also significantly higher than the distal semitendinosus tendon. Interpretation The results of this study demonstrate differences between the semitendinosus and gracilis tendons in terms of their quasi-static mechanical and nonlinear viscoelastic properties. These results are important for establishing surgical preconditioning protocols and graft selection. PMID:20092917

Static Holes in Geometrically Frustrated Bow Tie Ladder

NASA Astrophysics Data System (ADS)

Martins, George; Brenig, Wolfram

2007-03-01

Doping of the geometrically frustrated bow-tie spin ladder with static holes is investigated by a complementary approach using exact diagonalization and hard-core quantum dimers. Results for the thermodynamics in the undoped case, the singlet density of states, the hole-binding energy, and the spin correlations will be presented. We find that the static holes polarize their vicinity by a localization of singlets in order to reduce the frustration. As a consequence the singlet polarization cloud induces short range repulsive forces between the holes with oscillatory longer range behavior. For those systems we have studied, most results for the quantum dimer approach are found to be qualitatively if not quantitatively in agreement with exact diagonalization. The ground state of the undoped system is non-degenerate with translationally invariant nearest-neighbor spin correlations up to a few unit cells, which is consistent with a spin liquid state or a valence bond crystal with very large unit cell. C. Waldtmann, A. Kreutzmann, U. Schollwock, K. Maisinger, and H.-U. Everts, Phys. Rev. B 62, 9472 (2000).

Evaluation of magnetic resonance imaging issues for implantable microfabricated magnetic actuators.

PubMed

Lee, Hyowon; Xu, Qing; Shellock, Frank G; Bergsneider, Marvin; Judy, Jack W

2014-02-01

The mechanical robustness of microfabricated torsional magnetic actuators in withstanding the strong static fields (7 T) and time-varying field gradients (17 T/m) produced by an MR system was studied in this investigation. The static and dynamic mechanical characteristics of 30 devices were quantitatively measured before and after exposure to both strong uniform and non-uniform magnetic fields. The results showed no statistically significant change in both the static and dynamic mechanical performance, which mitigate concerns about the mechanical stability of these devices in association with MR systems under the conditions used for this assessment. The MR-induced heating was also measured in a 3-T/128-MHz MR system. The results showed a minimal increase (1.6 °C) in temperature due to the presence of the magnetic microactuator array. Finally, the size of the MR-image artifacts created by the magnetic microdevices were quantified. The signal loss caused by the devices was approximately four times greater than the size of the device.

The fluid trampoline: droplets bouncing on a soap film

NASA Astrophysics Data System (ADS)

Bush, John; Gilet, Tristan

2008-11-01

We present the results of a combined experimental and theoretical investigation of droplets falling onto a horizontal soap film. Both static and vertically vibrated soap films are considered. A quasi-static description of the soap film shape yields a force-displacement relation that provides excellent agreement with experiment, and allows us to model the film as a nonlinear spring. This approach yields an accurate criterion for the transition between droplet bouncing and crossing on the static film; moreover, it allows us to rationalize the observed constancy of the contact time and scaling for the coefficient of restitution in the bouncing states. On the vibrating film, a variety of bouncing behaviours were observed, including simple and complex periodic states, multiperiodicity and chaos. A simple theoretical model is developed that captures the essential physics of the bouncing process, reproducing all observed bouncing states. Quantitative agreement between model and experiment is deduced for simple periodic modes, and qualitative agreement for more complex periodic and chaotic bouncing states.

[Health and hygiene characteristics of the manned environment of the Saliut-7 orbital station].

PubMed

Zaloguev, S N; Savina, V P; Mukhamedieva, L N; Nefedov, Iu G; Viktorov, A N

1984-01-01

The Salyut-7 cabin environment was investigated with respect to the chemical, biological and physical factors. The gas composition was measured qualitatively and quantitatively. This determination showed a higher content of acetone and acetaldehyde when the cosmonauts worked on various trainers and unloaded the Progress cargo vehicles. The time-course study of the toxic impurities indicated that the increase in their content was transient (no more than 4 h). The microbial content was lower than in the Salyut-6 cabin environment. The study did not show a correlation between the microbial content in the environment and the time the prime crew remained onboard. There was a correlation between the microbial content, temperature variations, and conduct of certain experiments. On the whole, the Salyut-7 cabin environment was normal for the life and work of the crewmembers.

Molecular assessment of the sensitivity of sulfate-reducing microbial communities remediating mine drainage to aerobic stress.

PubMed

Lefèvre, Emilie; Pereyra, Luciana P; Hiibel, Sage R; Perrault, Elizabeth M; De Long, Susan K; Reardon, Kenneth F; Pruden, Amy

2013-09-15

Sulfate-reducing permeable reactive zones (SR-PRZs) are microbially-driven anaerobic systems designed for the removal of heavy metals and sulfate in mine drainage. Environmental perturbations, such as oxygen exposure, may adversely affect system stability and long-term performance. The objective of this study was to examine the effect of two successive aerobic stress events on the performance and microbial community composition of duplicate laboratory-scale lignocellulosic SR-PRZs operated using the following microbial community management strategies: biostimulation with ethanol or carboxymethylcellulose; bioaugmentation with sulfate-reducing or cellulose-degrading enrichments; inoculation with dairy manure only; and no inoculation. A functional gene-based approach employing terminal restriction fragment length polymorphism and quantitative polymerase chain reaction targeting genes of sulfate-reducing (dsrA), cellulose-degrading (cel5, cel48), fermentative (hydA), and methanogenic (mcrA) microbes was applied. In terms of performance (i.e., sulfate removal), biostimulation with ethanol was the only strategy that clearly had an effect (positive) following exposure to oxygen. In terms of microbial community composition, significant shifts were observed over the course of the experiment. Results suggest that exposure to oxygen more strongly influenced microbial community shifts than the different microbial community management strategies. Sensitivity to oxygen exposure varied among different populations and was particularly pronounced for fermentative bacteria. Although the community structure remained altered after exposure, system performance recovered, indicating that SR-PRZ microbial communities were functionally redundant. Results suggest that pre-exposure to oxygen might be a more effective strategy to improve the resilience of SR-PRZ microbial communities relative to bioaugmentation or biostimulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Time-resolved imaging refractometry of microbicidal films using quantitative phase microscopy.

PubMed

Rinehart, Matthew T; Drake, Tyler K; Robles, Francisco E; Rohan, Lisa C; Katz, David; Wax, Adam

2011-12-01

Quantitative phase microscopy is applied to image temporal changes in the refractive index (RI) distributions of solutions created by microbicidal films undergoing hydration. We present a novel method of using an engineered polydimethylsiloxane structure as a static phase reference to facilitate calibration of the absolute RI across the entire field. We present a study of dynamic structural changes in microbicidal films during hydration and subsequent dissolution. With assumptions about the smoothness of the phase changes induced by these films, we calculate absolute changes in the percentage of film in regions across the field of view.

Time-resolved imaging refractometry of microbicidal films using quantitative phase microscopy

PubMed Central

Rinehart, Matthew T.; Drake, Tyler K.; Robles, Francisco E.; Rohan, Lisa C.; Katz, David; Wax, Adam

2011-01-01

Quantitative phase microscopy is applied to image temporal changes in the refractive index (RI) distributions of solutions created by microbicidal films undergoing hydration. We present a novel method of using an engineered polydimethylsiloxane structure as a static phase reference to facilitate calibration of the absolute RI across the entire field. We present a study of dynamic structural changes in microbicidal films during hydration and subsequent dissolution. With assumptions about the smoothness of the phase changes induced by these films, we calculate absolute changes in the percentage of film in regions across the field of view. PMID:22191912

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

PubMed Central

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

2015-01-01

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

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-10-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Extraction of Dynamic Features from Hand Drawn Data for the Identification of Children with Handwriting Difficulty

ERIC Educational Resources Information Center

Khalid, Puspa Inayat; Yunus, Jasmy; Adnan, Robiah

2010-01-01

Studies have shown that differences between children with and without handwriting difficulties lie not only in the written product (static data) but also in dynamic data of handwriting process. Since writing system varies among countries and individuals, this study was conducted to determine the feasibility of using quantitative outcome measures…

The effects of changing land cover on streamflow simulation in Puerto Rico

Treesearch

A.E. Van Beusekom; L.E. Hay; R.J. Viger; W.A. Gould; J.A. Collazo; A. Henareh Khalyani

2014-01-01

This study quantitatively explores whether land cover changes have a substantive impact on simulated streamflow within the tropical island setting of Puerto Rico. The Precipitation Runoff Modeling System (PRMS) was used to compare streamflow simulations based on five static parameterizations of land cover with those based on dynamically varying parameters derived from...

Finding the Rose Among the Thorns: Some Thoughts on Integrating Media Research.

ERIC Educational Resources Information Center

Angert, Jay F.; Clark, Francis E.

A meta-analysis procedure was used to review research on pictorial effectiveness which focused on the use of static iconic visuals in instructional materials. The purpose of this exploratory study was to provide a means for forming future hypotheses based upon a quantitative aggregation of past research. The study was concerned with differential…

Students' Understanding and Perceptions of Assigned Team Roles in a Classroom Laboratory Environment

ERIC Educational Resources Information Center

Ott, Laura E.; Kephart, Kerrie; Stolle-McAllister, Kathleen; LaCourse, William R.

2018-01-01

Using a cooperative learning framework in a quantitative reasoning laboratory course, students were assigned to static teams of four in which they adopted roles that rotated regularly. The roles included: team leader, protocol manager, data recorder, and researcher. Using a mixed-methods approach, we investigated students' perceptions of the team…

Environmental Control on Microbial Turnover of Leaf Carbon in Streams – Ecological Function of Phototrophic-Heterotrophic Interactions

PubMed Central

Fabian, Jenny; Zlatanović, Sanja; Mutz, Michael; Grossart, Hans-Peter; van Geldern, Robert; Ulrich, Andreas; Gleixner, Gerd; Premke, Katrin

2018-01-01

In aquatic ecosystems, light availability can significantly influence microbial turnover of terrestrial organic matter through associated metabolic interactions between phototrophic and heterotrophic communities. However, particularly in streams, microbial functions vary significantly with the structure of the streambed, that is the distribution and spatial arrangement of sediment grains in the streambed. It is therefore essential to elucidate how environmental factors synergistically define the microbial turnover of terrestrial organic matter in order to better understand the ecological role of photo-heterotrophic interactions in stream ecosystem processes. In outdoor experimental streams, we examined how the structure of streambeds modifies the influence of light availability on microbial turnover of leaf carbon (C). Furthermore, we investigated whether the studied relationships of microbial leaf C turnover to environmental conditions are affected by flow intermittency commonly occurring in streams. We applied leaves enriched with a 13C-stable isotope tracer and combined quantitative and isotope analyses. We thereby elucidated whether treatment induced changes in C turnover were associated with altered use of leaf C within the microbial food web. Moreover, isotope analyses were combined with measurements of microbial community composition to determine whether changes in community function were associated with a change in community composition. In this study, we present evidence, that environmental factors interactively determine how phototrophs and heterotrophs contribute to leaf C turnover. Light availability promoted the utilization of leaf C within the microbial food web, which was likely associated with a promoted availability of highly bioavailable metabolites of phototrophic origin. However, our results additionally confirm that the structure of the streambed modifies light-related changes in microbial C turnover. From our observations, we conclude that the streambed structure influences the strength of photo-heterotrophic interactions by defining the spatial availability of algal metabolites in the streambed and the composition of microbial communities. Collectively, our multifactorial approach provides valuable insights into environmental controls on the functioning of stream ecosystems.

Monitoring the dynamics of syntrophic β-oxidizing bacteria during anaerobic degradation of oleic acid by quantitative PCR.

PubMed

Ziels, Ryan M; Beck, David A C; Martí, Magalí; Gough, Heidi L; Stensel, H David; Svensson, Bo H

2015-04-01

The ecophysiology of long-chain fatty acid-degrading syntrophic β-oxidizing bacteria has been poorly understood due to a lack of quantitative abundance data. Here, TaqMan quantitative PCR (qPCR) assays targeting the 16S rRNA gene of the known mesophilic syntrophic β-oxidizing bacterial genera Syntrophomonas and Syntrophus were developed and validated. Microbial community dynamics were followed using qPCR and Illumina-based high-throughput amplicon sequencing in triplicate methanogenic bioreactors subjected to five consecutive batch feedings of oleic acid. With repeated oleic acid feeding, the initial specific methane production rate significantly increased along with the relative abundances of Syntrophomonas and methanogenic archaea in the bioreactor communities. The novel qPCR assays showed that Syntrophomonas increased from 7 to 31% of the bacterial community 16S rRNA gene concentration, whereas that of Syntrophus decreased from 0.02 to less than 0.005%. High-throughput amplicon sequencing also revealed that Syntrophomonas became the dominant genus within the bioreactor microbiomes. These results suggest that increased specific mineralization rates of oleic acid were attributed to quantitative shifts within the microbial communities toward higher abundances of syntrophic β-oxidizing bacteria and methanogenic archaea. The novel qPCR assays targeting syntrophic β-oxidizing bacteria may thus serve as monitoring tools to indicate the fatty acid β-oxidization potential of anaerobic digester communities. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2013-09-07

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated withmore » microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).« less

Unravelling the active microbial community in a thermophilic anaerobic digester-microbial electrolysis cell coupled system under different conditions.

PubMed

Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

2017-03-01

Thermophilic anaerobic digestion (AD) of pig slurry coupled to a microbial electrolysis cell (MEC) with a recirculation loop was studied at lab-scale as a strategy to increase AD stability when submitted to organic and nitrogen overloads. The system performance was studied, with the recirculation loop both connected and disconnected, in terms of AD methane production, chemical oxygen demand removal (COD) and volatile fatty acid (VFA) concentrations. Furthermore, the microbial population was quantitatively and qualitatively assessed through DNA and RNA-based qPCR and high throughput sequencing (MiSeq), respectively to identify the RNA-based active microbial populations from the total DNA-based microbial community composition both in the AD and MEC reactors under different operational conditions. Suppression of the recirculation loop reduced the AD COD removal efficiency (from 40% to 22%) and the methane production (from 0.32 to 0.03 m 3  m -3  d -1 ). Restoring the recirculation loop led to a methane production of 0.55 m 3  m -3  d -1 concomitant with maximum MEC COD and ammonium removal efficiencies of 29% and 34%, respectively. Regarding microbial analysis, the composition of the AD and MEC anode populations differed from really active microorganisms. Desulfuromonadaceae was revealed as the most active family in the MEC (18%-19% of the RNA relative abundance), while hydrogenotrophic methanogens (Methanobacteriaceae) dominated the AD biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration

NASA Astrophysics Data System (ADS)

Alster, Charlotte J.; Koyama, Akihiro; Johnson, Nels G.; Wallenstein, Matthew D.; von Fischer, Joseph C.

2016-06-01

There is compelling evidence that microbial communities vary widely in their temperature sensitivity and may adapt to warming through time. To date, this sensitivity has been largely characterized using a range of models relying on versions of the Arrhenius equation, which predicts an exponential increase in reaction rate with temperature. However, there is growing evidence from laboratory and field studies that observe nonmonotonic responses of reaction rates to variation in temperature, indicating that Arrhenius is not an appropriate model for quantitatively characterizing temperature sensitivity. Recently, Hobbs et al. (2013) developed macromolecular rate theory (MMRT), which incorporates thermodynamic temperature optima as arising from heat capacity differences between isoenzymes. We applied MMRT to measurements of respiration from soils incubated at different temperatures. These soils were collected from three grassland sites across the U.S. Great Plains and reciprocally transplanted, allowing us to isolate the effects of microbial community type from edaphic factors. We found that microbial community type explained roughly 30% of the variation in the CO2 production rate from the labile C pool but that temperature and soil type were most important in explaining variation in labile and recalcitrant C pool size. For six out of the nine soil × inoculum combinations, MMRT was superior to Arrhenius. The MMRT analysis revealed that microbial communities have distinct heat capacity values and temperature sensitivities sometimes independent of soil type. These results challenge the current paradigm for modeling temperature sensitivity of soil C pools and understanding of microbial enzyme dynamics.

Soil Fluxomics: Disentangling Microbial Group Specific Metabolism by Modeling of 13C-Incorporation into PLFAs

NASA Astrophysics Data System (ADS)

Apostel, C.; Kuzyakov, Y.; Dippold, M. A.

2016-12-01

Soils are the largest terrestrial C sinks and microorganisms are the most important drivers of organic matter (OM) dynamics in soils: C allocation to ana- or catabolism in microbial cells is the decisive step, whether C gets oxidized to CO2 or whether it is allocated to microbial biomass, which, after cell death can be stabilized in soils. The metabolic parameter describing the ratio between the two fluxes is the carbon use efficiency (CUE), which can be assessed by position-specific labeling followed by metabolic flux modelling. However, to disentangle the single microbial groups' contribution to the bulk soil CUE, a tracing of individual groups metabolism is necessary. We assessed short-term (3 and 10 days) transformations of monosaccharides by adding position-specifically 13C labeled glucose to soil in a field experiment. Incorporation of 13C in the microbial PLFAs enabled us to distinguish individual microbial groups metabolic fluxes and compare their C-utilization efficiency using a quantitative C-flux model. The position-specific pattern in PLFAs revealed two sets of microorganisms: one metabolized glucose mainly by glycolysis and the other mainly by the pentose-phosphate pathway, which results in a higher CUE. Both of those sets included prokaryotic as well as eukaryotic microorganisms. This demonstrates that phylogenetic grouping is not decisive for the metabolic behavior of a microbial group and that the contribution of individual group members to the soil C fluxes cannot be concluded from their phylogeny.

Microbial Cellulose Utilization: Fundamentals and Biotechnology

PubMed Central

Lynd, Lee R.; Weimer, Paul J.; van Zyl, Willem H.; Pretorius, Isak S.

2002-01-01

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for “consolidated bioprocessing” (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts. PMID:12209002

Criteria For Evaluation of Proposed Protozoan Detection Methods

EPA Science Inventory

Currently, the only EPA approved method for detection and quantitation of protozoan cysts and oöcysts in source and drinking water, is the “ICR Protozoan Method for Detecting Giardia Cysts and Cryptosporidium Oöcysts in Water by a Fluorescent Antibody Procedure (ICR Microbial La...

ESTIMATING PATHOGEN EXPOSURES - THE CRITICAL CHALLENGE FOR QMRA TO SUPPORT REGULATION AND MANAGEMENT OF WATERS

EPA Science Inventory

Pathogen and indicator concentrations normally vary by several orders of magnitude in raw waters, and to an even greater extent during hazardous event periods. This variation in concentration typically dominate the estimate of infection generated in a quantitative microbial risk ...

Monitoring Fecal Indicators and Pathogens in Watersheds: Implementing a Quantitative Microbial Risk Assessment Approach

EPA Science Inventory

- Many of the nation's rivers, lakes, and estuaries are impaired with fecal indicator bacteria. - Fecal contamination from point and non-point sources is responsible for the presence of fecal pathogens in source and recreational waters - Effective compliance with TMDL regulatio...

Characterizing health risks associated with recreational swimming at Taiwanese beaches by using quantitative microbial risk assessment.

PubMed

Jang, Cheng-Shin; Liang, Ching-Ping

2018-01-01

Taiwan is surrounded by oceans, and therefore numerous pleasure beaches attract millions of tourists annually to participate in recreational swimming activities. However, impaired water quality because of fecal pollution poses a potential threat to the tourists' health. This study probabilistically characterized the health risks associated with recreational swimming engendered by waterborne enterococci at 13 Taiwanese beaches by using quantitative microbial risk assessment. First, data on enterococci concentrations at coastal beaches monitored by the Taiwan Environmental Protection Administration were reproduced using nonparametric Monte Carlo simulation (MCS). The ingestion volumes of recreational swimming based on uniform and gamma distributions were subsequently determined using MCS. Finally, after the distribution combination of the two parameters, the beta-Poisson dose-response function was employed to quantitatively estimate health risks to recreational swimmers. Moreover, various levels of risk to recreational swimmers were classified and spatially mapped to explore feasible recreational and environmental management strategies at the beaches. The study results revealed that although the health risks associated with recreational swimming did not exceed an acceptable benchmark of 0.019 illnesses daily at all beaches, they approached to this benchmark at certain beaches. Beaches with relatively high risks are located in Northwestern Taiwan owing to the current movements.

The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate

PubMed Central

Klesmith, Justin R.; Detwiler, Emily E.; Tomek, Kyle J.; Whitehead, Timothy A.

