Investigations of the microbial transformation of cortisol to prednisolone in urine samples.

Science.gov (United States)

Bredehöft, Michael; Baginski, Rainer; Parr, Maria-Kristina; Thevis, Mario; Schänzer, Wilhelm

2012-03-01

Doping control samples are normally collected under non-sterile conditions and sometimes, storage and transportation are influenced by parameters such as the temperature. Therefore, microbial contamination and subsequent alteration of a sample's composition are possible. Studies regarding sample collection in cattle breeding have already shown enzymatic transformation of endogenous testosterone to boldenone causing false-positive findings. The aim of the present study was to investigate whether positive doping cases with the synthetic corticosteroids prednisolone and prednisone may result from microbial transformation of the endogenous corticosteroids cortisol and cortisone, respectively. A method comprising parameters such as pH values and screening results for synthetic glucocorticosteroids as well as incubation experiments followed by liquid chromatographic and mass spectrometric analysis was employed to test for contaminating germs with Δ(1)-dehydrogenase activity. Over 700 urine samples comprising inpatient and doping control specimens were investigated. In none of them, 1,2-dehydrogenating activity was confirmed. These findings are in accordance with other studies. However, the problem of microbial alteration of doping control specimens with special respect to 1,2-dehydrogenation must not be underestimated. Article from a special issue on steroids and microorganisms. Copyright © 2010 Elsevier Ltd. All rights reserved.

Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs

Directory of Open Access Journals (Sweden)

P. K. Gao

2015-06-01

Full Text Available Microbial communities in injected water are expected to have significant influence on those of reservoir strata in long-term water flooding petroleum reservoirs. To investigate the similarities and differences in microbial communities in injected water and reservoir strata, high-throughput sequencing of microbial partial 16S rRNA of the water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous sandstone reservoir and a heterogeneous conglomerate reservoir were performed. The results indicate that a small number of microbial populations are shared between the water samples from the injection and production wells in the sandstone reservoir, whereas a large number of microbial populations are shared in the conglomerate reservoir. The bacterial and archaeal communities in the reservoir strata have high concentrations, which are similar to those in the injected water. However, microbial population abundance exhibited large differences between the water samples from the injection and production wells. The number of shared populations reflects the influence of microbial communities in injected water on those in reservoir strata to some extent, and show strong association with the unique variation of reservoir environments.

Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients.

Directory of Open Access Journals (Sweden)

Daniel Belstrøm

Full Text Available The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens.Site specific subgingival plaque samples (n = 54, pooled subgingival plaque samples (n = 18 and stimulated saliva samples (n = 18 were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing and microbial community profiles were compared using Spearman rank correlation coefficient.Pronounced intraindividual differences were recorded in site-specific microbial profiles, and site-specific information was in general not reflected by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94, compared to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94 in pooled subgingival samples.Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate for pooled subgingival samples when screening for presence of periopathogens. Future large-scale studies are needed to confirm findings from this study.

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

Directory of Open Access Journals (Sweden)

Gemma Henderson

Full Text Available 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

40 CFR 158.2172 - Experimental use permit microbial pesticides residue data requirements table.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Experimental use permit microbial....2172 Experimental use permit microbial pesticides residue data requirements table. (a) General. Sections 158.100 through 158.130 describe how to use this table to determine the residue chemistry data...

Relationships between processing delay and microbial load of broiler neck skin samples.

Science.gov (United States)

Lucianez, A; Holmes, M A; Tucker, A W

2010-01-01

The measurable microbial load on poultry carcasses during processing is determined by a number of factors including farm or origin, processing hygiene, and external temperature. This study investigated associations between carcass microbial load and progressive delays to processing. A total of 30 carcasses were delayed immediately after defeathering and before evisceration in a commercial abattoir in groups of five, and were held at ambient temperature for 1, 2, 3, 4, 6, and 8 h. Delayed carcasses were reintroduced to the processing line, and quantitative assessment of total viable count, coliforms, Staphylococcus aureus, and Pseudomonas spp. was undertaken on neck skin flap samples collected after carcass chilling and then pooled for each group. Sampling was repeated on 5 separate days, and the data were combined. Significant increases in total viable count (P = 0.001) and coliforms (P = 0.004), but not for S. aureus or Pseudomonas loads, were observed across the 8-h period of delay. In line with previous studies, there was significant variation in microbiological data according to sampling day. In conclusion, there is a significant and measurable decline in microbiological status of uneviscerated but defeathered poultry carcasses after an 8-h delay, but the variability of sampling results, reflecting the wide range of factors that impact microbial load, means that it is not possible to determine maximum or minimum acceptable periods of processing delay based on this criterion alone.

A method for sampling microbial aerosols using high altitude balloons.

Science.gov (United States)

Bryan, N C; Stewart, M; Granger, D; Guzik, T G; Christner, B C

2014-12-01

Owing to the challenges posed to microbial aerosol sampling at high altitudes, very little is known about the abundance, diversity, and extent of microbial taxa in the Earth-atmosphere system. To directly address this knowledge gap, we designed, constructed, and tested a system that passively samples aerosols during ascent through the atmosphere while tethered to a helium-filled latex sounding balloon. The sampling payload is ~ 2.7 kg and comprised of an electronics box and three sampling chambers (one serving as a procedural control). Each chamber is sealed with retractable doors that can be commanded to open and close at designated altitudes. The payload is deployed together with radio beacons that transmit GPS coordinates (latitude, longitude and altitude) in real time for tracking and recovery. A cut mechanism separates the payload string from the balloon at any desired altitude, returning all equipment safely to the ground on a parachute. When the chambers are opened, aerosol sampling is performed using the Rotorod® collection method (40 rods per chamber), with each rod passing through 0.035 m3 per km of altitude sampled. Based on quality control measurements, the collection of ~ 100 cells rod(-1) provided a 3-sigma confidence level of detection. The payload system described can be mated with any type of balloon platform and provides a tool for characterizing the vertical distribution of microorganisms in the troposphere and stratosphere. Copyright © 2014 Elsevier B.V. All rights reserved.

Biomarker Analysis of Samples Visually Identified as Microbial in the Eocene Green River Formation: An Analogue for Mars.

Science.gov (United States)

Olcott Marshall, Alison; Cestari, Nicholas A

2015-09-01

One of the major exploration targets for current and future Mars missions are lithofacies suggestive of biotic activity. Although such lithofacies are not confirmation of biotic activity, they provide a way to identify samples for further analyses. To test the efficacy of this approach, we identified carbonate samples from the Eocene Green River Formation as "microbial" or "non-microbial" based on the macroscale morphology of their laminations. These samples were then crushed and analyzed by gas chromatography/mass spectroscopy (GC/MS) to determine their lipid biomarker composition. GC/MS analysis revealed that carbonates visually identified as "microbial" contained a higher concentration of more diverse biomarkers than those identified as "non-microbial," suggesting that this could be a viable detection strategy for selecting samples for further analysis or caching on Mars.

Microbial processes and communities in sediment samples along a transect across the Lusi mud volcano, Indonesia

Science.gov (United States)

Krueger, Martin; Straaten, Nontje; Mazzini, Adriano

2015-04-01

The Lusi eruption represents one of the largest ongoing sedimentary hosted geothermal systems. This eruption started in 2006 following to a 6.3 M earthquake that stroke Java Island. Since then it has been spewing boiling mud from a central crater with peaks reaching 180.000 m3 per day. Today an area of about 8 km2 is covered by locally dried mud breccia where a network of hundreds of satellite seeping pools is active. Numerous investigations focused on the study of offshore microbial colonies that commonly thrive at offshore methane seeps and mud volcanoes, however very little has been done for onshore seeping structures. Lusi represents a unique opportunity to complete a comprehensive study of onshore microbial communities fed by the seepage of CH4 and CO2 as well as of heavier liquid hydrocarbons originating from several km below the surface. We conducted a sampling campaign at the Lusi site collecting samples of fresh mud close to the erupting crater using a remote controlled drone. In addition we completed a transect towards outer parts of the crater to collect older, weathered samples for comparison. In all samples active microorganisms were present. The highest activities for CO2 and CH4 production as well as for CH4 oxidation and hydrocarbon degradation were observed in medium-age mud samples collected roughly in the middle of the transect. Rates for aerobic methane oxidation were high, as was the potential of the microbial communities to degrade hydrocarbons (oils, alkanes, BTEX tested). The data suggests a transition of microbial populations from an anaerobic, hydrocarbon-driven metabolism in fresher samples from center or from small seeps to more generalistic, aerobic microbial communities in older, more consolidated sediments. Currently, the microbial communities in the different sediment samples are analyzed using quantitative PCR and T-RFLP combined with MiSeq sequencing. This study represents an initial step to better understand onshore seepage

Phosphatase Activity of Microbial Populations in Different Milk Samples in Relation to Protein and Carbohydrate Content

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Sosanka Protim SANDILYA

2014-12-01

Full Text Available Cattle milk is a rich source of protein, carbohydrate, vitamins, minerals and all other major and micro nutrients. At a moderate pH, milk is an excellent media for the growth of microbes and thus, intake of raw milk is precarious. In this study, attempt was made for a qualitative study of eight raw milk samples of different varieties of cow and goat milk, collected from Jorhat district of Assam, India, on the basis of nutritional value and microbial population. The highest microbial population was found in the milk collected from cross hybrid variety of cow, whereas microbial contamination was the least in Jersey cow milk. Samples of C1 (Jersey cow variety showed presence of the highest amount of protein and carbohydrate content as compared to the others. Almost all the milk samples showed positive acid and alkaline phosphatase activity. Maximum acid phosphatase activity was observed in cross hybrid cow milk, whereas local cow milk exhibited the highest alkaline phosphatase activity. Phosphatase activity did not show any co-relationship with microbial population of the milk samples. Similarly, the protein and carbohydrate content of the samples did not have any significant impact on both acid and alkaline phosphatase activity.

Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

KAUST Repository

Xue, Zheng

2014-07-15

Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community. © 2014 © 2014 Taylor & Francis.

Microbial activity in subsurface samples before and during nitrate-enhanced bioremediation

International Nuclear Information System (INIS)

Thomas, J.M.; Gordy, V.R.; Bruce, C.L.; Ward, C.H.; Hutchins, S.R.; Sinclair, J.L.

1995-01-01

A study was conducted to determine the microbial activity at a site contaminated with JP-4 jet fuel before and during nitrate-enhanced bioremediation. Samples at three depths from six different locations were collected aseptically under anaerobic conditions before and during treatment. Cores were located in or close to the source of contamination, downgradient of the source, or outside the zone of contamination. Parameters for microbial characterization included (1) viable counts of aerobic heterotrophic, JP-4 degrading, and oligotrophic bacteria; (2) the most probable number (MPN) of aerobic and anaerobic protozoa; (3) the MPN of total denitrifiers; and (4) the MPN of denitrifiers in hydrocarbon-amended microcosms. The results indicate that the total number of denitrifiers increased by an order of magnitude during nitrate-enhanced bioremediation in most samples. The number of total heterotrophs and JP-4-degrading microorganisms growing aerobically also increased. In addition, the first anaerobic protozoa associated with hydrocarbon-contaminated subsurface materials were detected

The Earth Microbiome Project and modeling the planets microbial potential (Invited)

Science.gov (United States)

Gilbert, J. A.

2013-12-01

The understanding of Earth's climate and ecology requires multiscale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date. To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts to target a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental parameter gradients. The EMP captures the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample. To date we have processed >17,000 samples from 40 different biomes. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important functional processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet. This is essential if we are to develop economically sound strategies to be good stewards of our Earth. The EMP recognizes that environments are comprised of complex sets of interdependent parameters and that the development of useful predictive computational models of both terrestrial and atmospheric systems requires

Sampling natural biofilms: a new route to build efficient microbial anodes.

Science.gov (United States)

Erable, Benjamin; Roncato, Marie-Anne; Achouak, Wafa; Bergel, Alain

2009-05-01

Electrochemically active biofilms were constructed on graphite anodes under constant polarization at -0.1V vs saturated calomel reference (SCE) with 10 mM acetate as substrate. The reactors were inoculated with three different microbial samples that were drawn from exactly the same place in a French Atlantic coastal port (i) by scraping the biofilm that had formed naturally on the surface of a floating bridge, (ii) by taking marine sediments just under the floating bridge, and (iii) by taking nearby beach sand. Current densities of 2.0 A/m2 were reached using the biofilm sample as inoculum while only 0.4 A/m2 and 0.8 A/m2 were obtained using the underlying sediments and the beach sand, respectively. The structure of bacterial communities forming biofilms was characterized by denaturing gradient gel electrophoresis (DGGE) analysis, and revealed differences between samples with the increase in relative intensities of some bands and the appearance of others. Bacteria close related to Bacteroidetes, Halomonas, and Marinobacterium were retrieved only from the efficient EA-biofilms formed from natural biofilms, whereas, bacteria close related to Mesoflavibacter were predominant on biofilm formed from sediments. The marine biofilm was selected as the inoculum to further optimize the microbial anode. Epifluorescence microscopy and SEM confirmed that maintaining the electrode under constant polarization promoted rapid settlement of the electrode surface by a bacterial monolayer film. The microbial anode was progressively adapted to the consumption of acetate by three serial additions of substrate, thus improving the Coulombic efficiency of acetate consumption from 31 to 89%. The possible oxidation of sulfide played only a very small part in the current production and the biofilm was not able to oxidize hydrogen. Graphite proved to be more efficient than dimensionally stable anode (DSA) or stainless steel butthis result might be due to differences in the surface roughness

Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization method.

Science.gov (United States)

do Nascimento, Cássio; dos Santos, Janine Navarro; Pedrazzi, Vinícius; Pita, Murillo Sucena; Monesi, Nadia; Ribeiro, Ricardo Faria; de Albuquerque, Rubens Ferreira

2014-01-01

Molecular diagnosis methods have been largely used in epidemiological or clinical studies to detect and quantify microbial species that may colonize the oral cavity in healthy or disease. The preservation of genetic material from samples remains the major challenge to ensure the feasibility of these methodologies. Long-term storage may compromise the final result. The aim of this study was to evaluate the effect of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization. Saliva and supragingival biofilm were taken from 10 healthy subjects, aliquoted (n=364) and processed according to proposed protocols: immediate processing and processed after 2 or 4 weeks, and 6 or 12 months of storage at 4°C, -20°C and -80°C. Either total or individual microbial counts were recorded in lower values for samples processed after 12 months of storage, irrespective of temperatures tested. Samples stored up to 6 months at cold temperatures showed similar counts to those immediately processed. The microbial incidence was also significantly reduced in samples stored during 12 months in all temperatures. Temperature and time of oral samples storage have relevant impact in the detection and quantification of bacterial and fungal species by Checkerboard DNA-DNA hybridization method. Samples should be processed immediately after collection or up to 6 months if conserved at cold temperatures to avoid false-negative results. Copyright © 2013 Elsevier Ltd. All rights reserved.

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.

Directory of Open Access Journals (Sweden)

Ilma Tapio

Full Text Available Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

Microbial Indicator Profiling of Fresh Produce and Environmental Samples from Farms and Packing Facilities in Northern Mexico.

Science.gov (United States)

Heredia, Norma; Caballero, Cindy; Cárdenas, Carmen; Molina, Karina; García, Rafael; Solís, Luisa; Burrowes, Vanessa; Bartz, Faith E; de Aceituno, Anna Fabiszewski; Jaykus, Lee-Ann; García, Santos; Leon, Juan

2016-07-01

To compare microbiological indicator and pathogen contamination among different types of fresh produce and environmental samples along the production chain, 636 samples of produce (rinsates from cantaloupe melons, jalapeño peppers, and tomatoes) and environmental samples (rinsates from hands of workers, soil, and water) were collected at four successive steps in the production process (from the field before harvest through the packing facility) on 11 farms in northern Mexico during 2011 and 2012. Samples were assayed for enteric pathogens (Escherichia coli O157:H7, other Shiga toxigenic E. coli, Salmonella, and Listeria monocytogenes) and microbial indicators (coliforms, other E. coli strains, and Enterococcus spp.). Salmonella was the only pathogen detected; it was found in one preharvest jalapeño sample (detection limits: 0.0033 CFU/ml in produce and hand samples, 0.0013 CFU/ml in water, and 0.04 CFU/g in soil). Microbial indicator profiles for produce, worker hands, and soil from jalapeño and tomato farms were similar, but cantaloupe farm samples had higher indicator levels (P soil (indicators were significantly more prevalent (70 to 89% of samples were positive; P = 0.01 to 0.02), and geometric mean levels were higher (0.3 to 0.6 log CFU/100 ml) than those in cantaloupe farm water (32 to 38% of samples were positive, geometric mean indicators were present during all production steps, but prevalence and levels were generally highest at the final on-farm production step (the packing facility) (P type and production step can inform the design of effective approaches to mitigate microbial contamination.

Flow cytometric analysis of microbial contamination in food industry technological lines--initial study.

Science.gov (United States)

Józwa, Wojciech; Czaczyk, Katarzyna

2012-04-02

Flow cytometry constitutes an alternative for traditional methods of microorganisms identification and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a significant reduction of time required for analysis allowing monitoring of production processes and immediate reaction in case of contamination or any disruption occurs. Apart from the analysis of raw materials or products on different stages of manufacturing process, the flow cytometry seems to constitute an ideal tool for the assessment of microbial contamination on the surface of technological lines. In the present work samples comprising smears from 3 different surfaces of technological lines from fruit and vegetable processing company from Greater Poland were analysed directly with flow cytometer. The measured parameters were forward and side scatter of laser light signals allowing the estimation of microbial cell contents in each sample. Flow cytometric analysis of the surface of food industry production lines enable the preliminary evaluation of microbial contamination within few minutes from the moment of sample arrival without the need of sample pretreatment. The presented method of fl ow cytometric initial evaluation of microbial state of food industry technological lines demonstrated its potential for developing a robust, routine method for the rapid and labor-saving detection of microbial contamination in food industry.

A human monocytic NF-κB fluorescent reporter cell line for detection of microbial contaminants in biological samples.

Directory of Open Access Journals (Sweden)

Claire Battin

Full Text Available Sensing of pathogens by innate immune cells is essential for the initiation of appropriate immune responses. Toll-like receptors (TLRs, which are highly sensitive for various structurally and evolutionary conserved molecules derived from microbes have a prominent role in this process. TLR engagement results in the activation of the transcription factor NF-κB, which induces the expression of cytokines and other inflammatory mediators. The exquisite sensitivity of TLR signalling can be exploited for the detection of bacteria and microbial contaminants in tissue cultures and in protein preparations. Here we describe a cellular reporter system for the detection of TLR ligands in biological samples. The well-characterized human monocytic THP-1 cell line was chosen as host for an NF-ᴋB-inducible enhanced green fluorescent protein reporter gene. We studied the sensitivity of the resultant reporter cells for a variety of microbial components and observed a strong reactivity towards TLR1/2 and TLR2/6 ligands. Mycoplasma lipoproteins are potent TLR2/6 agonists and we demonstrate that our reporter cells can be used as reliable and robust detection system for mycoplasma contaminations in cell cultures. In addition, a TLR4-sensitive subline of our reporters was engineered, and probed with recombinant proteins expressed in different host systems. Bacterially expressed but not mammalian expressed proteins induced strong reporter activity. We also tested proteins expressed in an E. coli strain engineered to lack TLR4 agonists. Such preparations also induced reporter activation in THP-1 cells highlighting the importance of testing recombinant protein preparations for microbial contaminations beyond endotoxins. Our results demonstrate the usefulness of monocytic reporter cells for high-throughput screening for microbial contaminations in diverse biological samples, including tissue culture supernatants and recombinant protein preparations. Fluorescent reporter

Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

Science.gov (United States)

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-03-05

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

KAUST Repository

Xue, Zheng; Lu, Huijie; Liu, Wen-Tso

2014-01-01

Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses

A novel derivation of a within-batch sampling plan based on a Poisson-gamma model characterising low microbial counts in foods.

Science.gov (United States)

Gonzales-Barron, Ursula; Zwietering, Marcel H; Butler, Francis

2013-02-01

This study proposes a novel step-wise methodology for the derivation of a sampling plan by variables for food production systems characterised by relatively low concentrations of the inspected microorganism. After representing the universe of contaminated batches by modelling the between-batch and within-batch variability in microbial counts, a tolerance criterion defining batch acceptability (i.e., up to a tolerance percentage of the food units having microbial concentrations lower or equal to a critical concentration) is established to delineate a limiting quality contour that separates satisfactory from unsatisfactory batches. The problem consists then of finding the optimum decision criterion - arithmetic mean of the analytical results (microbiological limit, m(L)) and the sample size (n) - that satisfies a pre-defined level of confidence measured on the samples' mean distributions from all possible true within-batch distributions. This is approached by obtaining decision landscape curves representing collectively the conditional and joint producer's and consumer's risks at different microbiological limits along with confidence intervals representing uncertainty due to the propagated between-batch variability. Whilst the method requires a number of risk management decisions to be made such as the objective of the sampling plan (GMP-based or risk-based), the modality of derivation, the tolerance criterion or level of safety, and the statistical level of confidence, the proposed method can be used when past monitoring data are available so as to produce statistically-sound dynamic sampling plans with optimised efficiency and discriminatory power. For the illustration of Enterobacteriaceae concentrations on Irish sheep carcasses, a sampling regime of n=10 and m(L)=17.5CFU/cm(2) is recommended to ensure that the producer has at least a 90% confidence of accepting a satisfactory batch whilst the consumer at least a 97.5% confidence that a batch will not be

Microbial Fluid-Rock Interactions in Chalk Samples and Salinity Factor in Divalent Ca2+ ions Release for Microbial Enhanced Oil Recovery Purposes

DEFF Research Database (Denmark)

Jimoh, Ismaila Adetunji; Rudyk, Svetlana Nikolayevna; Søgaard, Erik Gydesen

2011-01-01

In this study, laboratory experiments were performed on chalk samples from Danish sector of the North Sea to study microbial fluid-rock interactions with carbonate rock and to evaluate the dissolution of rock matrix (CaCO3). Result showed that the average concentration of Ca2+ ions after microbia...

Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

Directory of Open Access Journals (Sweden)

Koichi Fujie

2012-03-01

Full Text Available Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE and ultra performance liquid chromatography (UPLC method for the analysis of bacterial respiratory quinones (RQ in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA detector was successfully applied to the simultaneous determination of ubiquinones (UQ and menaquinones (MK without tedious pretreatment. Supercritical carbon dioxide (scCO2 extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost and biological samples (swine and Japanese quail feces.

30 CFR 71.201 - Sampling; general requirements.

Science.gov (United States)

2010-07-01

... MINES Sampling Procedures § 71.201 Sampling; general requirements. (a) Each operator shall take... required by this part with a sampling device approved by the Secretary and the Secretary of Health and Human Services under part 74 (Coal Mine Dust Personal Sampler Units) of this title. (b) Sampling devices...

The electric picnic: synergistic requirements for exoelectrogenic microbial communities

KAUST Repository

Kiely, Patrick D; Regan, John M; Logan, Bruce E

2011-01-01

(BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation

The Microbial DNA Index System (MiDIS): A tool for microbial pathogen source identification

Energy Technology Data Exchange (ETDEWEB)

Velsko, S. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2010-08-09

The microbial DNA Index System (MiDIS) is a concept for a microbial forensic database and investigative decision support system that can be used to help investigators identify the sources of microbial agents that have been used in a criminal or terrorist incident. The heart of the proposed system is a rigorous method for calculating source probabilities by using certain fundamental sampling distributions associated with the propagation and mutation of microbes on disease transmission networks. This formalism has a close relationship to mitochondrial and Y-chromosomal human DNA forensics, and the proposed decision support system is somewhat analogous to the CODIS and SWGDAM mtDNA databases. The MiDIS concept does not involve the use of opportunistic collections of microbial isolates and phylogenetic tree building as a basis for inference. A staged approach can be used to build MiDIS as an enduring capability, beginning with a pilot demonstration program that must meet user expectations for performance and validation before evolving into a continuing effort. Because MiDIS requires input from a a broad array of expertise including outbreak surveillance, field microbial isolate collection, microbial genome sequencing, disease transmission networks, and laboratory mutation rate studies, it will be necessary to assemble a national multi-laboratory team to develop such a system. The MiDIS effort would lend direction and focus to the national microbial genetics research program for microbial forensics, and would provide an appropriate forensic framework for interfacing to future national and international disease surveillance efforts.

The Indigo V Indian Ocean Expedition: a prototype for citizen microbial oceanography

DEFF Research Database (Denmark)

Lauro, Frederico; Senstius, Svend Jacob; Cullen, Jay

2014-01-01

Microbial Oceanography has long been an extremely expensive discipline, requiring ship time for sample collection and thereby economically constraining the number of samples collected. This is especially true for under-sampled water bodies such as the Indian Ocean. Specialised scientific equipmen...

Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome.

Science.gov (United States)

Andrade, Ana Camila; Fróes, Adriana; Lopes, Fabyano Álvares Cardoso; Thompson, Fabiano L; Krüger, Ricardo Henrique; Dinsdale, Elizabeth; Bruce, Thiago

2017-07-01

Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and

Trace Metal Requirements for Microbial Enzymes Involved in the Production and Consumption of Methane and Nitrous Oxide

Science.gov (United States)

Glass, Jennifer B.; Orphan, Victoria J.

2011-01-01

Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO2 cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH4), and nitrous oxide (N2O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH4 and N2O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH4 oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N2O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N2O reductase, the only known enzyme capable of microbial N2O conversion to N2, have only been found in classical denitrifiers. Accumulation of N2O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N2O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide

Microbial diversity in European and South American spacecraft assembly clean rooms

Science.gov (United States)

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

Quantitative comparison of the in situ microbial communities in different biomes

Energy Technology Data Exchange (ETDEWEB)

White, D.C. [Tennessee Univ., Knoxville, TN (United States)]|[Oak Ridge National Lab., TN (United States); Ringelberg, D.B.; Palmer, R.J. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

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 repeatedly 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/

30 CFR 70.201 - Sampling; general requirements.

Science.gov (United States)

2010-07-01

...; general requirements. (a) Each operator shall take respirable dust samples of the concentration of respirable dust in the active workings of the mine as required by this part with a sampling device approved... Personal Sampler Units) of this title. (b) Sampling devices shall be worn or carried directly to and from...

Childhood microbial keratitis

Directory of Open Access Journals (Sweden)

Abdullah G Al Otaibi

2012-01-01

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

Microbial flora analysis for the degradation of beta-cypermethrin.