2014-01-01

In exponentially growing bacteria, expression of heterologous protein impedes cellular growth rates. Quantitative understanding of the relationship between expression and growth rate will advance our ability to forward engineer bacteria, important for metabolic engineering and synthetic biology applications. Recently, a work described a scaling model based on optimal allocation of ribosomes for protein translation. This model quantitatively predicts a linear relationship between microbial growth rate and heterologous protein expression with no free parameters. With the aim of validating this model, we have rigorously quantified the fitness cost of gene expression by using a library of synthetic constitutive promoters to drive expression of two separate proteins (eGFP and amiE) in E. coli in different strains and growth media. In all cases, we demonstrate that the fitness cost is consistent with the previous findings. We expand upon the previous theory by introducing a simple promoter activity model to quantitatively predict how basal promoter strength relates to growth rate and protein expression. We then estimate the amount of protein expression needed to support high flux through a heterologous metabolic pathway and predict the sizable fitness cost associated with enzyme production. This work has broad implications across applied biological sciences because it allows for prediction of the interplay between promoter strength, protein expression, and the resulting cost to microbial growth rates. PMID:25286161

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence

USGS Publications Warehouse

Stoeckel, D.M.; Stelzer, E.A.; Stogner, R.W.; Mau, D.P.

2011-01-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections-augmented with local observations and land-use patterns-indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. ?? 2011 Elsevier Ltd.

Lipid biomarker analysis for the quantitative analysis of airborne microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Macnaughton, S.J.; Jenkins, T.L.; Cormier, M.R.

1997-08-01

There is an ever increasing concern regarding the presence of airborne microbial contaminants within indoor air environments. Exposure to such biocontaminants can give rise to large numbers of different health effects including infectious diseases, allergenic responses and respiratory problems, Biocontaminants typically round in indoor air environments include bacteria, fungi, algae, protozoa and dust mites. Mycotoxins, endotoxins, pollens and residues of organisms are also known to cause adverse health effects. A quantitative detection/identification technique independent of culturability that assays both culturable and non culturable biomass including endotoxin is critical in defining risks from indoor air biocontamination. Traditionally, methods employed for themore » monitoring of microorganism numbers in indoor air environments involve classical culture based techniques and/or direct microscopic counting. It has been repeatedly documented that viable microorganism counts only account for between 0.1-10% of the total community detectable by direct counting. The classic viable microbiologic approach doe`s not provide accurate estimates of microbial fragments or other indoor air components that can act as antigens and induce or potentiate allergic responses. Although bioaerosol samplers are designed to damage the microbes as little as possible, microbial stress has been shown to result from air sampling, aerosolization and microbial collection. Higher collection efficiency results in greater cell damage while less cell damage often results in lower collection efficiency. Filtration can collect particulates at almost 100% efficiency, but captured microorganisms may become dehydrated and damaged resulting in non-culturability, however, the lipid biomarker assays described herein do not rely on cell culture. Lipids are components that are universally distributed throughout cells providing a means to assess independent of culturability.« less

Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters

PubMed Central

Mueller, Jaclyn A.; Culley, Alexander I.

2014-01-01

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 μm) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ≥100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses. PMID:24747903

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

PubMed

Pasolli, Edoardo; Truong, Duy Tin; Malik, Faizan; Waldron, Levi; Segata, Nicola

2016-07-01

Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the "healthy" microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml.

Quantitative fluorescent in-situ hybridization: a hypothesized competition mode between two dominant bacteria groups in hydrogen-producing anaerobic sludge processes.

PubMed

Huang, C-L; Chen, C-C; Lin, C-Y; Liu, W-T

2009-01-01

Two hydrogen-producing continuous flow stirred tank reactors (CSTRs) fed respectively with glucose and sucrose were investigated by polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE) and fluorescent in-situ hybridization (FISH). The substrate was fed in a continuous mode decreased from hydraulic retention time (HRT) 10 hours to 6, 5, 4, 3, and 2 hours. Quantitative fluorescent in-situ hybridization (FISH) observations further demonstrated that two morphotypes of bacteria dominated both microbial communities. One was long rod bacteria which can be targeted either by Chis150 probe designed to hybridize the gram positive low G + C bacteria or the specific oligonucleotide probe Lg10-6. The probe Lg10-6, affiliated with Clostridium pasteurianum, was designed and then checked with other reference organisms. The other type, unknown group, which cannot be detected by Chis150 was curved rod bacteria. Notably, the population ratios of the two predominant groups reflected the different operational performance of the two reactors, such as hydrogen producing rates, substrate turnover rates and metabolites compositions. Therefore, a competition mode of the two dominant bacteria groups was hypothesized. In the study, 16S rRNA-based gene library of hydrogen-producing microbial communities was established. The efficiency of hydrogen yields was correlated with substrates (glucose or sucrose), HRT, metabolites compositions (acetate, propionate, butyrate and ethanol), thermal pre-treatment (seed biomass was heated at 100 degrees C for 45 minutes), and microbial communities in the bioreactor, not sludge sources (municipal sewage sludge, alcohol-processing sludge, or bean-processing sludge). The designed specific oligonucleotide probe Lg10-6 also provides us a useful and fast molecular tool to screen hydrogen-producing microbial communities in the future research.

Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics.

PubMed

Hosokawa-Muto, Junji; Fujinami, Yoshihito; Mizuno, Natsuko

2015-08-01

Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Visually observed mold and moldy odor versus quantitatively measured microbial exposure in homes

PubMed Central

Reponen, Tiina; Singh, Umesh; Schaffer, Chris; Vesper, Stephen; Johansson, Elisabet; Adhikari, Atin; Grinshpun, Sergey A.; Indugula, Reshmi; Ryan, Patrick; Levin, Linda; LeMasters, Grace

2010-01-01

The main study objective was to compare different methods for assessing mold exposure in conjunction with an epidemiologic study on the development of children’s asthma. Homes of 184 children were assessed for mold by visual observations and dust sampling at child’s age 1 (Year 1). Similar assessment supplemented with air sampling was conducted in Year 7. Samples were analyzed for endotoxin, (1–3)-β-D-glucan, and fungal spores. The Mold Specific Quantitative Polymerase Chain Reaction assay was used to analyze 36 mold species in dust samples, and the Environmental Relative Moldiness Index (ERMI) was calculated. Homes were categorized based on three criteria: 1) visible mold damage, 2) moldy odor, and 3) ERMI. Even for homes where families had not moved, Year 7 endotoxin and (1–3)-β-D-glucan exposures were significantly higher than those in Year 1 (p<0.001), whereas no difference was seen for ERMI (p=0.78). Microbial concentrations were not consistently associated with visible mold damage categories, but were consistently higher in homes with moldy odor and in homes that had high ERMI. Low correlations between results in air and dust samples indicate different types or durations of potential microbial exposures from dust vs. air. Future analysis will indicate which, if any, of the assessment methods is associated with the development of asthma. PMID:20810150

Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance.

PubMed

Paterson, Eric; Midwood, Andrew J; Millard, Peter

2009-01-01

For soils in carbon balance, losses of soil carbon from biological activity are balanced by organic inputs from vegetation. Perturbations, such as climate or land use change, have the potential to disrupt this balance and alter soil-atmosphere carbon exchanges. As the quantification of soil organic matter stocks is an insensitive means of detecting changes, certainly over short timescales, there is a need to apply methods that facilitate a quantitative understanding of the biological processes underlying soil carbon balance. We outline the processes by which plant carbon enters the soil and critically evaluate isotopic methods to quantify them. Then, we consider the balancing CO(2) flux from soil and detail the importance of partitioning the sources of this flux into those from recent plant assimilate and those from native soil organic matter. Finally, we consider the interactions between the inputs of carbon to soil and the losses from soil mediated by biological activity. We emphasize the key functional role of the microbiota in the concurrent processing of carbon from recent plant inputs and native soil organic matter. We conclude that quantitative isotope labelling and partitioning methods, coupled to those for the quantification of microbial community substrate use, offer the potential to resolve the functioning of the microbial control point of soil carbon balance in unprecedented detail.

Mixed culture models for predicting intestinal microbial interactions between Escherichia coli and Lactobacillus in the presence of probiotic Bacillus subtilis.

PubMed

Yang, J J; Niu, C C; Guo, X H

2015-01-01

Bacillus has been proposed as a probiotic due to its in vivo effectiveness in the gastrointestinal tract through antimicrobial activities. The present study investigates the effects of Lactobacillus alone or in the presence of Bacillus subtilis MA139 on the inhibition of pathogenic Escherichia coli K88. Mixed cultures were used to predict the possible interactions among these bacteria within the intestinal tract of animals. B. subtilis MA139 was first assayed for its inhibition against E. coli K88 both under shaking and static culture conditions. A co-culture assay was employed under static conditions to test the inhibitory effects of Lactobacillus reuteri on E. coli K88, with or without addition of B. subtilis MA139. The results showed that B. subtilis MA139 had marked inhibition against E. coli K88 under shaking conditions and weak inhibition under static conditions. Lactobacillus alone as well as in combination with B. subtilis MA139 spores exerted strong inhibition against E. coli K88 under static conditions. However, the inhibition by Lactobacillus in combination with B. subilis spores was much higher than that by Lactobacillus alone (P<0.01). B. subtilis MA139 significantly decreased the pH and oxidation-reduction potential values of the co-culture broth compared to that of Lactobacillus alone (P<0.05). The viability of Lactobacillus increased when co-cultured with B. subtilis MA139 because of significantly higher Lactobacillus counts and lower pH values in the broth (P<0.05). The role of Bacillus in the mixed culture models suggests that Bacillus may produce beneficial effects by increasing the viability of lactobacilli and subsequently inhibiting the growth of pathogenic E. coli. Therefore, the combination of Bacillus and Lactobacillus species as a probiotic is recommended.

Mechanical loading of bovine pericardium accelerates enzymatic degradation.

PubMed

Ellsmere, J C; Khanna, R A; Lee, J M

1999-06-01

Bioprosthetic heart valves fail as the result of two simultaneous processes: structural deterioration and calcification. Leaflet deterioration and perforation have been correlated with regions of highest stress in the tissue. The failures have long been assumed to be due to simple mechanical fatigue of the collagen fibre architecture; however, we have hypothesized that local stresses-and particularly dynamic stresses-accelerate local proteolysis, leading to tissue failure. This study addresses that hypothesis. Using a novel, custom-built microtensile culture system, strips of bovine pericardium were subjected to static and dynamic loads while being exposed to solutions of microbial collagenase or trypsin (a non-specific proteolytic enzyme). The time to extend to 30% strain (defined here as time to failure) was recorded. After failure, the percentage of collagen solubilized was calculated based on the amount of hydroxyproline present in solution. All data were analyzed by analysis of variance (ANOVA). In collagenase, exposure to static load significantly decreased the time to failure (P < 0.002) due to increased mean rate of collagen solubilization. Importantly, specimens exposed to collagenase and dynamic load failed faster than those exposed to collagenase under the same average static load (P = 0.02). In trypsin, by contrast, static load never led to failure and produced only minimal degradation. Under dynamic load, however, specimens exposed to collagenase, trypsin, and even Tris/CaCl2 buffer solution, all failed. Only samples exposed to Hanks' physiological solution did not fail. Failure of the specimens exposed to trypsin and Tris/CaCl2 suggests that the non-collagenous components and the calcium-dependent proteolytic enzymes present in pericardial tissue may play roles in the pathogenesis of bioprosthetic heart valve degeneration.

How Static is the Statics Classroom? An investigation into how innovations, specifically Research-Based Instructional Strategies, are adopted into the Statics Classroom

NASA Astrophysics Data System (ADS)

Cutler, Stephanie Leigh

The purpose of this dissertation is to investigate how educational research, specifically Research-Based Instructional Strategies (RBIS), is adopted by education practice, specifically within the engineering Statics classroom. Using a systematic approach, changes in classroom teaching practices were investigated from the instructors' perspective. Both researchers and practitioners are included in the process, combining efforts to improve student learning, which is a critical goal for engineering education. The study is divided into 3 stages and each is discussed in an individual manuscript. Manuscript 1 provides an assessment of current teaching practices; Manuscript 2 explores RBIS use by Statics instructors and perceived barriers of adoption; and Manuscript 3 evaluates adoption using Fidelity of Implementation. A common set of concurrent mixed methods was used for each stage of this study. A quantitative national survey of Statics instructors (n =166) and 18 qualitative interviews were conducted to examine activities used in the Statics classroom and familiarity with nine RBIS. The results of this study show that lecturing is the most common activity throughout Statics classrooms, but is not the only activity. Other common activities included working examples and students working on problems individually and in groups. As discussed by the interview participants, each of Rogers' characteristics influenced adoption for different reasons. For example, Complexity (level of difficulty with implementation of an RBIS) was most commonly identified as a barrier. His study also evaluated the Fidelity of Implementation for each RBIS and found it to be higher for RBIS that were less complex (in terms of the number of critical components). Many of the critical components (i.e. activities required for implementation, as described in the literature) were found to statistically distinguish RBIS users and non-users. This dissertation offers four contributions: (1) an understanding of current practices in Statics; (2) the instructor perspective of the barriers to using RBIS in the classroom; (3) the use of Fidelity of Implementation as a unique evaluation of RBIS adoption, which can be used by future engineering education researchers; and (4) a systematic approach of exploring change in the classroom, which offers new perspectives and approaches to accelerate the adoption process.

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

High-resolution phylogenetic microbial community profiling

DOE PAGES

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; ...

2016-02-09

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes.

PubMed

Toulza, Eve; Tagliabue, Alessandro; Blain, Stéphane; Piganeau, Gwenael

2012-01-01

Microbial metagenomes are DNA samples of the most abundant, and therefore most successful organisms at the sampling time and location for a given cell size range. The study of microbial communities via their DNA content has revolutionized our understanding of microbial ecology and evolution. Iron availability is a critical resource that limits microbial communities' growth in many oceanic areas. Here, we built a database of 2319 sequences, corresponding to 140 gene families of iron metabolism with a large phylogenetic spread, to explore the microbial strategies of iron acquisition in the ocean's bacterial community. We estimate iron metabolism strategies from metagenome gene content and investigate whether their prevalence varies with dissolved iron concentrations obtained from a biogeochemical model. We show significant quantitative and qualitative variations in iron metabolism pathways, with a higher proportion of iron metabolism genes in low iron environments. We found a striking difference between coastal and open ocean sites regarding Fe(2+) versus Fe(3+) uptake gene prevalence. We also show that non-specific siderophore uptake increases in low iron open ocean environments, suggesting bacteria may acquire iron from natural siderophore-like organic complexes. Despite the lack of knowledge of iron uptake mechanisms in most marine microorganisms, our approach provides insights into how the iron metabolic pathways of microbial communities may vary with seawater iron concentrations.

Static, Mixed-Array Total Evaporation for Improved Quantitation of Plutonium Minor Isotopes in Small Samples

NASA Astrophysics Data System (ADS)

Stanley, F. E.; Byerly, Benjamin L.; Thomas, Mariam R.; Spencer, Khalil J.

2016-06-01

Actinide isotope measurements are a critical signature capability in the modern nuclear forensics "toolbox", especially when interrogating anthropogenic constituents in real-world scenarios. Unfortunately, established methodologies, such as traditional total evaporation via thermal ionization mass spectrometry, struggle to confidently measure low abundance isotope ratios (<10-6) within already limited quantities of sample. Herein, we investigate the application of static, mixed array total evaporation techniques as a straightforward means of improving plutonium minor isotope measurements, which have been resistant to enhancement in recent years because of elevated radiologic concerns. Results are presented for small sample (~20 ng) applications involving a well-known plutonium isotope reference material, CRM-126a, and compared with traditional total evaporation methods.

Static, Mixed-Array Total Evaporation for Improved Quantitation of Plutonium Minor Isotopes in Small Samples.

PubMed

Stanley, F E; Byerly, Benjamin L; Thomas, Mariam R; Spencer, Khalil J

2016-06-01

Actinide isotope measurements are a critical signature capability in the modern nuclear forensics "toolbox", especially when interrogating anthropogenic constituents in real-world scenarios. Unfortunately, established methodologies, such as traditional total evaporation via thermal ionization mass spectrometry, struggle to confidently measure low abundance isotope ratios (<10(-6)) within already limited quantities of sample. Herein, we investigate the application of static, mixed array total evaporation techniques as a straightforward means of improving plutonium minor isotope measurements, which have been resistant to enhancement in recent years because of elevated radiologic concerns. Results are presented for small sample (~20 ng) applications involving a well-known plutonium isotope reference material, CRM-126a, and compared with traditional total evaporation methods. Graphical Abstract ᅟ.

EMERGING PATHOGENS OF ANIMAL ORIGIN: UNIQUE CHALLENGES FOR QUANTITATIVE MICROBIAL RISK ASSESSMENT

EPA Science Inventory

Recently severe human epidemics caused by waterborne Cryptosporidium parvum and Escherichia coli Strain (157:H7 of animal origin have attracted much attention in the national news media. Among the 130 diseases that can be transmitted to man from domestic and wild animals, a signi...

What is the relative health risk to swimmers from California Seagull feces compared to bather shedders?

EPA Science Inventory

Estimated infection risks to swimmers from California seagull and bather sources of fecal contamination at a beach in Southern California were compared using quantitative microbial risk assessment (QMRA). The risk to swimmers of gastro-intestinal infections was estimated from Ca...

Novel technologies in rumen microbiology: What have we learned?

USDA-ARS?s Scientific Manuscript database

Beginning in the 1950s, rumen microbiology enjoyed a golden age in which the secrets of the rumen began to be teased out through the isolation of numerous new microbial species and the discovery of such important concepts as interspecies hydrogen transfer and the quantitative aspects of bacterial gr...

Rapid and Specific Method for Evaluating Streptomyces Competitive Dynamics in Complex Soil Communities

USDA-ARS?s Scientific Manuscript database

Quantifying target microbial populations in complex communities remains a barrier to studying species interactions in soil environments. Quantitative real-time PCR (qPCR) offers a rapid and specific means to assess populations of target microorganisms. SYBR Green and TaqMan-based qPCR assays were de...

VISUALLY OBSERVED MOLD AND MOLDY ODOR VERSUS QUANTITATIVELY MEASURED MICROBIAL EXPOSURE IN HOMES

EPA Science Inventory

The main study objective was to compare different methods for assessing mold exposure in conjunction with an epidemiologic study on the development of children's asthma. Homes of 184 children were assessed for mold by visual observations and dust sampling at child's age 1 (Year ...

Can QMRA be used to Discount Pathogen Risk to Swimmers from Animal Fecal Contamination? Doheny Beach, CA Case Study

EPA Science Inventory

Estimated health risks to swimmers from seagull and bather sources of fecal contamination at Doheny Beach, California were compared using quantitative microbial risk assessment (QMRA) with a view to aiding beach closure decisions. Surfzone pathogens from seagulls were thought to...

Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study

EPA Science Inventory

The contribution of fecal pollution from dogs in urbanized areas can be significant and is an often underestimated problem. Microbial source tracking methods (MST) utilizing quantitative PCR of dog-associated gene sequences encoding 16S rRNA of Bacteroidales are a useful tool to ...

Simulated Moving Bed Chromatography: Separation and Recovery of Sugars and Ionic Liquid from Biomass Hydrolysates

PubMed Central

Caes, Benjamin R.; Van Oosbree, Thomas R.; Lu, Fachuang; Ralph, John; Maravelias, Christos T.

2015-01-01

Simulated moving bed chromatography, a continuous separation method, enables the nearly quantitative recovery of sugar products and ionic liquid solvent from chemical hydrolysates of biomass. The ensuing sugars support microbial growth, and the residual lignin from the process is intact. PMID:23939991

Quantitative analyses for elucidating mechanisms of cell fate commitment in the mouse blastocyst

NASA Astrophysics Data System (ADS)

Saiz, Néstor; Kang, Minjung; Puliafito, Alberto; Schrode, Nadine; Xenopoulos, Panagiotis; Lou, Xinghua; Di Talia, Stefano; Hadjantonakis, Anna-Katerina

2015-03-01

In recent years we have witnessed a shift from qualitative image analysis towards higher resolution, quantitative analyses of imaging data in developmental biology. This shift has been fueled by technological advances in both imaging and analysis software. We have recently developed a tool for accurate, semi-automated nuclear segmentation of imaging data from early mouse embryos and embryonic stem cells. We have applied this software to the study of the first lineage decisions that take place during mouse development and established analysis pipelines for both static and time-lapse imaging experiments. In this paper we summarize the conclusions from these studies to illustrate how quantitative, single-cell level analysis of imaging data can unveil biological processes that cannot be revealed by traditional qualitative studies.

Stoichiometric modelling of assimilatory and dissimilatory biomass utilisation in a microbial community

PubMed Central

Hunt, Kristopher A.; Jennings, Ryan deM.; Inskeep, William P.; Carlson, Ross P.

2017-01-01

Summary Assimilatory and dissimilatory utilisation of autotroph biomass by heterotrophs is a fundamental mechanism for the transfer of nutrients and energy across trophic levels. Metagenome data from a tractable, thermoacidophilic microbial community in Yellowstone National Park was used to build an in silico model to study heterotrophic utilisation of autotroph biomass using elementary flux mode analysis and flux balance analysis. Assimilatory and dissimilatory biomass utilisation was investigated using 29 forms of biomass-derived dissolved organic carbon (DOC) including individual monomer pools, individual macromolecular pools and aggregate biomass. The simulations identified ecologically competitive strategies for utilizing DOC under conditions of varying electron donor, electron acceptor or enzyme limitation. The simulated growth environment affected which form of DOC was the most competitive use of nutrients; for instance, oxygen limitation favoured utilisation of less reduced and fermentable DOC while carbon-limited environments favoured more reduced DOC. Additionally, metabolism was studied considering two encompassing metabolic strategies: simultaneous versus sequential use of DOC. Results of this study bound the transfer of nutrients and energy through microbial food webs, providing a quantitative foundation relevant to most microbial ecosystems. PMID:27387069

Application of clone library analysis and real-time PCR for comparison of microbial communities in a low-grade copper sulfide ore bioheap leachate.