Science.gov (United States)

Qi, Zhang; Wei, Zhang

2017-03-01

In the Xinjiang region of Eurasia, sustained long-term and continuous cropping of cotton over a wide expanse of land is practiced, which requires application of high levels of pyrethroid and other classes of pesticides-resulting in high levels of pesticide residues in the soil. In this study, soil samples were collected from areas of long-term continuous cotton crops with the aim of obtaining microbial resources applicable for remediation of pyrethroid pesticide contamination suitable for the soil type and climate of that area. Soil samples were first used to culture microbial flora capable of degrading beta-cypermethrin using an enrichment culture method. Structural changes and ultimate microbial floral composition during enrichment were analyzed by high-throughput sequencing. Four strains capable of degrading beta-cypermethrin were isolated and preliminarily classified. Finally, comparative rates and speeds of degradation of beta-cypermethrin between relevant microbial flora and single strains were determined. After continuous subculture for 3 weeks, soil sample microbial flora formed a new type of microbial flora by rapid succession, which showed stable growth by utilizing beta-cypermethrin as the sole carbon source (GXzq). This microbial flora mainly consisted of Pseudomonas, Hyphomicrobium, Dokdonella, and Methyloversatilis. Analysis of the microbial flora also permitted separation of four additional strains; i.e., GXZQ4, GXZQ6, GXZQ7, and GXZQ13 that, respectively, belonged to Streptomyces, Enterobacter, Streptomyces, and Pseudomonas. Under culture conditions of 37 °C and 180 rpm, the degradation rate of beta-cypermethrin by GXzq was as high as 89.84% within 96 h, which exceeded that achieved by the single strains GXZQ4, GXZQ6, GXZQ7, and GXZQ13 and their derived microbial flora GXh.

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

Science.gov (United States)

Pérez-Losada, Marcos; Crandall, Keith A; Freishtat, Robert J

2016-06-16

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity. We used targeted 16S rRNA MiSeq sequencing and two different sampling strategies [nasal washes (NW) and nasal brushes (NB)] to characterize the nasopharyngeal microbiota in 30 asthmatic children. Nasal brushing is more abrasive than nasal washing and targeted the inner portion of the inferior turbinate. This region is expected to be different from other nasal microenvironments. Nasal washing is not spatially specific. Our 30 × 2 nasal microbiomes generated 1,474,497 sequences, from which we identified an average of 157 and 186 OTUs per sample in the NW and NB groups, respectively. Microbiotas from NB showed significantly higher alpha-diversity than microbiotas from NW. Similarly, both nasal microbiotas were distinct from each other (PCoA) and significantly differed in their community composition and abundance in at least 9 genera (effective size ≥1 %). Nasopharyngeal microenvironments in asthmatic children contain microbiotas with different diversity and structure. Nasal washes and brushes capture that diversity differently. Future microbial studies of the nasopharynx need to be aware of potential spatial variation (biogeography).

Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India.

Science.gov (United States)

Dhasarathan, P; Theriappan, P; Ashokraja, C

2010-03-01

Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 10(4) CFU/g and 5.6 × 10(4) CFU/ml respectively), compared to the THB of cultivable area soil and water samples (98 × 10(7) CFU/g and 38.6 × 10(7) CFU/ml). The generic composition the THB of the pyrochemicals exposed samples too exhibited considerable change compared to other samples. Pseudomonas sp. was the predominant one (41.6%) followed by Achromobacter sp. (25%) in pyrochemical exposed soil and Pseudomonas sp. was the predominant one (25%) in pyrochemical exposed water samples followed by Bacillus sp. (25%) and Micrococcus sp. (16.6%). It was observed that Cornybacterium sp. and Micrococcus sp. were absent completely in pyrochemical exposed soil and Achromobacter sp. was missing in the pyrochemical exposed water samples, which were present in the other samples. The outcome of this study clearly demonstrates that pollutants such as chemicals used in pyrotechniques affect the microbial biodiversity and suitable measures have to be taken to control the pollution level and to save biodiversity.

Genomic Sequencing of Single Microbial Cells from Environmental Samples

Energy Technology Data Exchange (ETDEWEB)

Ishoey, Thomas; Woyke, Tanja; Stepanauskas, Ramunas; Novotny, Mark; Lasken, Roger S.

2008-02-01

Recently developed techniques allow genomic DNA sequencing from single microbial cells [Lasken RS: Single-cell genomic sequencing using multiple displacement amplification, Curr Opin Microbiol 2007, 10:510-516]. Here, we focus on research strategies for putting these methods into practice in the laboratory setting. An immediate consequence of single-cell sequencing is that it provides an alternative to culturing organisms as a prerequisite for genomic sequencing. The microgram amounts of DNA required as template are amplified from a single bacterium by a method called multiple displacement amplification (MDA) avoiding the need to grow cells. The ability to sequence DNA from individual cells will likely have an immense impact on microbiology considering the vast numbers of novel organisms, which have been inaccessible unless culture-independent methods could be used. However, special approaches have been necessary to work with amplified DNA. MDA may not recover the entire genome from the single copy present in most bacteria. Also, some sequence rearrangements can occur during the DNA amplification reaction. Over the past two years many research groups have begun to use MDA, and some practical approaches to single-cell sequencing have been developed. We review the consensus that is emerging on optimum methods, reliability of amplified template, and the proper interpretation of 'composite' genomes which result from the necessity of combining data from several single-cell MDA reactions in order to complete the assembly. Preferred laboratory methods are considered on the basis of experience at several large sequencing centers where >70% of genomes are now often recovered from single cells. Methods are reviewed for preparation of bacterial fractions from environmental samples, single-cell isolation, DNA amplification by MDA, and DNA sequencing.

40 CFR 158.2171 - Experimental use permit microbial pesticides product analysis data requirements table.

Science.gov (United States)

2010-07-01

... conducted at the point in the production process after which there would be no potential for microbial... Identity R MP EP -- 885.1200 Manufacturing process R TGAI and MP TGAI and EP 1, 2 Deposition of a sample in... -- 830.6313 Stability to normal and elevated temperatures, metals and metal ions R TGAI TGAI -- 830.6317...

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

Science.gov (United States)

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

Erratum: potential microbial contamination during sampling of permafrost soil assessed by tracers

DEFF Research Database (Denmark)

Bang-Andreasen, Toke; Schostag, Morten Dencker; Priemé, Anders

2017-01-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial b...

Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

Science.gov (United States)

Saingam, Prakit; Li, Bo; Yan, Tao

2018-06-01

DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

30 CFR 75.336 - Sampling and monitoring requirements.

Science.gov (United States)

2010-07-01

... concentration of other sampling locations in the sealed area and other required information. Before miners... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Sampling and monitoring requirements. 75.336... SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Ventilation § 75.336 Sampling and...

Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

OpenAIRE

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-01-01

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysi...

Treatability studies on different refinery wastewater samples using high-throughput microbial electrolysis cells (MECs)

KAUST Repository

Ren, Lijiao; Siegert, Michael; Ivanov, Ivan; Pisciotta, John M.; Logan, Bruce E.

2013-01-01

High-throughput microbial electrolysis cells (MECs) were used to perform treatability studies on many different refinery wastewater samples all having appreciably different characteristics, which resulted in large differences in current generation. A de-oiled refinery wastewater sample from one site (DOW1) produced the best results, with 2.1±0.2A/m2 (maximum current density), 79% chemical oxygen demand removal, and 82% headspace biological oxygen demand removal. These results were similar to those obtained using domestic wastewater. Two other de-oiled refinery wastewater samples also showed good performance, with a de-oiled oily sewer sample producing less current. A stabilization lagoon sample and a stripped sour wastewater sample failed to produce appreciable current. Electricity production, organics removal, and startup time were improved when the anode was first acclimated to domestic wastewater. These results show mini-MECs are an effective method for evaluating treatability of different wastewaters. © 2013 Elsevier Ltd.

Treatability studies on different refinery wastewater samples using high-throughput microbial electrolysis cells (MECs)

KAUST Repository

Ren, Lijiao

2013-05-01

High-throughput microbial electrolysis cells (MECs) were used to perform treatability studies on many different refinery wastewater samples all having appreciably different characteristics, which resulted in large differences in current generation. A de-oiled refinery wastewater sample from one site (DOW1) produced the best results, with 2.1±0.2A/m2 (maximum current density), 79% chemical oxygen demand removal, and 82% headspace biological oxygen demand removal. These results were similar to those obtained using domestic wastewater. Two other de-oiled refinery wastewater samples also showed good performance, with a de-oiled oily sewer sample producing less current. A stabilization lagoon sample and a stripped sour wastewater sample failed to produce appreciable current. Electricity production, organics removal, and startup time were improved when the anode was first acclimated to domestic wastewater. These results show mini-MECs are an effective method for evaluating treatability of different wastewaters. © 2013 Elsevier Ltd.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Science.gov (United States)

Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

Influence of acid mine drainage on microbial communities in stream and groundwater samples at Guryong Mine, South Korea

Science.gov (United States)

Kim, Jaisoo; Koo, So-Yeon; Kim, Ji-Young; Lee, Eun-Hee; Lee, Sang-Don; Ko, Kyung-Seok; Ko, Dong-Chan; Cho, Kyung-Suk

2009-10-01

The effects of acid mine drainage (AMD) in a stream and groundwater near an abandoned copper mine were characterized by physicochemical properties, bacterial community structure using denaturing gel gradient electrophoresis (DGGE), and microbial activity/diversity using Ecoplate technique. Based on DGGE fingerprints, the eubacterial community structures grouped into the stream water (GRS1, GRS2 and GRS3) and groundwater samples (GW1 and GW2), apparently based on differences in water temperature and the concentrations of dissolved oxygen, nitrate and sulfate. The most highly AMD-contaminated sample (GRS1) had additional α-Proteobacteria whereas the groundwater samples included additional β-Proteobacteria, suggesting the development of populations resistant to AMD toxicity under aerobic and anaerobic conditions, respectively. Community level physiological activities on the 31 Ecoplate substrates suggested that the activities decreased with increasing concentrations of sulfate and heavy metals derived from AMD. The Shannon index showed that microbial diversity was greatest in GRS2, and lowest in GRS1, and was probably related to the level of AMD.