PubMed

Bowei, Chen; Xingyu, Liu; Wenyan, Liu; Jiankang, Wen

2009-11-01

The microbial communities of leachate from a bioleaching heap located in China were analyzed using the 16S rRNA gene clone library and real-time quantitative PCR. Both methods showed that Leptospirillum spp. were the dominant bacteria, and Ferroplasma acidiphilum were the only archaea detected in the leachate. Clone library results indicated that nine operational taxonomic units (OTUs) were obtained, which fell into four divisions, the Nitrospirae (74%), the gamma-Proteobacteria (14%), the Actinobacteria (6%) and the Euryarchaeota (6%). The results obtained by real-time PCR in some ways were the same as clone library analysis. Furthermore, Sulfobacillus spp., detected only by real-time PCR, suggests that real-time PCR was a reliable technology to study the microbial communities in bioleaching environments. It is a useful tool to assist clone library analysis, to further understand microbial consortia and to have comprehensive and exact microbiological information about bioleaching environments. Finally, the interactions among the microorganisms detected in the leachate were summarized according to the characteristics of these species.

Influence of air quality on the composition of microbial pathogens in fresh rainwater.

PubMed

Kaushik, Rajni; Balasubramanian, Rajasekhar; de la Cruz, Armah A

2012-04-01

In this study, the microbiological quality of fresh rainwater was assessed from 50 rain events under tropical weather conditions for a year. The levels of four major opportunistic waterborne pathogens, namely, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Aeromonas hydrophila, in rainwater samples were quantified by using a robust and sensitive quantitative PCR (qPCR) method. Of the 50 rainwater samples, 25 were found to be positive for at least one pathogen: 21 for E. coli, 16 for P. aeruginosa, 6 for K. pneumoniae, and 1 for A. hydrophila. In addition to the microbiological assessment of rainwater samples, we also studied the influence of prevailing air quality on the microbial quality of rainwater over the sampling period. A significant change in the diversity and relative abundance of the basic microbial indicator organisms in rainwater was observed during a major regional air pollution episode in Southeast Asia due to biomass-burning emissions.

Constraining Biomarkers of Dissolved Organic Matter Sourcing Using Microbial Incubations of Vascular Plant Leachates of the California landscape

NASA Astrophysics Data System (ADS)

Harfmann, J.; Hernes, P.; Chuang, C. Y.; Kaiser, K.; Spencer, R. G.; Guillemette, F.

2017-12-01

Source origin of dissolved organic matter (DOM) is crucial in determining reactivity, driving chemical and biological processing of carbon. DOM source biomarkers such as lignin (a vascular plant marker) and D-amino acids (bacterial markers) are well-established tools in tracing DOM origin and fate. The development of high-resolution mass spectrometry and optical studies has expanded our toolkit; yet despite these advances, our understanding of DOM sources and fate remains largely qualitative. Quantitative data on DOM pools and fluxes become increasingly necessary as we refine our comprehension of its composition. In this study, we aim to calibrate and quantify DOM source endmembers by performing microbial incubations of multiple vascular plant leachates, where total DOM is constrained by initial vascular plant input and microbial production. Derived endmembers may be applied to endmember mixing models to quantify DOM source contributions in aquatic systems.

Correlation of Shiga Toxin Gene Frequency with Commonly Used Microbial Indicators of Recreational Water Quality▿ †

PubMed Central

Smith, Cody J.; Olszewski, Adam M.; Mauro, Steven A.

2009-01-01

Shiga toxin (Stx) genes produce proteins that are pathogenic to humans, leading to severe gastrointestinal illness. This work focuses on examining the abundance and distribution of stx genes in relation to common microbial indicators in beach water and streams in the vicinity of Presque Isle State Park in Erie, PA. By use of quantitative PCR, the relative abundance levels of stx DNA in over 700 samples in the sampling area were determined. The results demonstrate that the abundance and distribution of stx genes are variable and do not correlate with the abundance of Escherichia coli bacteria, enterococci, or viral particles. These results suggest that microbial indicators of water quality are not adequate in predicting the occurrence of organisms that harbor stx genes and highlight the need for standardized pathogen-specific detection protocols for waters utilized for recreational swimming. PMID:19011065

Standing variation in spatially growing populations

NASA Astrophysics Data System (ADS)

Fusco, Diana; Gralka, Matti; Kayser, Jona; Hallatschek, Oskar

Patterns of genetic diversity not only reflect the evolutionary history of a species but they can also determine the evolutionary response to environmental change. For instance, the standing genetic diversity of a microbial population can be key to rescue in the face of an antibiotic attack. While genetic diversity is in general shaped by both demography and evolution, very little is understood when both factors matter, as e.g. for biofilms with pronounced spatial organization. Here, we quantitatively explore patterns of genetic diversity by using microbial colonies and well-mixed test tube populations as antipodal model systems with extreme and very little spatial structure, respectively. We find that Eden model simulations and KPZ theory can remarkably reproduce the genetic diversity in microbial colonies obtained via population sequencing. The excellent agreement allows to draw conclusions on the resilience of spatially-organized populations and to uncover new strategies to contain antibiotic resistance.

Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research.

PubMed

Vorholt, Julia A; Vogel, Christine; Carlström, Charlotte I; Müller, Daniel B

2017-08-09

Plant microbiome research highlights the importance of indigenous microbial communities for host phenotypes such as growth and health. It aims to discover the molecular basis by which host-microbe and microbe-microbe interactions shape and maintain microbial communities and to understand the role of individual microorganisms, as well as their collective ecosystem function. Here, we discuss reductionist approaches to disentangle the inherent complexity of interactions in situ. Experimentally tractable, synthetic communities enable testing of hypotheses by targeted manipulation in gnotobiotic systems. Modifications of microbial, host, and environmental parameters allow for the quantitative assessment of host and microbe characteristics with dynamic and spatial resolution. We summarize first insights from this emerging field and discuss current challenges and limitations. Using multifaceted approaches to detect interactions and functions will provide new insights into the fundamental biology of plant-microbe interactions and help to harness the power of the microbiome. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology.

PubMed

Ju, Feng; Zhang, Tong

2015-11-03

Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.

Experimental design and quantitative analysis of microbial community multiomics.

PubMed

Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

2017-11-30

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

PubMed Central

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J.; Waghorn, Garry C.; Janssen, Peter H.

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided. PMID:24040342

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

PubMed

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

A High Performance Piezoelectric Sensor for Dynamic Force Monitoring of Landslide

PubMed Central

Li, Ming; Cheng, Wei; Chen, Jiangpan; Xie, Ruili; Li, Xiongfei

2017-01-01

Due to the increasing influence of human engineering activities, it is important to monitor the transient disturbance during the evolution process of landslide. For this purpose, a high-performance piezoelectric sensor is presented in this paper. To adapt the high static and dynamic stress environment in slope engineering, two key techniques, namely, the self-structure pressure distribution method (SSPDM) and the capacitive circuit voltage distribution method (CCVDM) are employed in the design of the sensor. The SSPDM can greatly improve the compressive capacity and the CCVDM can quantitatively decrease the high direct response voltage. Then, the calibration experiments are conducted via the independently invented static and transient mechanism since the conventional testing machines cannot match the calibration requirements. The sensitivity coefficient is obtained and the results reveal that the sensor has the characteristics of high compressive capacity, stable sensitivities under different static preload levels and wide-range dynamic measuring linearity. Finally, to reduce the measuring error caused by charge leakage of the piezoelectric element, a low-frequency correction method is proposed and experimental verified. Therefore, with the satisfactory static and dynamic properties and the improving low-frequency measuring reliability, the sensor can complement dynamic monitoring capability of the existing landslide monitoring and forecasting system. PMID:28218673

Quantifying dynamic characteristics of human walking for comprehensive gait cycle.

PubMed

Mummolo, Carlotta; Mangialardi, Luigi; Kim, Joo H

2013-09-01

Normal human walking typically consists of phases during which the body is statically unbalanced while maintaining dynamic stability. Quantifying the dynamic characteristics of human walking can provide better understanding of gait principles. We introduce a novel quantitative index, the dynamic gait measure (DGM), for comprehensive gait cycle. The DGM quantifies the effects of inertia and the static balance instability in terms of zero-moment point and ground projection of center of mass and incorporates the time-varying foot support region (FSR) and the threshold between static and dynamic walking. Also, a framework of determining the DGM from experimental data is introduced, in which the gait cycle segmentation is further refined. A multisegmental foot model is integrated into a biped system to reconstruct the walking motion from experiments, which demonstrates the time-varying FSR for different subphases. The proof-of-concept results of the DGM from a gait experiment are demonstrated. The DGM results are analyzed along with other established features and indices of normal human walking. The DGM provides a measure of static balance instability of biped walking during each (sub)phase as well as the entire gait cycle. The DGM of normal human walking has the potential to provide some scientific insights in understanding biped walking principles, which can also be useful for their engineering and clinical applications.

Foot-Ground Interaction during Upright Standing in Children with Down Syndrome

ERIC Educational Resources Information Center

Pau, Massimiliano; Galli, Manuela; Crivellini, Marcello; Albertini, Giorgio

2012-01-01

This study aimed to quantitatively characterize the main foot-ground contact parameters during static upright standing and to assess foot evolution with increasing age in young individuals affected by Down syndrome (DS). To this end, 99 children with DS of mean age 9.7 (1.7) were tested using a pressure sensitive mat, and the raw data were…

Ambiguity, logic, simplicity, and dynamics: Wittgensteinian evaluative criteria in peer review of quantitative research on categorization.

PubMed

Shimp, Charles P

2004-06-30

Research on categorization has changed over time, and some of these changes resemble how Wittgenstein's views changed from his Tractatus Logico-Philosophicus to his Philosophical Investigations. Wittgenstein initially focused on unambiguous, abstract, parsimonious, logical propositions and rules, and on independent, static, "atomic facts." This approach subsequently influenced the development of logical positivism and thereby may have indirectly influenced method and theory in research on categorization: much animal research on categorization has focused on learning simple, static, logical rules unambiguously interrelating small numbers of independent features. He later rejected logical simplicity and rigor and focused instead on Gestalt ideas about figure-ground reversals and context, the ambiguity of family resemblance, and the function of details of everyday language. Contemporary contextualism has been influenced by this latter position, some features of which appear in contemporary empirical research on categorization. These developmental changes are illustrated by research on avian local and global levels of visual perceptual analysis, categorization of rectangles and moving objects, and artificial grammar learning. Implications are described for peer review of quantitative theory in which ambiguity, logical rigor, simplicity, or dynamics are designed to play important roles.

Quantitative assessment of dynamic PET imaging data in cancer imaging.

PubMed

Muzi, Mark; O'Sullivan, Finbarr; Mankoff, David A; Doot, Robert K; Pierce, Larry A; Kurland, Brenda F; Linden, Hannah M; Kinahan, Paul E

2012-11-01

Clinical imaging in positron emission tomography (PET) is often performed using single-time-point estimates of tracer uptake or static imaging that provides a spatial map of regional tracer concentration. However, dynamic tracer imaging can provide considerably more information about in vivo biology by delineating both the temporal and spatial pattern of tracer uptake. In addition, several potential sources of error that occur in static imaging can be mitigated. This review focuses on the application of dynamic PET imaging to measuring regional cancer biologic features and especially in using dynamic PET imaging for quantitative therapeutic response monitoring for cancer clinical trials. Dynamic PET imaging output parameters, particularly transport (flow) and overall metabolic rate, have provided imaging end points for clinical trials at single-center institutions for years. However, dynamic imaging poses many challenges for multicenter clinical trial implementations from cross-center calibration to the inadequacy of a common informatics infrastructure. Underlying principles and methodology of PET dynamic imaging are first reviewed, followed by an examination of current approaches to dynamic PET image analysis with a specific case example of dynamic fluorothymidine imaging to illustrate the approach. Copyright © 2012 Elsevier Inc. All rights reserved.

The study on the parallel processing based time series correlation analysis of RBC membrane flickering in quantitative phase imaging

NASA Astrophysics Data System (ADS)

Lee, Minsuk; Won, Youngjae; Park, Byungjun; Lee, Seungrag

2017-02-01

Not only static characteristics but also dynamic characteristics of the red blood cell (RBC) contains useful information for the blood diagnosis. Quantitative phase imaging (QPI) can capture sample images with subnanometer scale depth resolution and millisecond scale temporal resolution. Various researches have been used QPI for the RBC diagnosis, and recently many researches has been developed to decrease the process time of RBC information extraction using QPI by the parallel computing algorithm, however previous studies are interested in the static parameters such as morphology of the cells or simple dynamic parameters such as root mean square (RMS) of the membrane fluctuations. Previously, we presented a practical blood test method using the time series correlation analysis of RBC membrane flickering with QPI. However, this method has shown that there is a limit to the clinical application because of the long computation time. In this study, we present an accelerated time series correlation analysis of RBC membrane flickering using the parallel computing algorithm. This method showed consistent fractal scaling exponent results of the surrounding medium and the normal RBC with our previous research.

Biogeochemical interactions between of coal mine water and gas well cement

NASA Astrophysics Data System (ADS)

Gulliver, D. M.; Gardiner, J. B.; Kutchko, B. G.; Hakala, A.; Spaulding, R.; Tkach, M. K.; Ross, D.

2017-12-01

Unconventional natural gas wells drilled in Northern Appalachia often pass through abandoned coal mines before reaching the Marcellus or Utica formations. Biogeochemical interactions between coal mine waters and gas well cements have the potential to alter the cement and compromise its sealing integrity. This study investigates the mineralogical, geochemical, and microbial changes of cement cores exposed to natural coal mine waters. Static reactors with Class H Portland cement cores and water samples from an abandoned bituminous Pittsburgh coal mine simulated the cement-fluid interactions at relevant temperature for time periods of 1, 2, 4, and 6 weeks. Fluids were analyzed for cation and anion concentrations and extracted DNA was analyzed by 16S rRNA gene sequencing and shotgun sequencing. Cement core material was evaluated via scanning electron microscope. Results suggest that the sampled coal mine water altered the permeability and matrix mineralogy of the cement cores. Scanning electron microscope images display an increase in mineral precipitates inside the cement matrix over the course of the experiment. Chemistry results from the reaction vessels' effluent waters display decreases in dissolved calcium, iron, silica, chloride, and sulfate. The microbial community decreased in diversity over the 6-week experiment, with Hydrogenophaga emerging as dominant. These results provide insight in the complex microbial-fluid-mineral interactions of these environments. This study begins to characterize the rarely documented biogeochemical impacts that coal waters may have on unconventional gas well integrity.

Cytotoxicity assessment of modified bioactive glasses with MLO-A5 osteogenic cells in vitro.

PubMed

Modglin, Vernon C; Brown, Roger F; Jung, Steven B; Day, Delbert E

2013-05-01

The primary objective of this study was to evaluate in vitro responses of MLO-A5 osteogenic cells to two modifications of the bioactive glass 13-93. The modified glasses, which were designed for use as cell support scaffolds and contained added boron to form the glasses 13-93 B1 and 13-93 B3, were made to accelerate formation of a bioactive hydroxyapatite surface layer and possibly enhance tissue growth. Quantitative MTT cytotoxicity tests revealed no inhibition of growth of MLO-A5 cells incubated with 13-93 glass extracts up to 10 mg/ml, moderate inhibition of growth with 13-93 B1 glass extracts, and noticeable inhibition of growth with 13-93 B3 glass extracts. A morphology-based biocompatibility test was also performed and yielded qualitative assessments of the relative biocompatibilities of glass extracts that agree with those obtained by the quantitative MTT test. However, as a proof of concept experiment, when MLO-A5 cells were seeded onto 13-93 B3 scaffolds in a dynamic in vitro environment, cell proliferation occurred as evidenced by qualitative and quantitative MTT labeling of scaffolds. Together these results demonstrate the in vitro toxicity of released borate ion in static experiments; however borate ion release can be mitigated in a dynamic environment similar to the human body where microvasculature is present. Here we argue that despite toxicity in static environments, boron-containing 13-93 compositions may warrant further study for use in tissue engineering applications.

Intestinal microbial variation may predict early acute rejection after liver transplantation in rats.

PubMed

Ren, Zhigang; Jiang, Jianwen; Lu, Haifeng; Chen, Xinhua; He, Yong; Zhang, Hua; Xie, Haiyang; Wang, Weilin; Zheng, Shusen; Zhou, Lin

2014-10-27

Acute rejection (AR) remains a life-threatening complication after orthotopic liver transplantation (OLT) and there are few available diagnostic biomarkers clinically for AR. This study aims to identify intestinal microbial profile and explore potential application of microbial profile as a biomarker for AR after OLT. The OLT models in rats were established. Hepatic graft histology, ultrastructure, function, and intestinal barrier function were tested. Ileocecal contents were collected for intestinal microbial analysis. Hepatic graft suffered from the ischemia-reperfusion (I/R) injury on day 1, initial AR on day 3, and severe AR on day 7 after OLT. Real-time quantitative polymerase chain reaction results showed that genus Faecalibacterium prausnitzii and Lactobacillus were decreased, whereas Clostridium bolteae was increased during AR. Notably, cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR. Microbial diversity and species richness were decreased during AR. Phylogenetic tree analysis showed that most of the decreased key bacteria belonged to phylum Firmicutes, whereas increased key bacteria belonged to phylum Bacteroidetes. Moreover, intestinal microvilli loss and tight junction damage were noted, and intestinal barrier dysfunction during AR presented a decrease of fecal secretory immunoglobulin A (sIgA) and increase of blood bacteremia, endotoxin, and tumor necrosis factor-α. We dynamically detail intestinal microbial characterization and find a high sensitivity of microbial change during AR after OLT, suggesting that intestinal microbial variation may predict AR in early phase and become an assistant therapeutic target to improve rejection after OLT.

Airborne bacterial contaminations in typical Chinese wet market with live poultry trade.

PubMed

Gao, Xin-Lei; Shao, Ming-Fei; Luo, Yi; Dong, Yu-Fang; Ouyang, Feng; Dong, Wen-Yi; Li, Ji

2016-12-01

Chinese wet markets with live poultry trade have been considered as major sources of pathogen dissemination, and sites for horizontal transfer of bacterial and viral pathogens. In this study, the pathogenic bacteria and antibiotic resistant genes (ARGs) in air samples collected at a typical Chinese wet market had been analysis and quantified. Corynebacterium minutissimum and other pathogenic bacteria accounted for 0.81-8.02% of the whole microbial community in different air samples. The four ARGs quantified in this study showed a comparable relative concentration (copies/ng_DNA) with municipal wastewater. Poultry manures were demonstrated to be important microbial contamination source in wet market, which was supported by both microbial composition based source tracking and the quantification of airborne microbial density. A series of Firmicutes and Bacteroidetes indicators of poultry area contamination were successfully screened, which will be useful for the more convenient monitoring of airborne poultry area contamination. Our results indicate bioaerosols acted as important route for the transmissions of pathogens and ARGs. Continued surveillance of airborne microbial contamination is required in poultry trade wet market. Urban live poultry markets are important sources of pathogen dissemination, and sites for horizontal transfer of viral and bacterial pathogens. In the present field-study, pathogenic bacteria and antibiotic resistance genes were focused to provide quantitative information on the levels of microbial contaminations at the indoor air of wet markets. Results demonstrated that poultry manures were important microbial contamination source in wet market, and in the meanwhile bioaerosols were identified as important route for the transmissions of microbial contaminants. A series of Firmicutes and Bacteroidetes indicators of poultry area contamination were successfully screened, which will be useful for the more convenient monitoring of airborne poultry area contamination. Copyright © 2016 Elsevier B.V. All rights reserved.