Microbial profile of a kefir sample preparations: grains in natura and lyophilized and fermented suspension

Directory of Open Access Journals (Sweden)

Rafaela Strada de Oliveira Bergmann

2010-12-01

Full Text Available Probiotics are supplementary foods developed by microbial strains that improve animal health beyond basic nutrition. Probiotics are consumed orally, regardless of being considered as normal inhabitants of the intestines, able to survive in enzimatic and biliary secretions. Kefir is a probiotic originated from the old continent, fermented by several bacteria and yeasts, encapsulated in a polyssacharide matrix, and resembles jelly grains. Kefir is also presented as its sourish product both in sugary or milky suspensions containing vitamins, aminoacids, peptides, carbohydrates, ethanol, and volatile compounds. Kefir is known to have a diverse microbial content depending on the country and fermentative substrates, which cause distinct probiotic effects. In this sense, the purpose of this work was to isolate, identify, and quantify the microbial content of a native sugary kefir sample (fermented suspension and lyophilized natural grains. Serial dilutions were plated on Rogosa agar (AR and De Man, Rogosa and Sharpe (MRS, for Lactobacillus; Brain Heart Infusion (BHI, for total bacteria; Sabouraud-Dextrose-Agar (SDA, for yeasts and filamentous fungi; Thioglycolate Agar (TA, for Streptococcus, Acetobacteria and Leuconostoc; and Coconut Water Agar (CWA, and CWA supplemented with yeast extract (CWAY, for various genera. Genera and species for all strains were identified through biochemical reactions and specific API systems. The microbial profile of kefir was different from other sources of grains despite the presence of similar microorganisms and others which have not been reported yet. The data obtained with the CWA and CWAE media suggest that both substrates are alternative and salutary media for culture of kefir strains.

Air sampling methods to evaluate microbial contamination in operating theatres: results of a comparative study in an orthopaedics department.

Science.gov (United States)

Napoli, C; Tafuri, S; Montenegro, L; Cassano, M; Notarnicola, A; Lattarulo, S; Montagna, M T; Moretti, B

2012-02-01

To evaluate the level of microbial contamination of air in operating theatres using active [i.e. surface air system (SAS)] and passive [i.e. index of microbial air contamination (IMA) and nitrocellulose membranes positioned near the wound] sampling systems. Sampling was performed between January 2010 and January 2011 in the operating theatre of the orthopaedics department in a university hospital in Southern Italy. During surgery, the mean bacterial loads recorded were 2232.9 colony-forming units (cfu)/m(2)/h with the IMA method, 123.2 cfu/m(3) with the SAS method and 2768.2 cfu/m(2)/h with the nitrocellulose membranes. Correlation was found between the results of the three methods. Staphylococcus aureus was detected in 12 of 60 operations (20%) with the membranes, five (8.3%) operations with the SAS method, and three operations (5%) with the IMA method. Use of nitrocellulose membranes placed near a wound is a valid method for measuring the microbial contamination of air. This method was more sensitive than the IMA method and was not subject to any calibration bias, unlike active air monitoring systems. Copyright © 2011 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems.

Science.gov (United States)

Jacxsens, L; Kussaga, J; Luning, P A; Van der Spiegel, M; Devlieghere, F; Uyttendaele, M

2009-08-31

A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the most emerging challenges is to assess the performance of a present FSMS. The objective of this work is to explain the development of a Microbial Assessment Scheme (MAS) as a tool for a systematic analysis of microbial counts in order to assess the current microbial performance of an implemented FSMS. It is assumed that low numbers of microorganisms and small variations in microbial counts indicate an effective FSMS. The MAS is a procedure that defines the identification of critical sampling locations, the selection of microbiological parameters, the assessment of sampling frequency, the selection of sampling method and method of analysis, and finally data processing and interpretation. Based on the MAS assessment, microbial safety level profiles can be derived, indicating which microorganisms and to what extent they contribute to food safety for a specific food processing company. The MAS concept is illustrated with a case study in the pork processing industry, where ready-to-eat meat products are produced (cured, cooked ham and cured, dried bacon).

Air sampling procedures to evaluate microbial contamination: a comparison between active and passive methods in operating theatres.

Science.gov (United States)

Napoli, Christian; Marcotrigiano, Vincenzo; Montagna, Maria Teresa

2012-08-02

Since air can play a central role as a reservoir for microorganisms, in controlled environments such as operating theatres regular microbial monitoring is useful to measure air quality and identify critical situations. The aim of this study is to assess microbial contamination levels in operating theatres using both an active and a passive sampling method and then to assess if there is a correlation between the results of the two different sampling methods. The study was performed in 32 turbulent air flow operating theatres of a University Hospital in Southern Italy. Active sampling was carried out using the Surface Air System and passive sampling with settle plates, in accordance with ISO 14698. The Total Viable Count (TVC) was evaluated at rest (in the morning before the beginning of surgical activity) and in operational (during surgery). The mean TVC at rest was 12.4 CFU/m3 and 722.5 CFU/m2/h for active and passive samplings respectively. The mean in operational TVC was 93.8 CFU/m3 (SD = 52.69; range = 22-256) and 10496.5 CFU/m2/h (SD = 7460.5; range = 1415.5-25479.7) for active and passive samplings respectively. Statistical analysis confirmed that the two methods correlate in a comparable way with the quality of air. It is possible to conclude that both methods can be used for general monitoring of air contamination, such as routine surveillance programs. However, the choice must be made between one or the other to obtain specific information.

Microbial Contamination of Pastry Cream: Evidence from Iran

Directory of Open Access Journals (Sweden)

Mohamadreza Pajohi-alamoti

2016-07-01

Full Text Available Background & Aims of the Study: Given the importance of microbial contamination in creating food-borne diseases, this study was conducted to assess level of microbial contamination of pastry creams in Hamedan, Iran. Materials and Methods: Totally, 80 samples were randomly collected from the confectioneries and analyzed for microbial contamination according to Iranian national standard microbial tests. Results: Data indicated that 49 (61.2% samples were contaminated, mostly comprised of Coliforms (92.5%. Moreover, the infection was seen to be higher in jelly roll compared to puff pastry. Yeast contamination was about 82.5 percent, which could accelerate the decay of such products. However, yeast contamination of puff pastries was higher than jelly roll. The microbial contamination with Staphylococcus aureus, total viable count and molds were 57.5%, 35% and 37.5%; respectively. Conclusion: Nevertheless, Salmonella, Escherichia coli and Listeria monocytogenes were not found in any of the samples. Abundance of microbial contamination in the puff pastry samples might put consumer’s health at risk.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Directory of Open Access Journals (Sweden)

D.C.A. Leite

2014-01-01

Full Text Available Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit, the PowerSoil® DNA Isolation Kit (PS kit and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit, for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

EVA Suit Microbial Leakage Investigation

Data.gov (United States)

National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

40 CFR 141.174 - Filtration sampling requirements.

Science.gov (United States)

2010-07-01

... PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Filtration and Disinfection... water system subject to the requirements of this subpart that provides conventional filtration treatment... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Filtration sampling requirements. 141...

Non-tuberculous mycobacteria and microbial populations in drinking water distribution systems

Directory of Open Access Journals (Sweden)

Rossella Briancesco

2010-01-01

Full Text Available Data on the occurrence of non-tuberculous mycobacteria (NTM, in parallel with those obtained for bacterial indicators and amoebae, are presented with the aim to collect information on the spread of NTM in drinking water distribution systems in Italy. Samples were collected from taps of hospitals and households in Central and Southern Italy. The concentration values obtained for the more traditional microbial parameters complied with the mandatory requirements for drinking water. Conversely, moderate-to-high microbial loads (till 300 CFU/L were observed for the NTM. Positive samples were obtained from 62% of the investigated water samples. Analogous results were observed for amoebae showing a higher percentage of positive samples (76%. In terms of public health, the presence of mycobacteria in water distribution systems may represent a potential risk especially for vulnerable people such as children, the elderly or immunocompromised individuals.

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

Science.gov (United States)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

Air sampling procedures to evaluate microbial contamination: a comparison between active and passive methods in operating theatres

Directory of Open Access Journals (Sweden)

Napoli Christian

2012-08-01

Full Text Available Abstract Background Since air can play a central role as a reservoir for microorganisms, in controlled environments such as operating theatres regular microbial monitoring is useful to measure air quality and identify critical situations. The aim of this study is to assess microbial contamination levels in operating theatres using both an active and a passive sampling method and then to assess if there is a correlation between the results of the two different sampling methods. Methods The study was performed in 32 turbulent air flow operating theatres of a University Hospital in Southern Italy. Active sampling was carried out using the Surface Air System and passive sampling with settle plates, in accordance with ISO 14698. The Total Viable Count (TVC was evaluated at rest (in the morning before the beginning of surgical activity and in operational (during surgery. Results The mean TVC at rest was 12.4 CFU/m3 and 722.5 CFU/m2/h for active and passive samplings respectively. The mean in operational TVC was 93.8 CFU/m3 (SD = 52.69; range = 22-256 and 10496.5 CFU/m2/h (SD = 7460.5; range = 1415.5-25479.7 for active and passive samplings respectively. Statistical analysis confirmed that the two methods correlate in a comparable way with the quality of air. Conclusion It is possible to conclude that both methods can be used for general monitoring of air contamination, such as routine surveillance programs. However, the choice must be made between one or the other to obtain specific information.