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats

PubMed Central

Ren, Zhigang; Jiang, Jianwen; Lu, Haifeng; Chen, Xinhua; He, Yong; Zhang, Hua; Xie, Haiyang; Wang, Weilin; Zheng, Shusen; Zhou, Lin

2014-01-01

Background Acute rejection (AR) remains a life-threatening complication after orthotopic liver transplantation (OLT) and there are few available diagnostic biomarkers clinically for AR. This study aims to identify intestinal microbial profile and explore potential application of microbial profile as a biomarker for AR after OLT. Methods The OLT models in rats were established. Hepatic graft histology, ultrastructure, function, and intestinal barrier function were tested. Ileocecal contents were collected for intestinal microbial analysis. Results Hepatic graft suffered from the ischemia-reperfusion (I/R) injury on day 1, initial AR on day 3, and severe AR on day 7 after OLT. Real-time quantitative polymerase chain reaction results showed that genus Faecalibacterium prausnitzii and Lactobacillus were decreased, whereas Clostridium bolteae was increased during AR. Notably, cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR. Microbial diversity and species richness were decreased during AR. Phylogenetic tree analysis showed that most of the decreased key bacteria belonged to phylum Firmicutes, whereas increased key bacteria belonged to phylum Bacteroidetes. Moreover, intestinal microvilli loss and tight junction damage were noted, and intestinal barrier dysfunction during AR presented a decrease of fecal secretory immunoglobulin A (sIgA) and increase of blood bacteremia, endotoxin, and tumor necrosis factor-α. Conclusion We dynamically detail intestinal microbial characterization and find a high sensitivity of microbial change during AR after OLT, suggesting that intestinal microbial variation may predict AR in early phase and become an assistant therapeutic target to improve rejection after OLT. PMID:25321166

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

(A)biotic processes control soil carbon dynamics: quantitative assessment of model complexity, stability and response to perturbations for improving ESMs

NASA Astrophysics Data System (ADS)

Georgiou, K.; Abramoff, R. Z.; Harte, J.; Riley, W. J.; Torn, M. S.

2016-12-01

As global temperatures and atmospheric CO2 concentrations continue to increase, soil microbial activity and decomposition of soil organic matter (SOM) are expected to follow suit, potentially limiting soil carbon storage. Traditional global- and ecosystem-scale models simulate SOM decomposition using linear kinetics, which are inherently unable to reproduce carbon-concentration feedbacks, such as priming of native SOM at elevated CO2 concentrations. Recent studies using nonlinear microbial models of SOM decomposition seek to capture these interactions, and several groups are currently integrating these microbial models into Earth System Models (ESMs). However, despite their widespread ability to exhibit nonlinear responses, these models vary tremendously in complexity and, consequently, dynamics. In this study, we explore, both analytically and numerically, the emergent oscillatory behavior and insensitivity of SOM stocks to carbon inputs that have been deemed `unrealistic' in recent microbial models. We discuss the sources of instability in four models of varying complexity, by sequentially reducing complexity of a detailed model that includes microbial physiology, a mineral sorption isotherm, and enzyme dynamics. We also present an alternative representation of microbial turnover that limits population sizes and, thus, reduces oscillations. We compare these models to several long-term carbon input manipulations, including the Detritus Input and Removal Treatment (DIRT) experiments, to show that there are clear metrics that can be used to distinguish and validate the inherent dynamics of each model structure. We find that traditional linear and nonlinear models cannot readily capture the range of long-term responses observed across the DIRT experiments as a direct consequence of their model structures, and that modifying microbial turnover results in more realistic predictions. Finally, we discuss our findings in the context of improving microbial model behavior for inclusion in ESMs.

A multivariable model for predicting the frictional behaviour and hydration of the human skin.

PubMed

Veijgen, N K; van der Heide, E; Masen, M A

2013-08-01

The frictional characteristics of skin-object interactions are important when handling objects, in the assessment of perception and comfort of products and materials and in the origins and prevention of skin injuries. In this study, based on statistical methods, a quantitative model is developed that describes the friction behaviour of human skin as a function of the subject characteristics, contact conditions, the properties of the counter material as well as environmental conditions. Although the frictional behaviour of human skin is a multivariable problem, in literature the variables that are associated with skin friction have been studied using univariable methods. In this work, multivariable models for the static and dynamic coefficients of friction as well as for the hydration of the skin are presented. A total of 634 skin-friction measurements were performed using a recently developed tribometer. Using a statistical analysis, previously defined potential influential variables were linked to the static and dynamic coefficient of friction and to the hydration of the skin, resulting in three predictive quantitative models that descibe the friction behaviour and the hydration of human skin respectively. Increased dynamic coefficients of friction were obtained from older subjects, on the index finger, with materials with a higher surface energy at higher room temperatures, whereas lower dynamic coefficients of friction were obtained at lower skin temperatures, on the temple with rougher contact materials. The static coefficient of friction increased with higher skin hydration, increasing age, on the index finger, with materials with a higher surface energy and at higher ambient temperatures. The hydration of the skin was associated with the skin temperature, anatomical location, presence of hair on the skin and the relative air humidity. Predictive models have been derived for the static and dynamic coefficient of friction using a multivariable approach. These two coefficients of friction show a strong correlation. Consequently the two multivariable models resemble, with the static coefficient of friction being on average 18% lower than the dynamic coefficient of friction. The multivariable models in this study can be used to describe the data set that was the basis for this study. Care should be taken when generalising these results. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Multiple syntrophic interactions drive biohythane production from waste sludge in microbial electrolysis cells.

PubMed

Liu, Qian; Ren, Zhiyong Jason; Huang, Cong; Liu, Bingfeng; Ren, Nanqi; Xing, Defeng

2016-01-01

Biohythane is a new and high-value transportation fuel present as a mixture of biomethane and biohydrogen. It has been produced from different organic matters using anaerobic digestion. Bioenergy can be recovered from waste activated sludge through methane production during anaerobic digestion, but energy yield is often insufficient to sludge disposal. Microbial electrolysis cell (MEC) is also a promising approach for bioenergy recovery and waste sludge disposal as higher energy efficiency and biogas production. The systematic understanding of microbial interactions and biohythane production in MEC is still limited. Here, we report biohythane production from waste sludge in biocathode microbial electrolysis cells and reveal syntrophic interactions in microbial communities based on high-throughput sequencing and quantitative PCR targeting 16S rRNA gene. The alkali-pretreated sludge fed MECs (AS-MEC) showed the highest biohythane production rate of 0.148 L·L(-1)-reactor·day(-1), which is 40 and 80 % higher than raw sludge fed MECs (RS-MEC) and anaerobic digestion (open circuit MEC, RS-OCMEC). Current density, metabolite profiles, and hydrogen-methane ratio results all confirm that alkali-pretreatment and microbial electrolysis greatly enhanced sludge hydrolysis and biohythane production. Illumina Miseq sequencing of 16S rRNA gene amplicons indicates that anode biofilm was dominated by exoelectrogenic Geobacter, fermentative bacteria and hydrogen-producing bacteria in the AS-MEC. The cathode biofilm was dominated by fermentative Clostridium. The dominant archaeal populations on the cathodes of AS-MEC and RS-MEC were affiliated with hydrogenotrophic Methanobacterium (98 %, relative abundance) and Methanocorpusculum (77 %), respectively. Multiple pathways of gas production were observed in the same MEC reactor, including fermentative and electrolytic H2 production, as well as hydrogenotrophic methanogenesis and electromethanogenesis. Real-time quantitative PCR analyses showed that higher amount of methanogens were enriched in AS-MEC than that in RS-MEC and RS-OCMEC, suggesting that alkali-pretreated sludge and MEC facilitated hydrogenotrophic methanogen enrichment. This study proves for the first time that biohythane could be produced directly in biocathode MECs using waste sludge. MEC and alkali-pretreatment accelerated enrichment of hydrogenotrophic methanogen and hydrolysis of waste sludge. The results indicate syntrophic interactions among fermentative bacteria, exoelectrogenic bacteria and methanogenic archaea in MECs are critical for highly efficient conversion of complex organics into biohythane, demonstrating that MECs can be more competitive than conventional anaerobic digestion for biohythane production using carbohydrate-deficient substrates. Biohythane production from waste sludge by MEC provides a promising new way for practical application of microbial electrochemical technology.

Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending.

PubMed

Chaudhry, Rabia M; Hamilton, Kerry A; Haas, Charles N; Nelson, Kara L

2017-06-13

Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium , and Salmonella . Consumer microbial risks of surface source water quality (impacted by 0-100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0-100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10 -4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10 -4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR.

Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis.

PubMed

Lang-Yona, Naama; Maier, Stefanie; Macholdt, Dorothea S; Müller-Germann, Isabell; Yordanova, Petya; Rodriguez-Caballero, Emilio; Jochum, Klaus P; Al-Amri, Abdullah; Andreae, Meinrat O; Fröhlich-Nowoisky, Janine; Weber, Bettina

2018-02-28

Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial community structure across a wastewater-impacted riparian buffer zone in the southeastern coastal plain.

PubMed

Ducey, T F; Johnson, P R; Shriner, A D; Matheny, T A; Hunt, P G

2013-01-01

Riparian buffer zones are important for both natural and developed ecosystems throughout the world because of their ability to retain nutrients, prevent soil erosion, protect aquatic environments from excessive sedimentation, and filter pollutants. Despite their importance, the microbial community structures of riparian buffer zones remains poorly defined. Our objectives for this study were twofold: first, to characterize the microbial populations found in riparian buffer zone soils; and second, to determine if microbial community structure could be linked to denitrification enzyme activity (DEA). To achieve these objectives, we investigated the microbial populations of a riparian buffer zone located downslope of a pasture irrigated with swine lagoon effluent, utilizing DNA sequencing of the 16S rDNA, DEA, and quantitative PCR (qPCR) of the denitrification genes nirK, nirS, and nosZ. Clone libraries of the 16S rDNA gene were generated from each of twelve sites across the riparian buffer with a total of 986 partial sequences grouped into 654 operational taxonomic units (OTUs). The Proteobacteria were the dominant group (49.8% of all OTUs), with the Acidobacteria also well represented (19.57% of all OTUs). Analysis of qPCR results identified spatial relationships between soil series, site location, and gene abundance, which could be used to infer both incomplete and total DEA rates.

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

PubMed Central

Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

2014-01-01

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

Estimation method for serial dilution experiments.

PubMed

Ben-David, Avishai; Davidson, Charles E

2014-12-01

Titration of microorganisms in infectious or environmental samples is a corner stone of quantitative microbiology. A simple method is presented to estimate the microbial counts obtained with the serial dilution technique for microorganisms that can grow on bacteriological media and develop into a colony. The number (concentration) of viable microbial organisms is estimated from a single dilution plate (assay) without a need for replicate plates. Our method selects the best agar plate with which to estimate the microbial counts, and takes into account the colony size and plate area that both contribute to the likelihood of miscounting the number of colonies on a plate. The estimate of the optimal count given by our method can be used to narrow the search for the best (optimal) dilution plate and saves time. The required inputs are the plate size, the microbial colony size, and the serial dilution factors. The proposed approach shows relative accuracy well within ±0.1log10 from data produced by computer simulations. The method maintains this accuracy even in the presence of dilution errors of up to 10% (for both the aliquot and diluent volumes), microbial counts between 10(4) and 10(12) colony-forming units, dilution ratios from 2 to 100, and plate size to colony size ratios between 6.25 to 200. Published by Elsevier B.V.

Uranium reduction and microbial community development in response to stimulation with different electron donors.

PubMed

Barlett, Melissa; Moon, Hee Sun; Peacock, Aaron A; Hedrick, David B; Williams, Kenneth H; Long, Philip E; Lovley, Derek; Jaffe, Peter R

2012-07-01

Stimulating microbial reduction of soluble U(VI) to less soluble U(IV) shows promise as an in situ bioremediation strategy for uranium contaminated groundwater, but the optimal electron donors for promoting this process have yet to be identified. The purpose of this study was to better understand how the addition of various electron donors to uranium-contaminated subsurface sediments affected U(VI) reduction and the composition of the microbial community. The simple electron donors, acetate or lactate, or the more complex donors, hydrogen-release compound (HRC) or vegetable oil, were added to the sediments incubated in flow-through columns. The composition of the microbial communities was evaluated with quantitative PCR probing specific 16S rRNA genes and functional genes, phospholipid fatty acid analysis, and clone libraries. All the electron donors promoted U(VI) removal, even though the composition of the microbial communities was different with each donor. In general, the overall biomass, rather than the specific bacterial species, was the factor most related to U(VI) removal. Vegetable oil and HRC were more effective in stimulating U(VI) removal than acetate. These results suggest that the addition of more complex organic electron donors could be an excellent option for in situ bioremediation of uranium-contaminated groundwater.

Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending

PubMed Central

Chaudhry, Rabia M.; Hamilton, Kerry A.; Haas, Charles N.; Nelson, Kara L.

2017-01-01

Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium, and Salmonella. Consumer microbial risks of surface source water quality (impacted by 0–100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0–100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10−4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10−4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR. PMID:28608808

Microbial load of umbilical cord blood Ureaplasma species and Mycoplasma hominis in preterm prelabor rupture of membranes.

PubMed

Kacerovsky, Marian; Pliskova, Lenka; Menon, Ramkumar; Kutova, Radka; Musilova, Ivana; Maly, Jan; Andrys, Ctirad

2014-11-01

To evaluate Ureaplasma species and M. hominis DNA in the umbilical cord blood and its correlation with its microbial load in the amniotic fluid, as a measure of microbial burden in fetal inflammatory response and neonatal outcome in pregnancies complicated by preterm prelabor rupture of membranes (pPROM). A retrospective study of 158 women with singleton pregnancies complicated by pPROM between 24(0/7) and 36(6/7) weeks was conducted. Amniotic fluid was obtained from all women by transabdominal amniocentesis, and umbilical cord blood was obtained by venipuncture from umbilical cords immediately after the delivery of the neonates. The Ureaplasma species and M. hominis DNA was quantitated using absolute quantification techniques. Ureaplasma species and M. hominis DNA was identified in 9% of the umbilical cord blood samples. No correlation between the amniotic fluid and umbilical cord blood microbial load was observed. The presence of Ureaplasma species and M. hominis DNA in the umbilical cord blood had no impact on short-term neonatal morbidity. A high microbial load of genital mycoplasma Ureaplasma species DNA in the umbilical cord in pregnancies complicated by pPROM is not associated with a high fetal inflammatory response and is therefore not associated with serious neonatal morbidity.

Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yuanyuan; Liu, Chongxuan; Nelson, William C.

Nitrogen (N) transformation in hyporheic zone (HZ) is an important component in N-cycling in ecosystems. A column study was conducted to investigate N transformation in a HZ sediment with a focus on how characteristic HZ properties including water chemistry, fluid residence time, and dynamic groundwater and surface water exchange affect on N transformation. Metagenomic and quantitative polymerase chain reaction (qPCR) analyses were performed to evaluate the dynamic changes in microbial community structure and its function in response to N transformation. The results indicated that N transformation in the HZ sediment was collectively controlled by microbial community functions including: denitrification, dissimilatorymore » nitrate reduction to ammonium (DNRA), nitrification, and anaerobic ammonium oxidation (anammox). However, the spatial distribution of the microbial community functions and associated biogeochemical reaction rates and products changed quickly in response to experimental perturbation, and was influenced by various factors including water chemistry (dissolved O2 and N species), desorption of sediment associated organic carbon, ion exchange reactions of NH4+, and fluid residence time. The results of this study implied that the microbial community in the HZ would exhibit strong function zonation along N and O gradients, which in turn would control the rates and products of N transformation.« less

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions.

PubMed

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

PubMed Central

Pereira-Marques, Joana; Pinto-Ribeiro, Ines; Costa, Jose L; Carneiro, Fatima; Machado, Jose C

2018-01-01

Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. Design The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. Results The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. Conclusions Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis. PMID:29102920

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

PubMed Central

Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y.-H.; Thompson, Janelle R.

2015-01-01

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools. PMID:26441948

The changes of bacterial communities and antibiotic resistance genes in microbial fuel cells during long-term oxytetracycline processing.

PubMed

Yan, Weifu; Guo, Yunyan; Xiao, Yong; Wang, Shuhua; Ding, Rui; Jiang, Jiaqi; Gang, Haiyin; Wang, Han; Yang, Jun; Zhao, Feng

2018-05-28

Microbial fuel cell (MFC) is regarded as a promising alternative for enhancing the removal of antibiotic pollutants. In this study, oxytetracycline served as an electron donor in the anode chamber of MFCs, and after continuous operation for 330 days, the efficiency of removal of 10 mg/L oxytetracycline in MFCs increased to 99.00% in 78 h, whereas removal efficiency of only 58.26% was achieved in microbial controls. Compared to microbial controls, higher ATP concentration and persistent electrical stimulation mainly contributed to bioelectrochemical reactions more rapidly to enhance oxytetracycline removal in MFCs. In addition, the analysis of bacterial communities revealed that Eubacterium spp.-as the main functional bacterial genus responsible for oxytetracycline biodegradation-flourished starting from merely 0.00%-91.69% ± 0.27% (mean ± SD) in MFCs. High-throughput quantitative PCR showed that the normalized copy numbers of total antibiotic resistance genes (ARGs) and mobile genetic elements in MFCs were 1.7364 and 0.0065 copies/cell respectively, which were markedly lower than those in the microbial controls. Furthermore, there was no significant correlation between oxytetracycline concentration in the influent and abundance of ARGs in effluent from MFCs. Nevertheless, Tp614, a transposase gene, was found to be enriched in both MFCs and microbial reactors, suggesting that it may be a common challenge for different biological processes for wastewater treatment. This study therefore showed a lower probability of upregulation and transmission of ARGs in MFCs when compared to a traditional anaerobic microbial treatment. Copyright © 2018. Published by Elsevier Ltd.

Differences in Hyporheic-Zone Microbial Community Structure along a Heavy-Metal Contamination Gradient

PubMed Central

Feris, Kevin; Ramsey, Philip; Frazar, Chris; Moore, Johnnie N.; Gannon, James E.; Holben, William E.

2003-01-01

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to α-, β-, and γ-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities. PMID:12957946

Nitrous oxide emissions and denitrification rates: A blueprint for smart management and remediation of agricultural landscapes.

NASA Astrophysics Data System (ADS)

Tomasek, A.; Hondzo, M.; Kozarek, J. L.

2015-12-01

Anthropogenic activities have greatly altered the global nitrogen cycle, especially in the agriculturally dominated Midwest, with severe consequences on human and aquatic health. Complete microbial denitrification can be viewed as a nitrogen sink, converting soluble nitrate into inert nitrogen gas. This research aims to quantify and correlate the driving parameters in microbial denitrification and explore the relationship to the abundance of denitrifying genes and the microbial communities at these sites. Denitrifying genes for each step in the denitrification process have been quantified. Data from a field site in Southern Minnesota has been collected throughout the season for two years enabling investigation into the temporal variability of denitrification. Data was collected at two cross-sections across the channel to determine the effect of bank location and moisture content on denitrification. Data were collected in an experimental basin in the summer of 2015 to determine the effect of flooding and benthic organic matter content and quality on microbial denitrification and nitrous oxide production. Four sediment types were investigated in three different flood regimes. After each raising or lowering of the water level, soil cores were taken to determine soil characteristics, the potential denitrification using the denitrification enzyme activity method, nitrous oxide production using a static core method, and the denitrifying gene abundance. Chambers were also deployed over each soil amendment in each flood regime to determine the nitrous oxide production over time. Results from these studies will convey a more complete explanation of denitrification and nitrous oxide production under varying environmental conditions. By determining the driving parameters for microbial denitrification, denitrification hot spots and hot moments can be created and enhanced. One potential consequence of increased denitrification is the possibility of incomplete denitrification resulting in the release of nitrous oxide, a greenhouse gas with 300 times the warming potential of carbon dioxide. The investigation of nitrous oxide emissions and correlation to denitrification rates will facilitate smart management and remediation efforts of agricultural landscapes.

Utilization of the water soluable fraction of wheat straw as a plant nutrient source

NASA Technical Reports Server (NTRS)

Mackowiak, C. L.; Garland, J. L.

1990-01-01

Recovery of water soluble, inorganic nutrients from the inedible portion of wheat was found to be an effective means of recycling nutrients within hydroponic systems. Through aqueous extraction (leaching), 60 percent of the total inorganic nutrient weight was removed from wheat straw and roots, although the recovery of individual nutrients varied. Leaching also removed about 20 percent of the total organic carbon from the biomass. In terms of dry weight, the leachate was comprised of approximately 60 percent organic and 40 percent inorganic compounds. Direct use of wheat straw leachate in static hydroponic systems had an inhibitory effect on wheat growth, both in the presence and absence of microorganisms. Biological treatment of leachate either with a mixed microbial community or the oyster mushroom Pleurotus ostreatus L., prior to use in hydroponic solutions, significantly reduced both the organic content and the inhibitory effects of the leachate. The inhibitory effects of unprocessed leachate appear to be a result of rapidly acting phytotoxic compounds that are detoxified by microbial activity. Leaching holds considerable promise as a method for nutrient recycling in a Controlled Ecological Life Support System (CELSS).

Development of an analytical microbial consortia method for enhancing performance monitoring at aerobic wastewater treatment plants.

PubMed

Razban, Behrooz; Nelson, Kristina Y; McMartin, Dena W; Cullimore, D Roy; Wall, Michelle; Wang, Dunling

2012-01-01

An analytical method to produce profiles of bacterial biomass fatty acid methyl esters (FAME) was developed employing rapid agitation followed by static incubation (RASI) using selective media of wastewater microbial communities. The results were compiled to produce a unique library for comparison and performance analysis at a Wastewater Treatment Plant (WWTP). A total of 146 samples from the aerated WWTP, comprising 73 samples of each secondary and tertiary effluent, were included analyzed. For comparison purposes, all samples were evaluated via a similarity index (SI) with secondary effluents producing an SI of 0.88 with 2.7% variation and tertiary samples producing an SI 0.86 with 5.0% variation. The results also highlighted significant differences between the fatty acid profiles of the tertiary and secondary effluents indicating considerable shifts in the bacterial community profile between these treatment phases. The WWTP performance results using this method were highly replicable and reproducible indicating that the protocol has potential as a performance-monitoring tool for aerated WWTPs. The results quickly and accurately reflect shifts in dominant bacterial communities that result when processes operations and performance change.

Fouling potential evaluation of soluble microbial products (SMP) with different membrane surfaces in a hybrid membrane bioreactor using worm reactor for sludge reduction.

PubMed

Li, Zhipeng; Tian, Yu; Ding, Yi; Chen, Lin; Wang, Haoyu

2013-07-01

The fouling characteristics of soluble microbial products (SMP) in the membrane bioreactor coupled with Static Sequencing Batch Worm Reactor (SSBWR-MBR) were tested with different types of membranes. It was noted that the flux decrements of S-SMP (SMP in SSBWR-MBR) with cellulose acetate (CA), polyvinylidene fluoride (PVDF) and polyether sulfones (PES) membranes were respectively 6.7%, 8.5% and 9.5% lower compared to those of C-SMP (SMP in Control-MBR) with corresponding membranes. However, for both the filtration of the C-SMP and S-SMP, the CA membrane exhibited the fastest diminishing rate of flux among the three types of membranes. The surface morphology analysis showed that the CA membrane exhibited more but smaller protuberances compared to the PVDF and PES. The second minimums surrounding each protruding asperity on CA membrane were more than those on the PVDF and PES membranes, enhancing the attachment of SMP onto the membrane surface. Copyright © 2013 Elsevier Ltd. All rights reserved.

Direct and indirect effects of vertical mixing, nutrients and ultraviolet radiation on the bacterioplankton metabolism in high-mountain lakes from southern Europe

NASA Astrophysics Data System (ADS)

Durán, C.; Medina-Sánchez, J. M.; Herrera, G.; Villar-Argaiz, M.; Villafañe, V. E.; Helbling, E. W.; Carrillo, P.

2014-05-01

As a consequence of global change, modifications in the interaction among abiotic stressors on aquatic ecosystems have been predicted. Among other factors, UVR transparency, nutrient inputs and shallower epilimnetic layers could alter the trophic links in the microbial food web. Currently, there are some evidences of higher sensitiveness of aquatic microbial organisms to UVR in opaque lakes. Our aim was to assess the interactive direct and indirect effects of UVR (through the excretion of organic carbon - EOC - by algae), mixing regime and nutrient input on bacterial metabolism. We performed in situ short-term experiments under the following treatments: full sunlight (UVR + PAR, >280 nm) vs. UVR exclusion (PAR only, >400 nm); ambient vs. nutrient addition (phosphorus (P; 30 μg PL-1) and nitrogen (N; up to final N : P molar ratio of 31)); and static vs. mixed regime. The experiments were conducted in three high-mountain lakes of Spain: Enol [LE], Las Yeguas [LY] and La Caldera [LC] which had contrasting UVR transparency characteristics (opaque (LE) vs. clear lakes (LY and LC)). Under ambient nutrient conditions and static regimes, UVR exerted a stimulatory effect on heterotrophic bacterial production (HBP) in the opaque lake but not in the clear ones. Under UVR, vertical mixing and nutrient addition HBP values were lower than under the static and ambient nutrient conditions, and the stimulatory effect that UVR exerted on HBP in the opaque lake disappeared. By contrast, vertical mixing and nutrient addition increased HBP values in the clear lakes, highlighting for a photoinhibitory effect of UVR on HBP. Mixed regime and nutrient addition resulted in negative effects of UVR on HBP more in the opaque than in the clear lakes. Moreover, in the opaque lake, bacterial respiration (BR) increased and EOC did not support the bacterial carbon demand (BCD). In contrast, bacterial metabolic costs did not increase in the clear lakes and the increased nutrient availability even led to higher HBP. Consequently, EOC satisfied BCD in the clear lakes, particularly in the clearest one [LC]. Our results suggest that the higher vulnerability of bacteria to the damaging effects of UVR may be particularly accentuated in the opaque lakes and further recognizes the relevance of light exposure history and biotic interactions on bacterioplankton metabolism when coping with fluctuating radiation and nutrient inputs.

Controls on northern wetland methane emissions: insights from regional synthesis studies and the Alaska Peatland Experiment (APEX)

NASA Astrophysics Data System (ADS)

Turetsky, M. R.; Euskirchen, E. S.; Czimczik, C. I.; Waldrop, M. P.; Olefeldt, D.; Fan, Z.; Kane, E. S.; McGuire, A. D.; Harden, J. W.

2014-12-01

Wetlands are the largest natural source of atmospheric methane. Static chambers have been used to quantify variation in wetland CH4 flux for many decades. Regional to global scale synthesis studies of static chamber measurements show that relationships between temperature, water availability and CH4 emissions depend on wetland type (bog, fen, swamp), region (tropical, temperate, arctic) and disturbance. For example, while water table position and temperature serve as the dominant controls on bog and swamp CH4 flux, vegetation is an important control on emissions from fens. These studies highlight the fact that wetland types have distinct controls on CH4 emissions; however, it is unlikely that modeling of wetland CH4 flux will improve without a better mechanistic understanding of the processes underlying CH4 production, transport, and oxidation. At the Alaska Peatland Experiment, we are quantifying CH4 emission using static chambers, automated chambers, and towers. Our sites vary in permafrost regime, including groundwater fens without permafrost, forested peat plateaus with intact permafrost, and collapse scar bogs formed through permafrost thaw. Experimental studies that examine plant and microbial responses to altered water table position and soil temperature are complemented by a gradient approach, where we use a space-for-time substitutions to examine the consequences of thaw on time-scales of decades to centuries. Our results thus far have documented the importance of soil rewetting in governing large CH4 fluxes from northern wetland soils. Accounting for CH4, our collapse scar bog significantly contributed to the global warming potential of the landscape. A major objective of our work is to explore the role of permafrost C release in greenhouse gas fluxes from wetland soils, which we are assessing using radiocarbon as a natural tracer. We have shown, for example, that ebullition of CH4 is dominated by recently fixed C, but a significant fraction of CH4 in bubbles is derived from old C released during thaw. The APEX time series datasets are being used in a variety of modeling studies, from small-scale soil pore and microbial controls on gas production and transport to regional scale assessments of how carbon cycle feedbacks to climate vary with wetland type and abundance.

Quantitative Microbial Risk Assessment (QMRA) as a Compliment to epidemiologic Studies Estimating Bather Risk at Recreational Beaches

EPA Science Inventory

The US EPA and WHO have set recreational water quality standards based on epidemiologic studies to protect human health at beaches. These studies have largely been limited to sewage-impacted sites and resources are unlikely to be available to assess the myriad of other impacted s...

Human-associated fecal qPCR measurements and predicted risk of gastrointestinal illness in recreational waters contaminated with raw sewage

EPA Science Inventory

We used quantitative microbial risk assessment (QMRA) to estimate the risk of gastrointestinal (GI) illness associated with swimming in recreational waters containing different concentrations of human-associated fecal qPCR markers from raw sewage– HF183 and HumM2. The volume/volu...

Risk-based enteric pathogen reduction targets for non-potable and direct potable use of roof runoff, stormwater, and greywater

EPA Science Inventory

This paper presents risk-based enteric pathogen log reduction targets for non-potable and potable uses of a variety of alternative source waters (i.e., locally-collected greywater, roof runoff, and stormwater). A probabilistic Quantitative Microbial Risk Assessment (QMRA) was use...

Quantitative microbial risk assessment for spray irrigation of dairy manure based on an empirical fate and transport model

USDA-ARS?s Scientific Manuscript database

Background: Spray irrigation for land-applying livestock manure is increasing in the United States as farms become larger and economies of scale make manure irrigation affordable. However, human health risks from exposure to zoonotic pathogens aerosolized during manure irrigation are not well-unders...

Estimation of infectious risks in residential populations exposed to airborne pathogens during center pivot irrigation of dairy wastewaters

USDA-ARS?s Scientific Manuscript database

In the western United States where dairy wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks after inhalation exposure of pathogens aero...

Using Real-time Quantitative PCR to Examine the Dynamics of Soil Fungi and Bacteria in Response to Ecosystem Warming

USDA-ARS?s Scientific Manuscript database

As atmospheric trace gas concentrations and global temperatures climb, scientists are challenged to determine how microbial communities may mediate plant response to future climate change. To this end, a Temperature Free-Air Controlled Enrichment (T-FACE) experiment was implemented in a spring wheat...

Predicting pathogen risks to aid beach management: the real value of quantitative microbial risk assessment (QMRA)

EPA Science Inventory

There has been an ongoing dilemma for agencies who set criteria for safe recreational waters in how to provide for a seasonal assessment of a beach site versus guidance for day-to-day management. Typically an overall 'safe' criterion level is derived from epidemiologic studies o...

COMPARATIVE POTENCY METHOD FOR CANCER RISK ASSESSMENT: APPLICATION TO THE QUANTITATIVE ASSESSMENT OF THE CONTRIBUTION OF COMBUSTION EMISSIONS TO LUNG CANCER RISK

EPA Science Inventory

Combustion sources emit soot particles containing carcinogenic polycyclic organic compounds which are mutagenic in short-term genetic bioassays in microbial and mammalian cells and are tumorigenic in animals. Although soot is considered to be a human carcinogen, soots from differ...

Patterns and drivers of fungal community depth stratification in Sphagnum peat

USDA-ARS?s Scientific Manuscript database

Peatlands store an immense pool of soil carbon vulnerable to microbial oxidation due to drought and intentional draining. We used amplicon sequencing and quantitative PCR to 1) examine how fungi are influenced by depth in the peat profile, water table (WT) and plant functional group (PFG) at the ons...

Comparison of recreational health risks associated with surfing and swimming in dry weather and post-storm conditions at Southern California beaches using quantitative microbial risk assessment (QMRA).

PubMed

Tseng, Linda Y; Jiang, Sunny C

2012-05-01

Southern California is an increasingly urbanized hotspot for surfing, thus it is of great interest to assess the human illness risks associated with this popular ocean recreational water sport from exposure to fecal bacteria contaminated coastal waters. Quantitative microbial risk assessments were applied to eight popular Southern California beaches using readily available enterococcus and fecal coliform data and dose-response models to compare health risks associated with surfing during dry weather and storm conditions. The results showed that the level of gastrointestinal illness risks from surfing post-storm events was elevated, with the probability of exceeding the US EPA health risk guideline up to 28% of the time. The surfing risk was also elevated in comparison with swimming at the same beach due to ingestion of greater volume of water. The study suggests that refinement of dose-response model, improving monitoring practice and better surfer behavior surveillance will improve the risk estimation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Characterizing the risk of infection from Mycobacterium tuberculosis in commercial passenger aircraft using quantitative microbial risk assessment.

PubMed

Jones, Rachael M; Masago, Yoshifumi; Bartrand, Timothy; Haas, Charles N; Nicas, Mark; Rose, Joan B

2009-03-01

Quantitative microbial risk assessment was used to predict the likelihood and spatial organization of Mycobacterium tuberculosis (Mtb) transmission in a commercial aircraft. Passenger exposure was predicted via a multizone Markov model in four scenarios: seated or moving infectious passengers and with or without filtration of recirculated cabin air. The traditional exponential (k = 1) and a new exponential (k = 0.0218) dose-response function were used to compute infection risk. Emission variability was included by Monte Carlo simulation. Infection risks were higher nearer and aft of the source; steady state airborne concentration levels were not attained. Expected incidence was low to moderate, with the central 95% ranging from 10(-6) to 10(-1) per 169 passengers in the four scenarios. Emission rates used were low compared to measurements from active TB patients in wards, thus a "superspreader" emitting 44 quanta/h could produce 6.2 cases or more under these scenarios. Use of respiratory protection by the infectious source and/or susceptible passengers reduced infection incidence up to one order of magnitude.

Quantitative microbial risk assessment of Cryptosporidium and Giardia in well water from a native community of Mexico.

PubMed

Balderrama-Carmona, Ana Paola; Gortáres-Moroyoqui, Pablo; Álvarez-Valencia, Luis Humberto; Castro-Espinoza, Luciano; Balderas-Cortés, José de Jesús; Mondaca-Fernández, Iram; Chaidez-Quiroz, Cristóbal; Meza-Montenegro, María Mercedes

2015-01-01

Cryptosporidium and Giardia are gastrointestinal disease-causing organisms transmitted by the fecal-oral route, zoonotic and prevalent in all socioeconomic segments with greater emphasis in rural communities. The goal of this study was to assess the risk of cryptosporidiosis and giardiasis of Potam dwellers consuming drinking water from communal well water. To achieve the goal, quantitative microbial risk assessment (QMRA) was carried out as follows: (a) identification of Cryptosporidium oocysts and Giardia cysts in well water samples by information collection rule method, (b) assessment of exposure to healthy Potam residents, (c) dose-response modelling, and (d) risk characterization using an exponential model. All well water samples tested were positive for Cryptosporidium and Giardia. The QMRA results indicate a mean of annual risks of 99:100 (0.99) for cryptosporidiosis and 1:1 (1.0) for giardiasis. The outcome of the present study may drive decision-makers to establish an educational and treatment program to reduce the incidence of parasite-borne intestinal infection in the Potam community, and to conduct risk analysis programs in other similar rural communities in Mexico.

High-sensitivity stable-isotope probing by a quantitative terminal restriction fragment length polymorphism protocol.

PubMed

Andeer, Peter; Strand, Stuart E; Stahl, David A

2012-01-01

Stable-isotope probing (SIP) has proved a valuable cultivation-independent tool for linking specific microbial populations to selected functions in various natural and engineered systems. However, application of SIP to microbial populations with relatively minor buoyant density increases, such as populations that utilize compounds as a nitrogen source, results in reduced resolution of labeled populations. We therefore developed a tandem quantitative PCR (qPCR)-TRFLP (terminal restriction fragment length polymorphism) protocol that improves resolution of detection by quantifying specific taxonomic groups in gradient fractions. This method combines well-controlled amplification with TRFLP analysis to quantify relative taxon abundance in amplicon pools of FAM-labeled PCR products, using the intercalating dye EvaGreen to monitor amplification. Method accuracy was evaluated using mixtures of cloned 16S rRNA genes, DNA extracted from low- and high-G+C bacterial isolates (Escherichia coli, Rhodococcus, Variovorax, and Microbacterium), and DNA from soil microcosms amended with known amounts of genomic DNA from bacterial isolates. Improved resolution of minor shifts in buoyant density relative to TRFLP analysis alone was confirmed using well-controlled SIP analyses.

Comparative study on occurrence characteristics of matrix water in static and gas double-dynamic solid-state fermentations using low-field NMR and MRI.

PubMed

He, Qin; Chen, Hong-zhang

2015-12-01

The water in a solid substrate is generally divided into three forms: hygroscopic, capillary, and free. However, there are few methods available for detecting the contents of different states of water in substrates. In this paper, low-field NMR and MRI were used to analyze the water occurrence characteristics of steam-exploded corn straw in solid-state fermentation (SSF). A significant linear relationship was found between the total NMR peak areas and the total water contents with a correlation coefficient of 0.993. It was further proved to be successful in comparing the contents and distributions of different states of water in static SSF and gas double-dynamic SSF (GDD-SSF). The results showed that among the three states of water, capillary water was the main form of water present and lost in substrates during fermentation. Total water and capillary water contents did not significantly differ as a result of different sample treatments, but hygroscopic water and free water contents in static SSF were respectively 0.38 and 2.98 times that in GDD-SSF with a packing height of 3 cm after fermentation. A relatively uniform water distribution and deep-depth region for microbial growth were found in GDD-SSF, suggesting that GDD-SSF was more suitable for industrialization. This technology has great potential for achieving efficient on-line water supply through water loss detection in SSF.

Chromosomal locus tracking with proper accounting of static and dynamic errors

PubMed Central

Backlund, Mikael P.; Joyner, Ryan; Moerner, W. E.

2015-01-01

The mean-squared displacement (MSD) and velocity autocorrelation (VAC) of tracked single particles or molecules are ubiquitous metrics for extracting parameters that describe the object’s motion, but they are both corrupted by experimental errors that hinder the quantitative extraction of underlying parameters. For the simple case of pure Brownian motion, the effects of localization error due to photon statistics (“static error”) and motion blur due to finite exposure time (“dynamic error”) on the MSD and VAC are already routinely treated. However, particles moving through complex environments such as cells, nuclei, or polymers often exhibit anomalous diffusion, for which the effects of these errors are less often sufficiently treated. We present data from tracked chromosomal loci in yeast that demonstrate the necessity of properly accounting for both static and dynamic error in the context of an anomalous diffusion that is consistent with a fractional Brownian motion (FBM). We compare these data to analytical forms of the expected values of the MSD and VAC for a general FBM in the presence of these errors. PMID:26172745

MATLAB Stability and Control Toolbox Trim and Static Stability Module

NASA Technical Reports Server (NTRS)

Kenny, Sean P.; Crespo, Luis

2012-01-01

MATLAB Stability and Control Toolbox (MASCOT) utilizes geometric, aerodynamic, and inertial inputs to calculate air vehicle stability in a variety of critical flight conditions. The code is based on fundamental, non-linear equations of motion and is able to translate results into a qualitative, graphical scale useful to the non-expert. MASCOT was created to provide the conceptual aircraft designer accurate predictions of air vehicle stability and control characteristics. The code takes as input mass property data in the form of an inertia tensor, aerodynamic loading data, and propulsion (i.e. thrust) loading data. Using fundamental nonlinear equations of motion, MASCOT then calculates vehicle trim and static stability data for the desired flight condition(s). Available flight conditions include six horizontal and six landing rotation conditions with varying options for engine out, crosswind, and sideslip, plus three take-off rotation conditions. Results are displayed through a unique graphical interface developed to provide the non-stability and control expert conceptual design engineer a qualitative scale indicating whether the vehicle has acceptable, marginal, or unacceptable static stability characteristics. If desired, the user can also examine the detailed, quantitative results.

Experimental and Numerical Analysis of Notched Composites Under Tension Loading

NASA Astrophysics Data System (ADS)

Aidi, Bilel; Case, Scott W.

2015-12-01

Experimental quasi-static tests were performed on center notched carbon fiber reinforced polymer (CFRP) composites having different stacking sequences made of G40-600/5245C prepreg. The three-dimensional Digital Image Correlation (DIC) technique was used during quasi-static tests conducted on quasi-isotropic notched samples to obtain the distribution of strains as a function of applied stress. A finite element model was built within Abaqus to predict the notched strength and the strain profiles for comparison with measured results. A user-material subroutine using the multi-continuum theory (MCT) as a failure initiation criterion and an energy-based damage evolution law as implemented by Autodesk Simulation Composite Analysis (ASCA) was used to conduct a quantitative comparison of strain components predicted by the analysis and obtained in the experiments. Good agreement between experimental data and numerical analyses results are observed. Modal analysis was carried out to investigate the effect of static damage on the dominant frequencies of the notched structure using the resulted degraded material elements. The first in-plane mode was found to be a good candidate for tracking the level of damage.

Monitoring protein hydrolysis by pepsin using pH-stat: In vitro gastric digestions in static and dynamic pH conditions.

PubMed

Mat, Damien J L; Cattenoz, Thomas; Souchon, Isabelle; Michon, Camille; Le Feunteun, Steven

2018-01-15

This study intends to demonstrate that acid titration at low pH is very well adapted to the monitoring of pepsin activity. After a description of the underlying principles, this approach was used during in vitro gastric digestions of a model of complex food containing 15wt% of whey proteins, according to both static (2h at pH = 3, Infogest protocol) and dynamic pH conditions (from pH 6.3 down to 2 in 1h). Pepsin activity was quantitatively assessed in all experiments through the calculation of degrees of hydrolysis (DH). Final values of 3.7 and 3.0% were obtained in static and dynamic pH conditions, respectively, and validated using an independent method. Results also show that about 92% of the peptides were detected at pH = 3, and 100% for pH≤2.5. Overall, the proposed approach proved to be very worthy to study protein hydrolysis during in vitro gastric digestions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Static, mixed-array total evaporation for improved quantitation of plutonium minor isotopes in small samples

DOE PAGES

Stanley, F. E.; Byerly, Benjamin L.; Thomas, Mariam R.; ...

2016-03-31

Actinide isotope measurements are a critical signature capability in the modern nuclear forensics “toolbox”, especially when interrogating anthropogenic constituents in real-world scenarios. Unfortunately, established methodologies, such as traditional total evaporation via thermal ionization mass spectrometry, struggle to confidently measure low abundance isotope ratios (<10 -6) within already limited quantities of sample. Herein, we investigate the application of static, mixed array total evaporation techniques as a straightforward means of improving plutonium minor isotope measurements, which have been resistant to enhancement in recent years because of elevated radiologic concerns. Furthermore, results are presented for small sample (~20 ng) applications involving a well-knownmore » plutonium isotope reference material, CRM-126a, and compared with traditional total evaporation methods.« less

Ares I Static Tests Design

NASA Technical Reports Server (NTRS)

Carson, William; Lindemuth, Kathleen; Mich, John; White, K. Preston; Parker, Peter A.