Microbial Forensics: A Scientific Assessment

Energy Technology Data Exchange (ETDEWEB)

Keim, Paul

2003-02-17

procedures and training to meet these initial challenges so as minimize disturbance of the evidence. While epidemiology and forensics are similar sciences with similar goals when applied to biocrimes, forensics has additional and more stringent requirements. Maintaining a chain of custody on evidentiary samples is one example of an extra requirement imposed on an investigation of a biocrime. Another issue is the intent in microbial forensics to identify a bioattack organism in greatest detail. If possible, forensic investigations will strive to identify the precise strain and substrain, rather than just to the species level, which might be sufficient in an epidemiological investigation. Although multiple groups have developed lists of bioterrorism target pathogens, these lists are too narrow. An expansion of microorganisms relevant to food and water threats should be considered. Computerized networks should be established to track infectious disease outbreaks in real time. These systems could alert public health and agricultural officials to the existence of a potential bioattack earlier than simply waiting for a report of a suspicious cluster of similar patients. Once a biocrime is suspected, a wide variety of methods are available to identify the microorganism used in the bioattack and to analyze features that might lead to the source of the event. A multi-pronged approach to such an investigation may be preferable, using many available methods-ranging from genomics to sequencing to physiology to analysis of substances in the sample. Microbial forensics will be most effective if there is sufficient basic scientific information concerning microbial genetics, evolution, physiology, and ecology. Strain subtyping analysis will be difficult to interpret if we do not understand some of the basic evolutionary mechanisms and population diversity of pathogens. Phenotypic features associated with evidentiary pathogens also may provide investigative leads, but full exploitation of

Microbial electrode sensor for alcohols

Energy Technology Data Exchange (ETDEWEB)

Hikuma, M [Ajinomoto Co., Inc., Kawasaki, Japan; Kubo, T; Yasuda, T; Karube, I; Suzuki, S

1979-10-01

A microbial electrode consisting of immobilized microorganisms, a gas permeable Teflon membrane, and an oxygen electrode was prepared for the continuous determination of methyl and ethyl alcohols. Immobilized Trichosporon brassicae was employed for a microbial electrode sensor for ethyl alcohol. When a sample solution containing ethyl alcohol was injected into a microbial electrode system, the current of the electrode decreased markedly with time until a steady state was reached. The response time was within 10 min by the steady state method and within 6 min by the pulse method. A linear relationship was observed between the current decrease and the concentration of ethyl alcohol below 22.5 mg/liter. The current was reproducible within +- 6% of the relative error when a sample solution containing 16.5 mg/liter ethyl alcohol. The standard deviation was 0.5 mg/liter in 40 experiments. The selectivity of the microbial electrode sensor for ethyl alcohol was satisfactory. The microbial electrode sensor was applied to a fermentation broth of yeasts and satisfactory comparative results were obtained (correlation coefficient 0.98). The current output of the microbial electrode sensor was almost constant for more than three weeks and 2100 assays. A microbial electrode sensor using immobilized bacteria for methyl alcohol was also described.

Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes

International Nuclear Information System (INIS)

Dunn, Warwick B

2008-01-01

The functional levels of biological cells or organisms can be separated into the genome, transcriptome, proteome and metabolome. Of these the metabolome offers specific advantages to the investigation of the phenotype of biological systems. The investigation of the metabolome (metabolomics) has only recently appeared as a mainstream scientific discipline and is currently developing rapidly for the study of microbial, plant and mammalian metabolomes. The metabolome pipeline or workflow encompasses the processes of sample collection and preparation, collection of analytical data, raw data pre-processing, data analysis and data storage. Of these processes the collection of analytical data will be discussed in this review with specific interest shown in the application of mass spectrometry in the metabolomics pipeline. The current developments in mass spectrometry platforms (GC–MS, LC–MS, DIMS and imaging MS) and applications of specific interest will be highlighted. The current limitations of these platforms and applications will be discussed with areas requiring further development also highlighted. These include the detectable coverage of the metabolome, the identification of metabolites and the process of converting raw data to biological knowledge. (review article)

40 CFR 141.22 - Turbidity sampling and analytical requirements.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Turbidity sampling and analytical... § 141.22 Turbidity sampling and analytical requirements. The requirements in this section apply to... the water distribution system at least once per day, for the purposes of making turbidity measurements...

Critique of Hanford Waste Vitrification Plant off-gas sampling requirements

International Nuclear Information System (INIS)

Goles, R.W.

1996-03-01

Off-gas sampling and monitoring activities needed to support operations safety, process control, waste form qualification, and environmental protection requirements of the Hanford Waste Vitrification Plant (HWVP) have been evaluated. The locations of necessary sampling sites have been identified on the basis of plant requirements, and the applicability of Defense Waste Processing Facility (DWPF) reference sampling equipment to these HWVP requirements has been assessed for all sampling sites. Equipment deficiencies, if present, have been described and the bases for modifications and/or alternative approaches have been developed

Evaluating the U.S. Food Safety Modernization Act Produce Safety Rule Standard for Microbial Quality of Agricultural Water for Growing Produce

NARCIS (Netherlands)

Havelaar, Arie H; Vazquez, Kathleen M; Topalcengiz, Zeynal; Muñoz-Carpena, Rafael; Danyluk, Michelle D

2017-01-01

The U.S. Food and Drug Administration (FDA) has defined standards for the microbial quality of agricultural surface water used for irrigation. According to the FDA produce safety rule (PSR), a microbial water quality profile requires analysis of a minimum of 20 samples for Escherichia coli over 2 to

Research of radiation-resistant microbial organisms

Energy Technology Data Exchange (ETDEWEB)

Kim, Dongho; Lim, Sangyong; Joe, Minho; Park, Haejoon; Song, Hyunpa; Im, Seunghun; Kim, Haram; Kim, Whajung; Choi, Jinsu; Park, Jongchun

2012-01-15

Many extremophiles including radiation-resistant bacteria Deinococcus radiodurans have special characteristics such as novel enzymes and physiological active substances different from known biological materials and are being in the spotlight of biotechnology science. In this research, basic technologies for the production of new genetic resources and microbial strains by a series of studies in radiation-resistant microbial organisms were investigated and developed. Mechanisms required for radiation-resistant in Deinococcus radiodurans were partly defined by analyzing the function of dinB, pprI, recG, DRA{sub 0}279, pprM, and two-component signal transduction systems. To apply genetic resource and functional materials from Deinococcus species, omics analysis in response to cadmium, construction of macroscopic biosensor, and characterization of carotenoids and chaperon protein were performed. Additionally, potential use of D. geothermalis in monosaccharide production from non-biodegradable plant materials was evaluated. Novel radiation resistant yeasts and bacteria were isolated and identified from environmental samples to obtain microbial and genomic resources. An optimal radiation mutant breeding method was set up for efficient and rapid isolation of target microbial mutants. Furthermore, an efficient ethanol producing mutant strain with high production yield and productivity was constructed using the breeding method in collaboration with Korea Research Institute of Bioscience and Biotechnology. Three Deinococcal bioindicators for radiation dosage confirmation after radiation sterilization process were developed. These results provide a comprehensive information for novel functional genetic elements, enzymes, and physiological active substances production or application. Eventually, industrial microbial cell factories based on radiation resistant microbial genomes can be developed and the technologies can be diffused to bioindustry continuously by this project.

Research of radiation-resistant microbial organisms

International Nuclear Information System (INIS)

Kim, Dongho; Lim, Sangyong; Joe, Minho; Park, Haejoon; Song, Hyunpa; Im, Seunghun; Kim, Haram; Kim, Whajung; Choi, Jinsu; Park, Jongchun

2012-01-01

Many extremophiles including radiation-resistant bacteria Deinococcus radiodurans have special characteristics such as novel enzymes and physiological active substances different from known biological materials and are being in the spotlight of biotechnology science. In this research, basic technologies for the production of new genetic resources and microbial strains by a series of studies in radiation-resistant microbial organisms were investigated and developed. Mechanisms required for radiation-resistant in Deinococcus radiodurans were partly defined by analyzing the function of dinB, pprI, recG, DRA 0 279, pprM, and two-component signal transduction systems. To apply genetic resource and functional materials from Deinococcus species, omics analysis in response to cadmium, construction of macroscopic biosensor, and characterization of carotenoids and chaperon protein were performed. Additionally, potential use of D. geothermalis in monosaccharide production from non-biodegradable plant materials was evaluated. Novel radiation resistant yeasts and bacteria were isolated and identified from environmental samples to obtain microbial and genomic resources. An optimal radiation mutant breeding method was set up for efficient and rapid isolation of target microbial mutants. Furthermore, an efficient ethanol producing mutant strain with high production yield and productivity was constructed using the breeding method in collaboration with Korea Research Institute of Bioscience and Biotechnology. Three Deinococcal bioindicators for radiation dosage confirmation after radiation sterilization process were developed. These results provide a comprehensive information for novel functional genetic elements, enzymes, and physiological active substances production or application. Eventually, industrial microbial cell factories based on radiation resistant microbial genomes can be developed and the technologies can be diffused to bioindustry continuously by this project

40 CFR 761.130 - Sampling requirements.

Science.gov (United States)

2010-07-01

... 761.130 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL... sampling scheme is that it is designed to characterize the degree of contamination within the entire.... For this purpose, the numerical level of cleanup required for spills cleaned in accordance with § 761...

Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

Science.gov (United States)

Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

2015-12-01

Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

Signature of Microbial Dysbiosis in Periodontitis.

Science.gov (United States)

Meuric, Vincent; Le Gall-David, Sandrine; Boyer, Emile; Acuña-Amador, Luis; Martin, Bénédicte; Fong, Shao Bing; Barloy-Hubler, Frederique; Bonnaure-Mallet, Martine

2017-07-15

applied to a subgingival sample set with well-defined clinical data, the method showed a strong correlation between the dysbiosis ratio, as well as a simplified ratio ( Porphyromonas , Treponema , and Tannerella to Rothia and Corynebacterium ), and pocket depth. Microbial analysis of chronic periodontitis can be correlated with the pocket depth through specific signatures for microbial dysbiosis. IMPORTANCE Defining microbiota typical of oral health or chronic periodontitis is difficult. The evaluation of periodontal disease is currently based on probing of the periodontal pocket. However, the status of pockets "on the mend" or sulci at risk of periodontitis cannot be addressed solely through pocket depth measurements or current microbiological tests available for practitioners. Thus, a more specific microbiological measure of dysbiosis could help in future diagnoses of periodontitis. In this work, data from different studies were pooled, to improve the accuracy of the results. However, analysis of multiple species from different studies intensified the bacterial network and complicated the search for reproducible microbial signatures. Despite the use of different methods in each study, investigation of the microbiota at the genus level showed that some genera were prevalent (up to 95% of the samples) in health or disease, allowing the calculation of bacterial ratios (i.e., dysbiosis ratios). The correlation between the proposed ratios and the periodontal pocket depth was tested, which confirmed the link between dysbiosis ratios and the severity of the disease. The results of this work are promising, but longitudinal studies will be required to improve the ratios and to define the microbial signatures of the disease, which will allow monitoring of periodontal pocket recovery and, conceivably, determination of the potential risk of periodontitis among healthy patients. Copyright © 2017 American Society for Microbiology.

Microbial conversion technologies

Energy Technology Data Exchange (ETDEWEB)

Lau, P. [National Research Council of Canada, Ottawa, ON (Canada). Bioconversion and Sustainable Development

2006-07-01

Microbes are a biomass and an valuable resource. This presentation discussed microbial conversion technologies along with background information on microbial cells, their characteristics and microbial diversity. Untapped opportunities for microbial conversion were identified. Metagenomic and genome mining approaches were also discussed, as they can provide access to uncultivated or unculturable microorganisms in communal populations and are an unlimited resource for biocatalysts, novel genes and metabolites. Genome mining was seen as an economical approach. The presentation also emphasized that the development of microbial biorefineries would require significant insights into the relevant microorganisms and that biocatalysts were the ultimate in sustainability. In addition, the presentation discussed the natural fibres initiative for biochemicals and biomaterials. Anticipated outputs were identified and work in progress of a new enzyme-retting cocktail to provide diversity and/or consistency in fibre characteristics for various applications were also presented. It was concluded that it is necessary to leverage understanding of biological processes to produce bioproducts in a clean and sustainable manner. tabs., figs.

Instrument for Study of Microbial Thermal Inactivation

Science.gov (United States)

Dickerson, R. W.; Read, R. B.

1968-01-01

An instrument was designed for the study of thermal inactivation of microorganisms using heating times of less than 1 sec. The instrument operates on the principle of rapid automatic displacement of the microorganism to and from a saturated steam atmosphere, and the operating temperature range is 50 to 90 C. At a temperature of 70 C, thermometric lag (time required to respond to 63.2% of a step change) of the fluid sample containing microorganisms was 0.12 sec. Heating time required to heat the sample to within 0.1 C of the exposure temperature was less than 1 sec, permitting exposure periods as brief as 1 sec, provided the proper corrections are made for the lethal effect of heating. The instrument is most useful for heat exposure periods of less than 5 min, and, typically, more than 500 samples can be processed for microbial inactivation determinations within an 8-hr period. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 7 Fig. 8 PMID:4874466

Non-microbial sources of microbial volatile organic compounds.

Science.gov (United States)

Choi, Hyunok; Schmidbauer, Norbert; Bornehag, Carl-Gustaf

2016-07-01

The question regarding the true sources of the purported microbial volatile organic compounds (MVOCs) remains unanswered. To identify microbial, as well as non-microbial sources of 28 compounds, which are commonly accepted as microbial VOCs (i.e. primary outcome of interest is Σ 28 VOCs). In a cross-sectional investigation of 390 homes, six building inspectors assessed water/mold damage, took air and dust samples, and measured environmental conditions (i.e., absolute humidity (AH, g/m(3)), temperature (°C), ventilation rate (ACH)). The air sample was analyzed for volatile organic compounds (μg/m(3)) and; dust samples were analyzed for total viable fungal concentration (CFU/g) and six phthalates (mg/g dust). Four benchmark variables of the underlying sources were defined as highest quartile categories of: 1) the total concentration of 17 propylene glycol and propylene glycol ethers (Σ17 PGEs) in the air sample; 2) 2,2,4-trimethyl-1,3-pentanediol monoisobutyrate (TMPD-MIB) in the air sample; 3) semi-quantitative mold index; and 4) total fungal load (CFU/g). Within severely damp homes, co-occurrence of the highest quartile concentration of either Σ17 PGEs or TMPD-MIB were respectively associated with a significantly higher median concentration of Σ 28 VOCs (8.05 and 13.38μg/m(3), respectively) compared to the reference homes (4.30 and 4.86μg/m(3), respectively, both Ps ≤0.002). Furthermore, the homes within the highest quartile range for Σ fungal load as well as AH were associated with a significantly increased median Σ 28 VOCs compared to the reference group (8.74 vs. 4.32μg/m(3), P=0.001). Within the final model of multiple indoor sources on Σ 28 VOCs, one natural log-unit increase in summed concentration of Σ17 PGEs, plus TMPD-MIB (Σ 17 PGEs + TMPD-MIB) was associated with 1.8-times (95% CI, 1.3-2.5), greater likelihood of having a highest quartile of Σ 28 VOCs, after adjusting for absolute humidity, history of repainting at least one room

Microbial content of abattoir wastewater and its contaminated soil in ...

African Journals Online (AJOL)

Microbial content of wastewater in two abattoirs and the impact on microbial population of receiving soil was studied in Agege and Ojo Local Government Areas in Lagos State, Nigeria. Wastewater samples were collected from each of the abattoirs over three months period and examined for microbial content. Soil samples ...

Microbial incorporation of nitrogen in stream detritus

Science.gov (United States)

Diane M. Sanzone; Jennifer L. Tank; Judy L. Meyer; Patrick J. Mulholland; Stuart E.G. Findlay

2001-01-01

We adapted the chloroform fumigation method to determine microbial nitrogen (N) and microbial incorporation of 15N on three common substrates [leaves, wood and fine benthic organic matter (FBOM)] in three forest streams. We compared microbial N and 15 content of samples collected during a 6-week15N-NH...

ASSESSMENT OF THE BIODIVERSITY OF SAMPLES USED FOR ISOLATION OF MICROBIAL STRAINS CAPABLE OF CONVERTING STRAW DESTINED AS A SUBSTRATE FOR BIOGAS PLANT

Directory of Open Access Journals (Sweden)

Krystyna Cybulska

2016-01-01

Full Text Available In biogas plants, almost any type of organic matter can be used as a substrate to produce biogas. To make the process of methane fermentation more effective, these materials are pretreated. This applies in particular to a group of difficult substrates. Straw, due to its hemicellulose structure and saturation, is hardly fermented by biogas reactor microorganisms. The methods of post-harvest residue preparation for anaerobic digestion being applied so far are expensive, while their application has a negative effect on methanoegenic bacteria. Therefore, the microorganisms being able to degrade straw hemicellulose structure, utilisation of which could precede the proper fermentation process, have been searched for. This paper presents the results of microbial biodiversity analysis in the environmental samples being lupin, cereal, rape and maize straw as well as hay and haylage at different degradation stages. The analysis of biodiversity will help at a further stage of study to isolate active microbial strains showing cellulolytic, hemicellulolytic or ligninolytic activity which are desirable in the process of straw biodegradation. Analysis of the microbial count was performed by the method of deep inoculation on different microbiological culture media. The conducted tests include determination of the number of fungi, bacteria and actinomycetes. The results obtained confirm the usefulness of the analysed samples for isolation of microbial strains capable of converting straw preceding the biogas production.

Composition of microbial communities in aerosol, snow and ice samples from remote glaciated areas (Antarctica, Alps, Andes)

Science.gov (United States)

Elster, J.; Delmas, R. J.; Petit, J.-R.; Řeháková, K.