2009-01-01

Probabilistic engineering design enhances safety and reduces costs by incorporating risk assessment directly into the design process. In this paper, we assess the format of the quantitative metrics for the vehicle which will replace the Space Shuttle, the Ares I rocket. Specifically, we address the metrics for in-flight measurement error in the vector position of the motor nozzle, dictated by limits on guidance, navigation, and control systems. Analyses include the propagation of error from measured to derived parameters, the time-series of dwell points for the duty cycle during static tests, and commanded versus achieved yaw angle during tests. Based on these analyses, we recommend a probabilistic template for specifying the maximum error in angular displacement and radial offset for the nozzle-position vector. Criteria for evaluating individual tests and risky decisions also are developed.

Red blood cell dynamics: from cell deformation to ATP release.

PubMed

Wan, Jiandi; Forsyth, Alison M; Stone, Howard A

2011-10-01

The mechanisms of red blood cell (RBC) deformation under both static and dynamic, i.e., flow, conditions have been studied extensively since the mid 1960s. Deformation-induced biochemical reactions and possible signaling in RBCs, however, were proposed only fifteen years ago. Therefore, the fundamental relationship between RBC deformation and cellular signaling dynamics i.e., mechanotransduction, remains incompletely understood. Quantitative understanding of the mechanotransductive pathways in RBCs requires integrative studies of physical models of RBC deformation and cellular biochemical reactions. In this article we review the physical models of RBC deformation, spanning from continuum membrane mechanics to cellular skeleton dynamics under both static and flow conditions, and elaborate the mechanistic links involved in deformation-induced ATP release. This journal is © The Royal Society of Chemistry 2011

An Approach to Extract Moving Objects from Mls Data Using a Volumetric Background Representation

NASA Astrophysics Data System (ADS)

Gehrung, J.; Hebel, M.; Arens, M.; Stilla, U.

2017-05-01

Data recorded by mobile LiDAR systems (MLS) can be used for the generation and refinement of city models or for the automatic detection of long-term changes in the public road space. Since for this task only static structures are of interest, all mobile objects need to be removed. This work presents a straightforward but powerful approach to remove the subclass of moving objects. A probabilistic volumetric representation is utilized to separate MLS measurements recorded by a Velodyne HDL-64E into mobile objects and static background. The method was subjected to a quantitative and a qualitative examination using multiple datasets recorded by a mobile mapping platform. The results show that depending on the chosen octree resolution 87-95% of the measurements are labeled correctly.

Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

2002-12-01

In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

Microbial facies distribution and its geological and geochemical controls at the Hanford 300 area

NASA Astrophysics Data System (ADS)

Hou, Z.; Nelson, W.; Stegen, J.; Murray, C. J.; Arntzen, E.

2015-12-01

Efforts have been made by various scientific disciplines to study hyporheic zones and characterize their associated processes. One way to approach the study of the hyporheic zone is to define facies, which are elements of a (hydrobio) geologic classification scheme that groups components of a complex system with high variability into a manageable set of discrete classes. In this study, we try to classify the hyporheic zone based on the geology, geochemistry, microbiology, and understand their interactive influences on the integrated biogeochemical distributions and processes. A number of measurements have been taken for 21 freeze core samples along the Columbia River bank in the Hanford 300 Area, and unique datasets have been obtained on biomass, pH, number of microbial taxa, percentage of N/C/H/S, microbial activity parameters, as well as microbial community attributes/modules. In order to gain a complete understanding of the geological control on these variables and processes, the explanatory variables are set to include quantitative gravel/sand/mud/silt/clay percentages, statistical moments of grain size distributions, as well as geological (e.g., Folk-Wentworth) and statistical (e.g., hierarchical) clusters. The dominant factors for major microbial and geochemical variables are identified and summarized using exploratory data analysis approaches (e.g., principal component analysis, hierarchical clustering, factor analysis, multivariate analysis of variance). The feasibility of extending the facies definition and its control of microbial and geochemical properties to larger scales is discussed.

The Environment and the Microbial Ecology of Human Skin

PubMed Central

McBride, Mollie E.; Duncan, W. Christopher; Knox, J. M.

1977-01-01

Microbial flora of the skin of three human population groups representing different natural environments was examined quantitatively and qualitatively to determine whether environmental differences in temperature and humidity can influence the microbial flora of normal skin. Five anatomical skin sites - hands, back, axillae, groin, and feet - were sampled from 10 subjects working in a high-humidity, high-temperature environment, 10 subjects from a low-temperature, high-humidity environment, and 10 subjects working in a moderate-temperature and low-humidity environment. Bacterial populations were significantly larger from the back, axillae, and feet in individuals from the high-temperature and high-humidity environment as compared to the moderate-temperature, low-humidity environment. High humidity and low temperature had no significant effect on total populations, but this group showed a higher frequency of isolation of fungi, and gram-negative bacteria from the back and feet. Although there was an indication that increase in the environmental humidity could result in an increased frequency of isolation of gram-negative bacteria, there was no evidence that an increase in either temperature or humidity altered the relative proportions of gram-negative bacteria in the predominantly gram-positive microbial flora found on normal skin. It was concluded that, although climatic changes may cause fluctation in microbial populations from certain sites, they are not a major influence on the ecology of the microbial flora of normal skin in the natural environment. The variables introduced by studying individuals in their natural environment and the influence of these on the results are discussed. PMID:16345214

In situ detection of microbial c-type cytochrome based on intrinsic peroxidase-like activity using screen-printed carbon electrode.

PubMed

Wen, Junlin; He, Daigui; Yu, Zhen; Zhou, Shungui

2018-08-15

C-type cytochromes (c-cyts) facilitate microbial extracellular electron transfer and play critical roles in biogeochemical cycling, bioelectricity generation and bioremediation. In this study, a simple and effective method has been developed to detect microbial c-cyts by means of peroxidase mimetic reaction on screen-printed carbon electrode (SPCE). To this end, bacteria cells were immobilized onto the working electrode surface of SPCE by a simple drop casting. After introducing 3,3',5,5'-tetramethylbenzidine (TMB) solution, microbial c-cyts with peroxidase-like activity catalyze the oxidation of TMB in the presence of hydrogen peroxide. The oxidized TMB was electrochemically determined and the current signal was employed to calculate the c-cyts content. This electrochemical method is highly sensitive for microbial c-cyts with a low detection limit of 40.78 fmol and a wide detection range between 51.70 fmol and 6.64 pmol. Moreover, the proposed technique can be universally expanded to detect c-cyts in other bacteria species such as Fontibacter ferrireducens, Pseudomonas aeruginosa, Comamonas guangdongensis and Escherichia coli. Furthermore, the proposed method confers an in situ facile and quantitative c-cyts detection without any destructive sample preparations, complex electrode modifications and expensive enzyme- or metal particle- based signal amplification. The suggested method advances an intelligent strategy for in situ quantification of microbial c-cyts and consequently holds promising application potential in microbiology and environmental science. Copyright © 2018 Elsevier B.V. All rights reserved.

Pharmaceutical container/closure integrity. II: The relationship between microbial ingress and helium leak rates in rubber-stoppered glass vials.

PubMed

Kirsch, L E; Nguyen, L; Moeckly, C S; Gerth, R

1997-01-01

Helium leak rate measurements were quantitatively correlated to the probability of microbial ingress for rubber-stoppered glass vials subjected to immersion challenge. Standard 10-mL tubing glass vials were modified by inserting micropipettes of various sizes (0.1 to 10 microns nominal diameter) into a side wall hole and securing them with epoxy. Butyl rubber closures and aluminum crimps were used to seal the vials. The test units were sealed in a helium-filled glove bag, then the absolute helium leak rates were determined. The test units were disassembled, filled with media, resealed, and autoclaved. The test units were thermally treated to eliminate airlocks within the micropipette lumen and establish a liquid path between microbial challenge media and the test units' contents. Microbial challenge was performed by immersing the test units in a 35 degrees C bath containing magnesium ion and 8 to 10 logs of viable P. diminuta and E. coli for 24 hours. The test units were then incubated at 35 degrees C for an additional 13 days. Microbial ingress was detected by turbidity and plating on blood agar. The elimination of airlocks was confirmed by the presence of magnesium ions in the vial contents by atomic absorption spectrometry. A total of 288 vials were subjected to microbial challenge testing. Those test units whose contents failed to show detectable magnesium ions were eliminated from further analysis. At large leak rates, the probability of microbial ingress approached 100% and at very low leak rates microbial ingress rates were 0%. A dramatic increase in microbial failure occurred in the leak rate region 10(-4.5) to 10(-3) std cc/sec, which roughly corresponded to leak diameters ranging from 0.4 to 2 microns. Below a leak rate of 10(-4.5) std cc/sec the microbial failure rate was < 10%. The critical leak rate in our studies, i.e. the value below which microbial ingress cannot occur because the leak is too small, was observed to be between 10(-5) and 10(-5.8) std cc/sec, which corresponds to an approximate leak diameter of 0.2-0.3 micron.

Nucleic acid based quantitative microbial community analysis in different marine and terrestrial sediments

NASA Astrophysics Data System (ADS)

Schippers, A.; Blazejak, A.; Köweker, G.

2009-12-01

Sub-seafloor sediments harbour over half of all prokaryotic cells on Earth. This immense cell number is calculated from numerous microscopic cell counts (AODC) in ODP sediment cores. Since AODC can not differentiate between living or dead cells, the population size of living microorganisms and the abundance of different prokaryotic groups are unknown. Recent molecular nucleic acid and biomarker analyses showed that a high proportion of the cells are alive and that the microbial communities of deep marine sediments harbour members of distinct, uncultured bacterial and archaeal lineages. The main objective of our project is the quantification of living prokaryotes in various sediments. Deep sediment samples from the Pacific and the Atlantic Oceans (ODP Legs 201 and 207, IODP Exp. 307 and 308), sediments from the Indian Ocean (RV Sonne 189-2) and the Black Sea (RV Meteor 51/4) as well as terrestrial Chesapeake Bay Sediments (ICDP) were analyzed using Catalyzed Reporter Deposition - Fluorescence In Situ Hybridisation (CARD - FISH) and quantitative, real-time PCR (Q-PCR), targeting either the 16S rRNA gene or the functional genes dsrA, mcrA and aprA to quantify microorganisms of various phylogenetic or physiological groups (e.g. JS1 cluster and Chloroflexi). At all sediment sites, cell numbers decreased with depth, however, the abundance of particular microbial groups varied at different sites and depths. The results indicate that global estimates of the deep biosphere should be reconsidered.

Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities.

PubMed

Lettat, A; Hassanat, F; Benchaar, C

2013-08-01

Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable enough to reflect changes in ruminal methanogenesis. A more robust technique to characterize changes in archaeal community structures will help to better understand the microbial process involved in ruminal methanogenesis and, hence, enabling the development of more effective dietary CH4 mitigation strategies. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems.

PubMed

Gomaa, Ahmed A; Klumpe, Heidi E; Luo, Michelle L; Selle, Kurt; Barrangou, Rodolphe; Beisel, Chase L

2014-01-28

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of "smart" antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms. Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.

Quantitative microbial risk assessment of microbial source tracking markers in recreational water contaminated with fresh untreated and secondary treated sewage.

PubMed

Ahmed, Warish; Hamilton, Kerry A; Lobos, Aldo; Hughes, Bridie; Staley, Christopher; Sadowsky, Michael J; Harwood, Valerie J

2018-05-14

Microbial source tracking (MST) methods have provided the means to identify sewage contamination in recreational waters, but the risk associated with elevated levels of MST targets such as sewage-associated Bacteroides HF183 and other markers is uncertain. Quantitative microbial risk assessment (QMRA) modeling allows interpretation of MST data in the context of the risk of gastrointestinal (GI) illness caused by exposure to known reference pathogens. In this study, five sewage-associated, quantitative PCR (qPCR) MST markers [Bacteroides HF183 (HF183), Methanobrevibacter smithii nifH (nifH), human adenovirus (HAdV), human polyomavirus (HPyV) and pepper mild mottle virus (PMMoV)] were evaluated to determine at what concentration these nucleic acid markers reflected a significant health risk from exposure to fresh untreated or secondary treated sewage in beach water. The QMRA models were evaluated for a target probability of illness of 36 GI illnesses/1000 swimming events (i.e., risk benchmark 0.036) for the reference pathogens norovirus (NoV) and human adenovirus 40/41 (HAdV 40/41). Sewage markers at several dilutions exceeded the risk benchmark for reference pathogens NoV and HAdV 40/41. HF183 concentrations 3.22 × 10 3 (for both NoV and HAdV 40/41) gene copies (GC)/100 mL of water contaminated with fresh untreated sewage represented risk >0.036. Similarly, HF183 concentrations 3.66 × 10 3 (for NoV and HAdV 40/41) GC/100 mL of water contaminated with secondary treated sewage represented risk >0.036. HAdV concentration as low as 4.11 × 10 1 GC/100 mL of water represented risk >0.036 when water was contaminated with secondary treated sewage. Results of this study provide a valuable context for water quality managers to evaluate human health risks associated with contamination from fresh sewage. The approach described here may also be useful in the future for evaluating health risks from contamination with aged or treated sewage or feces from other animal sources as more data are made available. Copyright © 2018 Elsevier Ltd. All rights reserved.

Soil temperature and water content drive microbial carbon fixation in grassland of permafrost area on the Tibetan plateau

NASA Astrophysics Data System (ADS)

Kong, W.; Guo, G.; Liu, J.

2014-12-01

Soil microbial communities underpin terrestrial biogeochemical cycles and are greatly influenced by global warming and global-warming-induced dryness. However, the response of soil microbial community function to global change remains largely uncertain, particularly in the ecologically vulnerable Tibetan plateau permafrost area with large carbon storage. With the concept of space for time substitution, we investigated the responses of soil CO2-fixing microbial community and its enzyme activity to climate change along an elevation gradient (4400-5100 m) of alpine grassland on the central Tibetan plateau. The elevation gradient in a south-facing hill slope leads to variation in climate and soil physicochemical parameters. The autotrophic microbial communities were characterized by quantitative PCR (qPCR), terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning/sequencing targeting the CO2-fixing gene (RubisCO). The results demonstrated that the autotrophic microbial community abundance, structure and its enzyme activity were mainly driven by soil temperature and water content. Soil temperature increase and water decrease dramatically reduced the abundance of the outnumbered form IC RubisCO-containing microbes, and significantly changed the structure of form IC, IAB and ID RubisCO-containing microbial community. Structural equation model revealed that the RubisCO enzyme was directly derived from RubisCO-containing microbes and its activity was significantly reduced by soil temperature increase and water content decrease. Thus our results provide a novel positive feedback loop of climate warming and warming-induced dryness by that soil microbial carbon fixing potential will reduce by 3.77%-8.86% with the soil temperature increase of 1.94oC and water content decrease of 60%-70%. This positive feedback could be capable of amplifying the climate change given the significant contribution of soil microbial CO2-fixing up to 4.9% of total soil organic carbon.

Systems for Lung Volume Standardization during Static and Dynamic MDCT-based Quantitative Assessment of Pulmonary Structure and Function

PubMed Central

Fuld, Matthew K.; Grout, Randall; Guo, Junfeng; Morgan, John H.; Hoffman, Eric A.

2013-01-01

Rationale and Objectives Multidetector-row Computed Tomography (MDCT) has emerged as a tool for quantitative assessment of parenchymal destruction, air trapping (density metrics) and airway remodeling (metrics relating airway wall and lumen geometry) in chronic obstructive pulmonary disease (COPD) and asthma. Critical to the accuracy and interpretability of these MDCT-derived metrics is the assurance that the lungs are scanned during a breath-hold at a standardized volume. Materials and Methods A computer monitored turbine-based flow meter system was developed to control patient breath-holds and facilitate static imaging at fixed percentages of the vital capacity. Due to calibration challenges with gas density changes during multi-breath xenon-CT an alternative system was required. The design incorporated dual rolling seal pistons. Both systems were tested in a laboratory environment and human subject trials. Results The turbine-based system successfully controlled lung volumes in 32/37 subjects, having a linear relationship for CT measured air volume between repeated scans: for all scans, the mean and confidence interval of the differences (scan1-scan2) was −9 ml (−169, 151); for TLC alone 6 ml (−164, 177); for FRC alone, −23 ml (−172, 126). The dual-piston system successfully controlled lung volume in 31/41 subjects. Study failures related largely to subject non-compliance with verbal instruction and gas leaks around the mouthpiece. Conclusion We demonstrate the successful use of a turbine-based system for static lung volume control and demonstrate its inadequacies for dynamic xenon-CT studies. Implementation of a dual-rolling seal spirometer has been shown to adequately control lung volume for multi-breath wash-in xenon-CT studies. These systems coupled with proper patient coaching provide the tools for the use of CT to quantitate regional lung structure and function. The wash-in xenon-CT method for assessing regional lung function, while not necessarily practical for routine clinical studies, provides for a dynamic protocol against which newly emerging single breath, dual-energy xenon-CT measures can be validated. PMID:22555001

Systems for lung volume standardization during static and dynamic MDCT-based quantitative assessment of pulmonary structure and function.

PubMed

Fuld, Matthew K; Grout, Randall W; Guo, Junfeng; Morgan, John H; Hoffman, Eric A

2012-08-01

Multidetector-row computed tomography (MDCT) has emerged as a tool for quantitative assessment of parenchymal destruction, air trapping (density metrics), and airway remodeling (metrics relating airway wall and lumen geometry) in chronic obstructive pulmonary disease (COPD) and asthma. Critical to the accuracy and interpretability of these MDCT-derived metrics is the assurance that the lungs are scanned during a breathhold at a standardized volume. A computer monitored turbine-based flow meter system was developed to control patient breathholds and facilitate static imaging at fixed percentages of the vital capacity. Because of calibration challenges with gas density changes during multibreath xenon CT, an alternative system was required. The design incorporated dual rolling seal pistons. Both systems were tested in a laboratory environment and human subject trials. The turbine-based system successfully controlled lung volumes in 32/37 subjects, having a linear relationship for CT measured air volume between repeated scans: for all scans, the mean and confidence interval of the differences (scan1-scan2) was -9 mL (-169, 151); for total lung capacity alone 6 mL (-164, 177); for functional residual capacity alone, -23 mL (-172, 126). The dual-piston system successfully controlled lung volume in 31/41 subjects. Study failures related largely to subject noncompliance with verbal instruction and gas leaks around the mouthpiece. We demonstrate the successful use of a turbine-based system for static lung volume control and demonstrate its inadequacies for dynamic xenon CT studies. Implementation of a dual-rolling seal spirometer has been shown to adequately control lung volume for multibreath wash-in xenon CT studies. These systems coupled with proper patient coaching provide the tools for the use of CT to quantitate regional lung structure and function. The wash-in xenon CT method for assessing regional lung function, although not necessarily practical for routine clinical studies, provides for a dynamic protocol against which newly emerging single breath, dual-energy xenon CT measures can be validated. Copyright © 2012 AUR. Published by Elsevier Inc. All rights reserved.

Global and local health burden trade-off through the hybridisation of quantitative microbial risk assessment and life cycle assessment to aid water management.

PubMed

Kobayashi, Yumi; Peters, Greg M; Ashbolt, Nicholas J; Heimersson, Sara; Svanström, Magdalena; Khan, Stuart J

2015-08-01

Life cycle assessment (LCA) and quantitative risk assessment (QRA) are commonly used to evaluate potential human health impacts associated with proposed or existing infrastructure and products. Each approach has a distinct objective and, consequently, their conclusions may be inconsistent or contradictory. It is proposed that the integration of elements of QRA and LCA may provide a more holistic approach to health impact assessment. Here we examine the possibility of merging LCA assessed human health impacts with quantitative microbial risk assessment (QMRA) for waterborne pathogen impacts, expressed with the common health metric, disability adjusted life years (DALYs). The example of a recent large-scale water recycling project in Sydney, Australia was used to identify and demonstrate the potential advantages and current limitations of this approach. A comparative analysis of two scenarios - with and without the development of this project - was undertaken for this purpose. LCA and QMRA were carried out independently for the two scenarios to compare human health impacts, as measured by DALYs lost per year. LCA results suggested that construction of the project would lead to an increased number of DALYs lost per year, while estimated disease burden resulting from microbial exposures indicated that it would result in the loss of fewer DALYs per year than the alternative scenario. By merging the results of the LCA and QMRA, we demonstrate the advantages in providing a more comprehensive assessment of human disease burden for the two scenarios, in particular, the importance of considering the results of both LCA and QRA in a comparative assessment of decision alternatives to avoid problem shifting. The application of DALYs as a common measure between the two approaches was found to be useful for this purpose. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantification and enzyme targets of fatty acid amides from duckweed root exudates involved in the stimulation of denitrification.

PubMed

Sun, Li; Lu, Yufang; Kronzucker, Herbert J; Shi, Weiming

2016-07-01

Fatty acid amides from plant root exudates, such as oleamide and erucamide, have the ability to participate in strong plant-microbe interactions, stimulating nitrogen metabolism in rhizospheric bacteria. However, mechanisms of secretion of such fatty acid amides, and the nature of their stimulatory activities on microbial metabolism, have not been examined. In the present study, collection, pre-treatment, and determination methods of oleamide and erucamide in duckweed root exudates are compared. The detection limits of oleamide and erucamide by gas chromatography (GC) (10.3ngmL(-1) and 16.1ngmL(-1), respectively) are shown to be much lower than those by liquid chromatography (LC) (1.7 and 5.0μgmL(-1), respectively). Quantitative GC analysis yielded five times larger amounts of oleamide and erucamide in root exudates of Spirodela polyrrhiza when using a continuous collection method (50.20±4.32 and 76.79±13.92μgkg(-1) FW day(-1)), compared to static collection (10.88±0.66 and 15.27±0.58μgkg(-1) FW day(-1)). Furthermore, fatty acid amide secretion was significantly enhanced under elevated nitrogen conditions (>300mgL(-1)), and was negatively correlated with the relative growth rate of duckweed. Mechanistic assays were conducted to show that erucamide stimulates nitrogen removal by enhancing denitrification, targeting two key denitrifying enzymes, nitrate and nitrite reductases, in bacteria. Our findings significantly contribute to our understanding of the regulation of nitrogen dynamics by plant root exudates in natural ecosystems. Copyright © 2016 Elsevier GmbH. All rights reserved.

The concept of "buffering" in systems and control theory: from metaphor to math.

PubMed

Schmitt, Bernhard M

2004-10-04

The paradigm of "buffering" is used increasingly for the description of diverse "systemic" phenomena encountered in evolutionary genetics, ecology, integrative physiology, and other areas. However, in this new context, the paradigm has not yet matured into a truly quantitative concept inasmuch as it lacks a corresponding quantitative measure of "systems-level buffering strength". Here, I develop such measures on the basis of a formal and general approach to the quantitation of buffering action. "Systems-level buffering" is shown to be synonymous with "disturbance rejection" in feedback-control systems, and can be quantitated by means of dimensionless proportions between partial flows in two-partitioned systems. The units allow either the time-independent, "static" buffering properties or the time-dependent, "dynamic" ones to be measured. Analogous to this "resistance to change", one can define and measure the "conductance to change"; this quantity corresponds to "set-point tracking" in feedback-control systems. Together, these units provide a systematic framework for the quantitation of buffering action in systems biology, and reveal the common principle behind systems-level buffering, classical acid-base buffering, and multiple other manifestations of buffering.

Human perceptual overestimation of whole body roll tilt in hypergravity

PubMed Central

Newman, Michael C.; Oman, Charles M.; Merfeld, Daniel M.; Young, Laurence R.

2014-01-01

Hypergravity provides a unique environment to study human perception of orientation. We utilized a long-radius centrifuge to study perception of both static and dynamic whole body roll tilt in hypergravity, across a range of angles, frequencies, and net gravito-inertial levels (referred to as G levels). While studies of static tilt perception in hypergravity have been published, this is the first to measure dynamic tilt perception (i.e., with time-varying canal stimulation) in hypergravity using a continuous matching task. In complete darkness, subjects reported their orientation perception using a haptic task, whereby they attempted to align a hand-held bar with their perceived horizontal. Static roll tilt was overestimated in hypergravity, with more overestimation at larger angles and higher G levels, across the conditions tested (overestimated by ∼35% per additional G level, P < 0.001). As our primary contribution, we show that dynamic roll tilt was also consistently overestimated in hypergravity (P < 0.001) at all angles and frequencies tested, again with more overestimation at higher G levels. The overestimation was similar to that for static tilts at low angular velocities but decreased at higher angular velocities (P = 0.006), consistent with semicircular canal sensory integration. To match our findings, we propose a modification to a previous Observer-type canal-otolith interaction model. Specifically, our data were better modeled by including the hypothesis that the central nervous system treats otolith stimulation in the utricular plane differently than stimulation out of the utricular plane. This modified model was able to simulate quantitatively both the static and the dynamic roll tilt overestimation in hypergravity measured experimentally. PMID:25540216

Modified wound dressing with phyto-nanostructured coating to prevent staphylococcal and pseudomonal biofilm development

NASA Astrophysics Data System (ADS)

Anghel, Ion; Holban, Alina Maria; Grumezescu, Alexandru Mihai; Andronescu, Ecaterina; Ficai, Anton; Anghel, Alina Georgiana; Maganu, Maria; Lazǎr, Veronica; Chifiriuc, Mariana Carmen

2012-12-01

This paper reports a newly fabricated nanophyto-modified wound dressing with microbicidal and anti-adherence properties. Nanofluid-based magnetite doped with eugenol or limonene was used to fabricate modified wound dressings. Nanostructure coated materials were characterized by TEM, XRD, and FT-IR. For the quantitative measurement of biofilm-embedded microbial cells, a culture-based method for viable cell count was used. The optimized textile dressing samples proved to be more resistant to staphylococcal and pseudomonal colonization and biofilm formation compared to the uncoated controls. The functionalized surfaces for wound dressing seems to be a very useful tool for the prevention of wound microbial contamination on viable tissues.

Modified wound dressing with phyto-nanostructured coating to prevent staphylococcal and pseudomonal biofilm development

PubMed Central

2012-01-01

This paper reports a newly fabricated nanophyto-modified wound dressing with microbicidal and anti-adherence properties. Nanofluid-based magnetite doped with eugenol or limonene was used to fabricate modified wound dressings. Nanostructure coated materials were characterized by TEM, XRD, and FT-IR. For the quantitative measurement of biofilm-embedded microbial cells, a culture-based method for viable cell count was used. The optimized textile dressing samples proved to be more resistant to staphylococcal and pseudomonal colonization and biofilm formation compared to the uncoated controls. The functionalized surfaces for wound dressing seems to be a very useful tool for the prevention of wound microbial contamination on viable tissues. PMID:23272823

Modified wound dressing with phyto-nanostructured coating to prevent staphylococcal and pseudomonal biofilm development.

PubMed

Anghel, Ion; Holban, Alina Maria; Grumezescu, Alexandru Mihai; Andronescu, Ecaterina; Ficai, Anton; Anghel, Alina Georgiana; Maganu, Maria; Laz R, Veronica; Chifiriuc, Mariana Carmen

2012-12-31

This paper reports a newly fabricated nanophyto-modified wound dressing with microbicidal and anti-adherence properties. Nanofluid-based magnetite doped with eugenol or limonene was used to fabricate modified wound dressings. Nanostructure coated materials were characterized by TEM, XRD, and FT-IR. For the quantitative measurement of biofilm-embedded microbial cells, a culture-based method for viable cell count was used. The optimized textile dressing samples proved to be more resistant to staphylococcal and pseudomonal colonization and biofilm formation compared to the uncoated controls. The functionalized surfaces for wound dressing seems to be a very useful tool for the prevention of wound microbial contamination on viable tissues.

Status and future of Quantitative Microbiological Risk Assessment in China

PubMed Central

Dong, Q.L.; Barker, G.C.; Gorris, L.G.M.; Tian, M.S.; Song, X.Y.; Malakar, P.K.

2015-01-01

Since the implementation of the Food Safety Law of the People's Republic of China in 2009 use of Quantitative Microbiological Risk Assessment (QMRA) has increased. QMRA is used to assess the risk posed to consumers by pathogenic bacteria which cause the majority of foodborne outbreaks in China. This review analyses the progress of QMRA research in China from 2000 to 2013 and discusses 3 possible improvements for the future. These improvements include planning and scoping to initiate QMRA, effectiveness of microbial risk assessment utility for risk management decision making, and application of QMRA to establish appropriate Food Safety Objectives. PMID:26089594

Quantification of Microbial Phenotypes

PubMed Central

Martínez, Verónica S.; Krömer, Jens O.

2016-01-01

Metabolite profiling technologies have improved to generate close to quantitative metabolomics data, which can be employed to quantitatively describe the metabolic phenotype of an organism. Here, we review the current technologies available for quantitative metabolomics, present their advantages and drawbacks, and the current challenges to generate fully quantitative metabolomics data. Metabolomics data can be integrated into metabolic networks using thermodynamic principles to constrain the directionality of reactions. Here we explain how to estimate Gibbs energy under physiological conditions, including examples of the estimations, and the different methods for thermodynamics-based network analysis. The fundamentals of the methods and how to perform the analyses are described. Finally, an example applying quantitative metabolomics to a yeast model by 13C fluxomics and thermodynamics-based network analysis is presented. The example shows that (1) these two methods are complementary to each other; and (2) there is a need to take into account Gibbs energy errors. Better estimations of metabolic phenotypes will be obtained when further constraints are included in the analysis. PMID:27941694

Quantitative Evaluation of Tumor Early Response to a Vascular-Disrupting Agent with Dynamic PET.

PubMed

Guo, Ning; Zhang, Fan; Zhang, Xiaomeng; Guo, Jinxia; Lang, Lixin; Kiesewetter, Dale O; Niu, Gang; Li, Quanzheng; Chen, Xiaoyuan

2015-12-01

The purpose of this study is to evaluate the early response of tumors to a vascular-disrupting agent (VDA) VEGF121/recombinant toxin gelonin (rGel) using dynamic [(18)F]FPPRGD2 positron emission tomography (PET) and kinetic parameter estimation. Two tumor xenograft models: U87MG (highly vascularized) and A549 (moderately vascularized), were selected, and both were randomized into treatment and control groups. Sixty-minute dynamic PET scans with [(18)F]FPPRGD2 that targets to integrin αvβ3 were performed at days 0 (baseline), 1, and 3 since VEGF121/rGel treatment started. Dynamic PET-derived binding potential (BPND) and parametric maps were compared with tumor uptake (%ID/g) and the static PET image at 1 h after the tracer administration. The growth of U87MG tumor was obviously delayed upon VEGF121/rGel treatment. A549 tumor was not responsive to the same treatment. BPND of treated U87MG tumors decreased significantly at day 1 (p < 0.05), and the difference was more significant at day 3 (p < 0.01), compared with the control group. However, the tracer uptake (%ID/g) derived from static images at 1-h time point did not show significant difference between the treated and control tumors until day 3. Little difference in tracer uptake (%ID/g) or BPND was found between treated and control A549 tumors. Considering the tracer retention in tumor and the slower clearance due to damaged tumor vasculature after treatment, BPND representing the actual specific binding portion appears to be more sensitive and accurate than the semiquantitative parameters (such as %ID/g) derived from static images to assess the early response of tumor to VDA treatment. Quantitative analysis based on dynamic PET with [(18)F]FPPRGD2 shows advantages in distinguishing effective from ineffective treatment during the course of VEGF121/rGel therapy at early stage and is therefore more sensitive in assessing therapy response than static PET.

Maple sap predominant microbial contaminants are correlated with the physicochemical and sensorial properties of maple syrup.

PubMed

Filteau, Marie; Lagacé, Luc; Lapointe, Gisèle; Roy, Denis

2012-03-01

Maple sap processing and microbial contamination are significant aspects that affect maple syrup quality. In this study, two sample sets from 2005 and 2008 were used to assess the maple syrup quality variation and its relationship to microbial populations, with respect to processing, production site and harvesting period. The abundance of maple sap predominant bacteria (Pseudomonas fluorescens group and two subgroups, Rahnella spp., Janthinobacterium spp., Leuconostoc mesenteroides) and yeast (Mrakia spp., Mrakiella spp.,Guehomyces pullulans) was assessed by quantitative PCR. Maple syrup properties were analyzed by physicochemical and sensorial methods. Results indicate that P. fluorescens, Mrakia spp., Mrakiella spp. G. pullulans and Rahnella spp. are stable contaminants of maple sap, as they were found for every production site throughout the flow period. Multiple factor analysis reports a link between the relative abundance of P. fluorescens group and Mrakia spp. in maple sap with maple and vanilla odor as well as flavor of maple syrup. This evidence supports the contribution of these microorganisms or a consortium of predominant microbial contaminants to the characteristic properties of maple syrup. Copyright © 2011 Elsevier B.V. All rights reserved.

Molecular-based environmental risk assessment of three varieties of genetically engineered cows.

PubMed

Xu, Jianxiang; Zhao, Jie; Wang, Jianwu; Zhao, Yaofeng; Zhang, Lei; Chu, Mingxing; Li, Ning

2011-10-01

The development of animal biotechnology has led to an increase in attention to biosafety issues. Here we evaluated the impact of genetically engineered cows on the environment. The probability of horizontal gene transfer and the impact on the microbial communities in cow gut and soil were tested using three varieties of genetically engineered cows that were previously transformed with a human gene encoding lysozyme, lactoferrin, or human alpha lactalbumin. The results showed that the transgenes were not detectable by polymerase chain reaction (PCR) or quantitative real-time PCR in gut microbial DNA extracts of manure or microbial DNA extracts of topsoil. In addition, the transgenes had no impact on the microbial communities in cow gut or soil as assessed by PCR-denaturing gradient gel electrophoresis or 16S rDNA sequencing. Furthermore, phylogenetic analyses showed that the manure bacteria sampled during each of the four seasons belonged primarily to two groups, Firmicutes and Bacteroidetes, and the soil bacteria belonged to four groups, Firmicutes, Bacteroidetes, Actinobacteria, and α-proteobacteria. Other groups, such as β-proteobacteria, γ-proteobacteria, δ-proteobacteria, ε-proteobacteria, Spirochaetes, Acidobacteria, Chloroflexi, and Nitrospira, were not dominant in the manure or soil.

Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions.

PubMed

Pourabedin, Mohsen; Xu, Zhengxin; Baurhoo, Bushansingh; Chevaux, Eric; Zhao, Xin

2014-05-01

There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.

FTIR as an easy and fast analytical approach to follow up microbial growth during fungal pretreatment of poplar wood with Phanerochaete chrysosporium.

PubMed

Cornet, I; Wittner, N; Tofani, G; Tavernier, S

2018-02-01

Since the determination of the fermentation kinetics is one of the main challenges in solid state fermentation, the quantitative measurement of biomass growth during microbial pretreatment by FTIR spectroscopy in Attenuated Total Reflectance mode was evaluated. Peaks at wave numbers of 1651 cm -1 and 1593 cm -1 showed to be affected during pretreatment of poplar wood particles by Phanerochaete chrysosporium MUCL 19343. Samples with different microbial biomass fractions were obtained from two different experiments, i.e., shake flask and fixed-bed reactor experiments. The glucosamine concentration was compared to the normalized absorbance ratio of the 1651 cm -1 to 1593 cm -1 peak, measured by FTIR-ATR, and resulted in a linear relationship. The application of a normalized absorbance ratio in function of time provided a graph that was similar to the microbial growth curve. Application of FTIR in ATR mode to follow-up kinetics during solid state fermentation seems to be a fast and easy alternative to laborious measurement techniques, such as glucosamine determination. Copyright © 2018 Elsevier B.V. All rights reserved.

Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils.

PubMed

Fang, Linchuan; Wang, Mengke; Cai, Lin; Cang, Long

2017-06-01

Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.

Microbial processing of carbon in hydrothermal systems (Invited)

NASA Astrophysics Data System (ADS)

LaRowe, D.; Amend, J. P.

2013-12-01

Microorganisms are known to be active in hydrothermal systems. They catalyze reactions that consume and produce carbon compounds as a result of their efforts to gain energy, grow and replace biomass. However, the rates of these processes, as well as the size of the active component of microbial populations, are poorly constrained in hydrothermal environments. In order to better characterize biogeochemical processes in these settings, a quantitative relationship between rates of microbial catalysis, energy supply and demand and population size is presented. Within this formulation, rates of biomass change are determined as a function of the proportion of catabolic power that is converted into biomass - either new microorganisms or the replacement of existing cell components - and the amount of energy that is required to synthesize biomass. The constraints that hydrothermal conditions place on power supply and demand are explicitly taken into account. The chemical composition, including the concentrations of organic compounds, of diffuse and focused flow hydrothermal fluids, hydrothermally influenced sediment pore water and fluids from the oceanic lithosphere are used in conjunction with cell count data and the model described above to constrain the rates of microbial processes that influence the carbon cycle in the Juan de Fuca hydrothermal system.

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Minjing; Qian, Wei-jun; Gao, Yuqian

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes asmore » time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates« less

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

PubMed

Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

Two-dimensional distribution of microbial activity and flow patterns within naturally fractured chalk.

PubMed

Arnon, Shai; Ronen, Zeev; Adar, Eilon; Yakirevich, Alexander; Nativ, Ronit

2005-10-01

The two-dimensional distribution of flow patterns and their dynamic change due to microbial activity were investigated in naturally fractured chalk cores. Long-term biodegradation experiments were conducted in two cores ( approximately 20 cm diameter, 31 and 44 cm long), intersected by a natural fracture. 2,4,6-tribromophenol (TBP) was used as a model contaminant and as the sole carbon source for aerobic microbial activity. The transmissivity of the fractures was continuously reduced due to biomass accumulation in the fracture concurrent with TBP biodegradation. From multi-tracer experiments conducted prior to and following the microbial activity, it was found that biomass accumulation causes redistribution of the preferential flow channels. Zones of slow flow near the fracture inlet were clogged, thus further diverting the flow through zones of fast flow, which were also partially clogged. Quantitative evaluation of biodegradation and bacterial counts supported the results of the multi-tracer tests, indicating that most of the bacterial activity occurs close to the inlet. The changing flow patterns, which control the nutrient supply, resulted in variations in the concentrations of the chemical constituents (TBP, bromide and oxygen), used as indicators of biodegradation.

Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review.

PubMed

Cárdenas, Juan Pablo; Quatrini, Raquel; Holmes, David S

2016-09-01

High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed. Copyright © 2016 The Author(s). Published by Elsevier Masson SAS.. All rights reserved.

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

PubMed Central

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

Microbial diversity in European and South American spacecraft assembly clean rooms

NASA Astrophysics Data System (ADS)

Moissl-Eichinger, Christine; Stieglmeier, Michaela; Schwendner, Petra

Spacecraft assembly clean rooms are unique environments for microbes: Due to low nutri-ent levels, desiccated, clean conditions, constant control of humidity and temperature, these environments are quite inhospitable to microbial life and even considered "extreme". Many procedures keep the contamination as low as possible, but these conditions are also highly se-lective for indigenous microbial communities. For space missions under planetary protection requirements, it is crucial to control the contaminating bioburden as much as possible; but for the development of novel cleaning/sterilization methods it is also important to identify and characterize (understand) the present microbial community of spacecraft clean rooms. In prepa-ration for the recently approved ESA ExoMars mission, two European and one South American spacecraft assembly clean rooms were analyzed with respect to their microbial diversity, using standard procedures, new cultivation approaches and molecular methods, that should shed light onto the presence of planetary protection relevant microorganisms. For this study, the Her-schel Space Observatory (launched in May 2009) and its housing clean rooms in Friedrichshafen (Germany), at ESTEC (The Netherlands) and CSG, Kourou (French Guyana) were sampled during assembly, test and launch operations. Although Herschel does not demand planetary protection requirements, all clean rooms were in a fully operating state during sampling. This gave us the opportunity to sample the microbial diversity under strict particulate and molecular contamination-control. Samples were collected from spacecraft and selected clean room surface areas and were subjected to cultivation assays (32 different media), molecular studies (based on 16S rRNA gene sequence analysis) and quantitative PCR. The results from different strategies will be compared and critically discussed, showing the advantages and limits of the selected methodologies. This talk will sum up the lessons learned from this microbial diversity project.

Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example

PubMed Central

Röling, Wilfred F. M.; van Bodegom, Peter M.

2014-01-01

Molecular ecology approaches are rapidly advancing our insights into the microorganisms involved in the degradation of marine oil spills and their metabolic potentials. Yet, many questions remain open: how do oil-degrading microbial communities assemble in terms of functional diversity, species abundances and organization and what are the drivers? How do the functional properties of microorganisms scale to processes at the ecosystem level? How does mass flow among species, and which factors and species control and regulate fluxes, stability and other ecosystem functions? Can generic rules on oil-degradation be derived, and what drivers underlie these rules? How can we engineer oil-degrading microbial communities such that toxic polycyclic aromatic hydrocarbons are degraded faster? These types of questions apply to the field of microbial ecology in general. We outline how recent advances in single-species systems biology might be extended to help answer these questions. We argue that bottom-up mechanistic modeling allows deciphering the respective roles and interactions among microorganisms. In particular constraint-based, metagenome-derived community-scale flux balance analysis appears suited for this goal as it allows calculating degradation-related fluxes based on physiological constraints and growth strategies, without needing detailed kinetic information. We subsequently discuss what is required to make these approaches successful, and identify a need to better understand microbial physiology in order to advance microbial ecology. We advocate the development of databases containing microbial physiological data. Answering the posed questions is far from trivial. Oil-degrading communities are, however, an attractive setting to start testing systems biology-derived models and hypotheses as they are relatively simple in diversity and key activities, with several key players being isolated and a high availability of experimental data and approaches. PMID:24723922

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments.

PubMed

Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

2017-01-01

Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO 2 ) and elevated temperature (ambient +4°C) on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase ( amoA ) and bacterial nitrite reductase ( nirS ) were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO 2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes ( amoA and nirS ) were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus▿ †

PubMed Central

Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; Raskin, Lutgarde

2010-01-01

Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors. PMID:20889793

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

PubMed

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metabolite recycling and bidirectional C fluxes: Revolutionizing our view on microbial C cycling in soils

NASA Astrophysics Data System (ADS)

Dippold, M. A.; Apostel, C.; Kuzyakov, Y.

2016-12-01

Biogeochemists' view on microbial C transformation in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the anabolism. However, life in a C limited environment as challenging as soil requires microbial adaptation strategies at all levels of metabolism. By coupling of position-specific labeling of core metabolites with compound-specific isotope analysis we demonstrated that catabolic oxidation of these metabolites exists in parallel to reductive, energy consuming pathways, reducing them for anabolic purposes. Up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in the citric acid cycle. Furthermore, position-specific labeling of rather `cost-intensive' biomass compounds such as fatty acids revealed that intact recycling of metabolites is a crucial microbial adaptation to C scarcity in soils. Both processes are unlikely to occur in pure cultures, where constant growth conditions under high C supply allow a straight unidirectional regulation of C metabolism. However, unstable environmental conditions, C scarcity and interactions between a still unknown diversity of microorganisms in soils are likely to induce the observed metabolic diversity. To understand how microorganisms catalyze the biogeochemical fluxes in soil, a profound understanding of their metabolic adaptation strategies such as recycling or switching between bidirectional fluxes is crucial. Metabolic flux models adapted to soil microbial communities and their regulatory strategies will not only deepen our understanding on the microorganims' reactions to environmental changes but also create the prerequisits for a quantitative prediction of biogeochemical fluxes based on the underlying microbial processes.

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

PubMed Central

Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

2014-01-01

Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

Toward quantitative understanding on microbial community structure and functioning: a modeling-centered approach using degradation of marine oil spills as example.

PubMed

Röling, Wilfred F M; van Bodegom, Peter M

2014-01-01

Molecular ecology approaches are rapidly advancing our insights into the microorganisms involved in the degradation of marine oil spills and their metabolic potentials. Yet, many questions remain open: how do oil-degrading microbial communities assemble in terms of functional diversity, species abundances and organization and what are the drivers? How do the functional properties of microorganisms scale to processes at the ecosystem level? How does mass flow among species, and which factors and species control and regulate fluxes, stability and other ecosystem functions? Can generic rules on oil-degradation be derived, and what drivers underlie these rules? How can we engineer oil-degrading microbial communities such that toxic polycyclic aromatic hydrocarbons are degraded faster? These types of questions apply to the field of microbial ecology in general. We outline how recent advances in single-species systems biology might be extended to help answer these questions. We argue that bottom-up mechanistic modeling allows deciphering the respective roles and interactions among microorganisms. In particular constraint-based, metagenome-derived community-scale flux balance analysis appears suited for this goal as it allows calculating degradation-related fluxes based on physiological constraints and growth strategies, without needing detailed kinetic information. We subsequently discuss what is required to make these approaches successful, and identify a need to better understand microbial physiology in order to advance microbial ecology. We advocate the development of databases containing microbial physiological data. Answering the posed questions is far from trivial. Oil-degrading communities are, however, an attractive setting to start testing systems biology-derived models and hypotheses as they are relatively simple in diversity and key activities, with several key players being isolated and a high availability of experimental data and approaches.

Early detection of cataract and response to pantethine therapy with non-invasive static and dynamic light scattering

NASA Astrophysics Data System (ADS)

Ansari, Rafat R.; King, James F.; Seeberger, Teri; Clark, John I.

2003-07-01

Cataractogenesis is a risk factor for space travelers. Here on earth, half of all blindness is due to cataracts. At this time, the only known treatment is surgical removal of the lens. In this paper, we present static and dynamic light scattering (DLS) measurements of early onset of cataract before it has any effect on vision and to test the effectiveness of pantethine as an anticataract agent in reversing cataracts. In this preliminary study, experiments were conducted on 12 rodents. Static measurements were performed by scanning the animal eye (cornea to retina) at a laser power of 80 microwatts to collect photons or scattered intensity in steps of 10 microns. The rodents studied were control, selenite injected, and selenite plus pantethine injected. Selenite was used to induce cataracts. Static and dynamic changes (increase in light scatter and crystalline size) in the lenses are quantitatively measured as early as 1 day post selenite injections. Scattering intensity and DLS measurements from lenses of animals administered pantethine resembled controls. These subtle molecular changes are not noticeable when the animals are examined with conventional ophthalmic instruments because their lenses remain transparent. Acknowledgements: Technical support from C.Ganders, University of Washington, Seattle, NEI research grant EY04542 (JIC) and support under a NASA-NEI/NIH interagency agreement (RRA) are greatly appreciated. JFK works for QSS Inc. at NASA GRC.

Quantitative kinetic analysis of lung nodules by temporal subtraction technique in dynamic chest radiography with a flat panel detector

NASA Astrophysics Data System (ADS)

Tsuchiya, Yuichiro; Kodera, Yoshie; Tanaka, Rie; Sanada, Shigeru

2007-03-01

Early detection and treatment of lung cancer is one of the most effective means to reduce cancer mortality; chest X-ray radiography has been widely used as a screening examination or health checkup. The new examination method and the development of computer analysis system allow obtaining respiratory kinetics by the use of flat panel detector (FPD), which is the expanded method of chest X-ray radiography. Through such changes functional evaluation of respiratory kinetics in chest has become available. Its introduction into clinical practice is expected in the future. In this study, we developed the computer analysis algorithm for the purpose of detecting lung nodules and evaluating quantitative kinetics. Breathing chest radiograph obtained by modified FPD was converted into 4 static images drawing the feature, by sequential temporal subtraction processing, morphologic enhancement processing, kinetic visualization processing, and lung region detection processing, after the breath synchronization process utilizing the diaphragmatic analysis of the vector movement. The artificial neural network used to analyze the density patterns detected the true nodules by analyzing these static images, and drew their kinetic tracks. For the algorithm performance and the evaluation of clinical effectiveness with 7 normal patients and simulated nodules, both showed sufficient detecting capability and kinetic imaging function without statistically significant difference. Our technique can quantitatively evaluate the kinetic range of nodules, and is effective in detecting a nodule on a breathing chest radiograph. Moreover, the application of this technique is expected to extend computer-aided diagnosis systems and facilitate the development of an automatic planning system for radiation therapy.

Rocket Immunoelectrophoresis of the Entomocidal Parasporal Crystal of Bacillus thuringiensis subsp. kurstaki†

PubMed Central

Andrews, R. E.; Iandolo, J. J.; Campbell, B. S.; Davidson, L. I.; Bulla, L. A.

1980-01-01

Rocket immunoelectrophoresis was used to quantitate the soluble parasporal crystal of Bacillus thuringiensis subsp. kurstaki. The method described is rapid, reliable, specific, and extremely accurate, and it can be used to measure crystal toxin in commercial microbial insecticides that contain a mixture of spores, vegetative cells, and carrier materials. Images PMID:16345656

Quantitative Microbial Risk Assessment Tutorial - SDMProjectBuilder: Import Local Data Files to Identify and Modify Contamination Sources and Input ParametersUpdated 2017

EPA Science Inventory

Twelve example local data support files are automatically downloaded when the SDMProjectBuilder is installed on a computer. They allow the user to modify values to parameters that impact the release, migration, fate, and transport of microbes within a watershed, and control delin...

Low Frequencies of Interference to EPA Quantitative Polymerase Chain Reaction (qPCR) Methods for Microbial Water Quality Monitoring in U.S. Rivers and Streams and Coastal Waters

EPA Science Inventory

In collaboration with U.S States and Tribes, the United States Environmental Protection Agency (EPA) conducts periodic and rotating, statistically based surveys of U.S. rivers and streams (National Rivers and Streams Assessment, NRSA), estuarine and Great Lakes nearshore coastal ...

Quantitative Microbial Risk Assessment Tutorial – SDMProjectBuilder: Import Local Data Files to Identify and Modify Contamination Sources and Input Parameters

EPA Science Inventory

Twelve example local data support files are automatically downloaded when the SDMProjectBuilder is installed on a computer. They allow the user to modify values to parameters that impact the release, migration, fate, and transport of microbes within a watershed, and control delin...

How to train your microbe: methods for dynamically characterizing gene networks

PubMed Central

Castillo-Hair, Sebastian M.; Igoshin, Oleg A.; Tabor, Jeffrey J.

2015-01-01

Gene networks regulate biological processes dynamically. However, researchers have largely relied upon static perturbations, such as growth media variations and gene knockouts, to elucidate gene network structure and function. Thus, much of the regulation on the path from DNA to phenotype remains poorly understood. Recent studies have utilized improved genetic tools, hardware, and computational control strategies to generate precise temporal perturbations outside and inside of live cells. These experiments have, in turn, provided new insights into the organizing principles of biology. Here, we introduce the major classes of dynamical perturbations that can be used to study gene networks, and discuss technologies available for creating them in a wide range of microbial pathways. PMID:25677419

Microbial Community Structure in the Rhizosphere of Rice Plants

PubMed Central

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

2016-01-01

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

Collective cell migration: a physics perspective

NASA Astrophysics Data System (ADS)

Hakim, Vincent; Silberzan, Pascal

2017-07-01

Cells have traditionally been viewed either as independently moving entities or as somewhat static parts of tissues. However, it is now clear that in many cases, multiple cells coordinate their motions and move as collective entities. Well-studied examples comprise development events, as well as physiological and pathological situations. Different ex vivo model systems have also been investigated. Several recent advances have taken place at the interface between biology and physics, and have benefitted from progress in imaging and microscopy, from the use of microfabrication techniques, as well as from the introduction of quantitative tools and models. We review these interesting developments in quantitative cell biology that also provide rich examples of collective out-of-equilibrium motion.

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali N.; Or, Dani

2014-09-01

The dispersal rates of self-propelled microorganisms affect their spatial interactions and the ecological functioning of microbial communities. Microbial dispersal rates affect risk of contamination of water resources by soil-borne pathogens, the inoculation of plant roots, or the rates of spoilage of food products. In contrast with the wealth of information on microbial dispersal in water replete systems, very little is known about their dispersal rates in unsaturated porous media. The fragmented aqueous phase occupying complex soil pore spaces suppress motility and limits dispersal ranges in unsaturated soil. The primary objective of this study was to systematically evaluate key factors that shape microbial dispersal in model unsaturated porous media to quantify effects of saturation, pore space geometry, and chemotaxis on characteristics of principles that govern motile microbial dispersion in unsaturated soil. We constructed a novel 3-D angular pore network model (PNM) to mimic aqueous pathways in soil for different hydration conditions; within the PNM, we employed an individual-based model that considers physiological and biophysical properties of motile and chemotactic bacteria. The effects of hydration conditions on first passage times in different pore networks were studied showing that fragmentation of aquatic habitats under dry conditions sharply suppresses nutrient transport and microbial dispersal rates in good agreement with limited experimental data. Chemotactically biased mean travel speed of microbial cells across 9 mm saturated PNM was ˜3 mm/h decreasing exponentially to 0.45 mm/h for the PNM at matric potential of -15 kPa (for -35 kPa, dispersal practically ceases and the mean travel time to traverse the 9 mm PNM exceeds 1 year). Results indicate that chemotaxis enhances dispersal rates by orders of magnitude relative to random (diffusive) motions. Model predictions considering microbial cell sizes relative to available liquid pathways sizes were in good agreement with experimental results for unsaturated soils. The new modeling platform enables quantitative consideration of key biophysical factors (e.g., pore space heterogeneities and hydration conditions) governing microbial interactions in 3-D soil pore spaces.

Effect of virgin olive oil and thyme phenolic compounds on blood lipid profile: implications of human gut microbiota.

PubMed

Martín-Peláez, Sandra; Mosele, Juana Ines; Pizarro, Neus; Farràs, Marta; de la Torre, Rafael; Subirana, Isaac; Pérez-Cano, Francisco José; Castañer, Olga; Solà, Rosa; Fernandez-Castillejo, Sara; Heredia, Saray; Farré, Magí; Motilva, María José; Fitó, Montserrat

2017-02-01

To investigate the effect of virgin olive oil phenolic compounds (PC) alone or in combination with thyme PC on blood lipid profile from hypercholesterolemic humans, and whether the changes generated are related with changes in gut microbiota populations and activities. A randomized, controlled, double-blind, crossover human trial (n = 12) was carried out. Participants ingested 25 mL/day for 3 weeks, preceded by 2-week washout periods, three raw virgin olive oils differing in the concentration and origin of PC: (1) a virgin olive oil (OO) naturally containing 80 mg PC/kg, (VOO), (2) a PC-enriched virgin olive oil containing 500 mg PC/kg, from OO (FVOO), and (3) a PC-enriched virgin olive oil containing a mixture of 500 mg PC/kg from OO and thyme, 1:1 (FVOOT). Blood lipid values and faecal quantitative changes in microbial populations, short chain fatty acids, cholesterol microbial metabolites, bile acids, and phenolic metabolites were analysed. FVOOT decreased seric ox-LDL concentrations compared with pre-FVOOT, and increased numbers of bifidobacteria and the levels of the phenolic metabolite protocatechuic acid compared to VOO (P < 0.05). FVOO did not lead to changes in blood lipid profile nor quantitative changes in the microbial populations analysed, but increased the coprostanone compared to FVOOT (P < 0.05), and the levels of the faecal hydroxytyrosol and dihydroxyphenylacetic acids, compared with pre-intervention values and to VOO, respectively (P < 0.05). The ingestion of a PC-enriched virgin olive oil, containing a mixture of olive oil and thyme PC for 3 weeks, decreases blood ox-LDL in hypercholesterolemic humans. This cardio-protective effect could be mediated by the increases in populations of bifidobacteria together with increases in PC microbial metabolites with antioxidant activities.

Relationships between soil microbial communities and soil carbon turnover along a vegetation and moisture gradient in interior Alaska

NASA Astrophysics Data System (ADS)

Waldrop, M. P.; Harden, J. W.; Turetsky, M. R.; Petersen, D. G.; McGuire, A. D.; Briones, M. J.; Churchill, A. C.; Doctor, D. H.; Pruett, L. E.

2010-12-01

Boreal landscapes are characterized by a mosaic of uplands and lowlands, which differ in plant species composition, litter biochemistry, and biogeochemical cycling rates. Boreal ecosystems, from upland black spruce stands to lowland fens, are structured largely by water table position and contain quantitatively and qualitatively different forms of soil organic matter. Differences in carbon (C) availability among ecosystems likely translate to differences in the structure of soil microbial communities, which in turn could affect rates of organic matter decomposition and turnover. We examined relationships between microbial communities and soil C turnover in near-surface soils along a topographic soil moisture and vegetation gradient in interior Alaska. We tested the hypothesis that upland black spruce sites would be dominated by soil fungi and have slow rates of C turnover, whereas lowland ecosystems would be dominated by bacteria and mesofauna (enchytraeids) and have more rapid rates of C turnover. We utilized several isotopic measures of soil C turnover including bomb radiocarbon techniques, the δ15N of SOM, and the difference between δ13C of SOM, DOC, and respired CO2. All three measures indicated greater C turnover rates in the surface soils of the lowland fen sites compared to the more upland locations. Quantitative PCR analyses of soil bacteria and archaea, combined with enchytraed counts, confirmed that surface soils from the lowland fen ecosystems had the highest abundances of these functional groups. Fungal biomass was highly variable and tended to be more abundant in the upland forest sites. Soil enzymatic results were mixed: potential cellulase activities were higher in the more upland soils even though rates of microbial activity were generally lower. Oxidative enzyme activities were higher in fens, even though these ecosystems are saturated and partly anaerobic. Overall our data support soil food web theory which argues that rapidly cycling systems are bacterial dominated with mesofaunal grazing, whereas slowly cycling systems have characteristic higher fungal:bacterial ratios.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence.

PubMed

Stoeckel, Donald M; Stelzer, Erin A; Stogner, Robert W; Mau, David P

2011-05-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections--augmented with local observations and land-use patterns--indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. Copyright © 2011 Elsevier Ltd. All rights reserved.

Introducing a novel interaction model structure for the combined effect of temperature and pH on the microbial growth rate.

PubMed

Akkermans, Simen; Noriega Fernandez, Estefanía; Logist, Filip; Van Impe, Jan F

2017-01-02

Efficient modelling of the microbial growth rate can be performed by combining the effects of individual conditions in a multiplicative way, known as the gamma concept. However, several studies have illustrated that interactions between different effects should be taken into account at stressing environmental conditions to achieve a more accurate description of the growth rate. In this research, a novel approach for modeling the interactions between the effects of environmental conditions on the microbial growth rate is introduced. As a case study, the effect of temperature and pH on the growth rate of Escherichia coli K12 is modeled, based on a set of computer controlled bioreactor experiments performed under static environmental conditions. The models compared in this case study are the gamma model, the model of Augustin and Carlier (2000), the model of Le Marc et al. (2002) and the novel multiplicative interaction model, developed in this paper. This novel model enables the separate identification of interactions between the effects of two (or more) environmental conditions. The comparison of these models focuses on the accuracy, interpretability and compatibility with efficient modeling approaches. Moreover, for the separate effects of temperature and pH, new cardinal parameter model structures are proposed. The novel interaction model contributes to a generic modeling approach, resulting in predictive models that are (i) accurate, (ii) easily identifiable with a limited work load, (iii) modular, and (iv) biologically interpretable. Copyright © 2016. Published by Elsevier B.V.

[Effects of grape seed addition in swine manure-wheat straw composting on the compost microbial community and carbon and nitrogen contents].

PubMed

Huang, Yi-Mei; Liu, Xue-Ling; Jiang, Ji-Shao; Huang, Hua; Liu, Dong

2012-08-01

Taking substrates swine manure and wheat straw (fresh mass ratio 10.5:1) as the control (PMW), a composting experiment was conducted in a self-made aerated static composting bin to study the effects of adding 8% grape seed (treatment PMW + G) on the succession of microbial community and the transformation of carbon and nitrogen in the substrates during the composting. Seven samples were collected from each treatment, according to the temperature of the compost during the 30 d composting period. The microbial population and physiological groups were determined, and the NH4(+)-N, NO3(-)-N, organic N, and organic C concentrations in the compost were measured. Grape seed addition induced a slight increase of bacterial count and a significant increase of actinomycetes count, but decreased the fungal count significantly. Grape seed addition also decreased the ratio of bacteria to actinomycetes and the counts of ammonifiers and denitrifiers, but increased the counts of nitrifiers, N-fixing bacteria, and cellulose-decomposing microorganisms. The contents of NH4(+)-N and organic C decreased, while that of NO3(-)-N increased obviously. The NO3(-)-N content in the compost was positively correlated with the actinomycetes count. During composting, the compost temperature in treatment PMW + G increased more rapidly, and remained steady in thermophilic phase, while the water content changed little, which provided a stable and higher population of actinomycetes and nitrifiers in thermophilic phase, being beneficial to the increase of compost nitrate N.

Responses of soluble microbial products and extracellular polymeric substances to the presence of toxic 2,6-dichlorophenol in aerobic granular sludge system.

PubMed

Li, Kai; Wei, Dong; Yan, Tao; Du, Bin; Wei, Qin

2016-12-01

The objective of this study was to evaluate the responses of soluble microbial products (SMP) and extracellular polymeric substances (EPS) to the presence of toxic 2,6-dichlorophenol (2,6-DCP) in aerobic granular sludge (AGS) system. Batch experiment showed that NH 4 + -N removal efficiency significantly decreased from 99.6% to 47.2% in the toxic 2,6-DCP of 20 mg/L. Moreover, the inhibition degrees of 2,6-DCP on (SOUR) H , [Formula: see text] and [Formula: see text] were 7.8%, 32.1% and 9.5%, respectively. The main components of SMP, including protein (PN) and polysaccharide (PS) increased from 2.3 ± 0.74 and 16.8 ± 0.12 mg/L to 66.4 ± 0.56 and 18.0 ± 0.19 mg/L in the presence of 2,6-DCP. Three-dimensional excitation-emission matrix (3D-EEM) spectroscopy identified tryptophan PN-like, humic acid-like and fulvic acid-like substances in the control SMP, and their fluorescence intensities increased after exposure to 2,6-DCP. Synchronous fluorescence spectra suggested that the fluorescence quenching between EPS and 2,6-DCP was a static quenching process. The obtained results could provide insightful information on the responses of microbial products to AGS in the presence of toxic chlorophenols. Copyright © 2016 Elsevier Ltd. All rights reserved.