2007-06-01

Taxonomical and ecological analyses were performed on micro-autotrophs (cyanobacteria and algae together with remnants of diatom valves), micro-fungi (hyphae and spores), bacteria (rod, cocci and red clusters), yeast, and plant pollen extracted from various samples: Alps snow (Mt. Blank area), Andean snow (Illimani, Bolivia), Antarctic aerosol filters (Dumont d'Urville, Terre Adélie), and Antarctic inland ice (Terre Adélie). Three methods for ice and snow sample's pre-concentration were tested (filtration, centrifugation and lyophilisation). Afterwards, cultivation methods for terrestrial, freshwater and marine microorganisms (micro-autotrophs and micro-fungi) were used in combination with liquid and solid media. The main goal of the study was to find out if micro-autotrophs are commonly transported by air masses, and later stored in snow and icecaps around the world. The most striking result of this study was the absence of culturable micro-autotrophs in all studied samples. However, an unusual culturable pigmented prokaryote was found in both alpine snow and aerosol samples. Analyses of many samples and proper statistical analyses (PCA, RDA- Monte Carlo permutation tests) showed that studied treatments highly significantly differ in both microbial community and biotic remnants composition F=9.33, p=0.001. In addition, GLM showed that studied treatments highly significantly differ in numbers of categories of microorganisms and remnants of biological material F=11.45, p=0.00005. The Antarctic aerosol samples were characterised by having red clusters of bacteria, the unusual prokaryote and yeasts. The high mountain snow from the Alps and Andes contained much more culturable heterotrophs. The unusual prokaryote was very abundant, as were coccoid bacteria, red clusters of bacteria, as well as yeasts. The Antarctic ice samples were quite different. These samples had higher numbers of rod bacteria and fungal hyphae. The microbial communities and biological remnants of

Microbial control of seawater by microfiltration

Directory of Open Access Journals (Sweden)

Wilmer Soler T

2010-08-01

Full Text Available Recent scientific literature presents seawater as a potential aid to solve a variety of health diseases in animals and human beings because by means of its mineral and trace elements content. In Colombia, Nicaragua and Spain it is collected in a natural way from de shore and drunk; however, this can represent a health risk because of the problems related to chemical and microbiological contamination. Microbial control of seawater allows the improvement of its microbiological quality. Objective: to compare the efficiency of three microbial control methods: microfiltration, solar exposition and quarantine. Methodology: 30 samples were collected in 20-liter high density polyethylene containers in three different places in the Colombian Atlantic coast. Results: 15 samples out of 30 showed the presence of bacteria such as E. coli and halophiles bacteria like Vibrio and Aeromonas. Microfiltration through ceramic filters of 0.5 µm produces disinfection in 100% of the samples but the quarantine for five months and solar disinfection are effective in 66 and 21% respectively. The latter requires certain weather conditions to achieve disinfection and it only allows managing small quantities of water. Dicussion: Considering chemical contamination in some places which cannot be controlled through disinfection methods, the collection of water offshore in clean places is suggested and then microfiltration treatment should be performed.

Imaging hydrated microbial extracellular polymers: Comparative analysis by electron microscopy

Energy Technology Data Exchange (ETDEWEB)

Dohnalkova, A.C.; Marshall, M. J.; Arey, B. W.; Williams, K. H.; Buck, E. C.; Fredrickson, J. K.

2011-01-01

Microbe-mineral and -metal interactions represent a major intersection between the biosphere and geosphere but require high-resolution imaging and analytical tools for investigating microscale associations. Electron microscopy has been used extensively for geomicrobial investigations and although used bona fide, the traditional methods of sample preparation do not preserve the native morphology of microbiological components, especially extracellular polymers. Herein, we present a direct comparative analysis of microbial interactions using conventional electron microscopy approaches of imaging at room temperature and a suite of cryogenic electron microscopy methods providing imaging in the close-to-natural hydrated state. In situ, we observed an irreversible transformation of the hydrated bacterial extracellular polymers during the traditional dehydration-based sample preparation that resulted in their collapse into filamentous structures. Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding nature of interactions between microbial extracellular polymers and their environment.

Hydrodynamics of microbial filter feeding

DEFF Research Database (Denmark)

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

2017-01-01

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate......-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude......; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet...

Efficacy of microbial sampling recommendations and practices in sub-Saharan Africa.

Science.gov (United States)

Taylor, David D J; Khush, Ranjiv; Peletz, Rachel; Kumpel, Emily

2018-05-01

Current guidelines for testing drinking water quality recommend that the sampling rate, which is the number of samples tested for fecal indicator bacteria (FIB) per year, increases as the population served by the drinking water system increases. However, in low-resource settings, prevalence of contamination tends to be higher, potentially requiring higher sampling rates and different statistical methods not addressed by current sampling recommendations. We analyzed 27,930 tests for FIB collected from 351 piped water systems in eight countries in sub-Saharan Africa to assess current sampling rates, observed contamination prevalences, and the ability of monitoring agencies to complete two common objectives of sampling programs: determine regulatory compliance and detect a change over time. Although FIB were never detected in samples from 75% of piped water systems, only 14% were sampled often enough to conclude with 90% confidence that the true contamination prevalence met an example guideline (≤5% chance of any sample positive for FIB). Similarly, after observing a ten percentage point increase in contaminated samples, 43% of PWS would still require more than a year before their monitoring agency could be confident that contamination had actually increased. We conclude that current sampling practices in these settings may provide insufficient information because they collect too few samples. We also conclude that current guidelines could be improved by specifying how to increase sampling after contamination has been detected. Our results suggest that future recommendations should explicitly consider the regulatory limit and desired confidence in results, and adapt when FIB is detected. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Next Generation Microbiology Requirements

Science.gov (United States)

Ott, C. M.; Oubre, C. M.; Elliott, T. F.; Castro, V. A.; Pierson, D. L.

2012-01-01

As humans continue to explore deep into space, microorganisms will travel with them. The primary means to mitigate the risk of infectious disease are a combination of prudent spacecraft design and rigorous operational controls. The effectiveness of these methods are evaluated by microbiological monitoring of spacecraft, food, water, and the crew that is performed preflight, in-flight, and post-flight. Current NASA requirements associated with microbiological monitoring are based on culture-based methodology where microorganisms are grown on a semi-solid growth medium and enumerated. Subsequent identification of the organisms requires specialized labor and large equipment, which historically has been performed on Earth. Requirements that rely strictly on culture-based units limit the use of non-culture based monitoring technology. Specifically, the culture-based "measurement criteria" are Colony Forming Units (CFU, representing the growth of one microorganism at a single location on the agar medium) per a given volume, area, or sample size. As the CFU unit by definition is culture-based, these requirements limit alternative technologies for spaceflight applications. As spaceflight missions such as those to Mars extend further into space, culture-based technology will become difficult to implement due to the (a) limited shelf life of the culture media, (b) mass/volume necessary to carry these consumables, and (c) problems associated with the production of biohazardous material in the habitable volume of the spacecraft. In addition, an extensive amount of new knowledge has been obtained during the Space Shuttle, NASA-Mir, and International Space Station Programs, which gave direction for new or modified microbial control requirements for vehicle design and mission operations. The goal of this task is to develop and recommend a new set of requirements for vehicle design and mission operations, including microbiological monitoring, based upon "lessons learned" and new

Dose requirements for microbial decontamination of botanical materials by irradiation

International Nuclear Information System (INIS)

Razem, D.; Katusin-Razem, Branka

2002-01-01

Microbial contamination levels and corresponding resistivities to irradiation (expressed as dose required for the first 90% reduction, D first 9 0% r ed ) were analyzed in a number of various botanical materials. The following generalizations could be made: total aerobic plate count is the most informative measure of contamination; the probability of contamination depends on available surface of the material and processing history: flowers and leaves usually contain more contamination than fruits and seeds, while crude herbs contain more than extracts; liquid extracts are more contaminated than dry ones. At the same time, resistivity to irradiation increases approximately in the reverse order of contamination level on going from flowers and leaves, to fruits and seeds, to liquid and dry extracts. The two quantities, probability of contamination and D first 9 0% r ed being inversely related, the treatment dose needed to reduce initial contamination to tolerable level amounts to between 4 and 30 kGy under a typical scenario, and between 8 and 40 kGy under the worst-case scenario for the whole range of raw materials and botanical products

Microbial analyses of clay and water from different samples from the Mont Terri Rock Laboratory (RL), Switzerland

International Nuclear Information System (INIS)

Sergeant, C.; Vesvres, M.H.; Barsotti, V.; Stroes-Gascoyne, S.; Hamon, C.J.; Neble, S.; Shippers, A.; Le Marrec, C.; Vinsot, A.; Schwyn, B.

2010-01-01

processes that may develop locally in Opalinus Clay upon disturbance by drilling and excavation (i.e., introduction of space, water, microbes and nutrients). In a second part of this work, results are presented here from detection and identification of microorganisms in water which accumulated in an open borehole drilled in the Opalinus Clay (BEZ-G5). Besides introduced (exogenous) microorganisms, such water may contain autochthonous species. The latter may be easier to detect in water samples than by direct analysis of the clay rock. Both culturing (aerobic and anaerobic media) and direct (DNA extraction and PCR-DGGE) methods were used. Pure cultures of bacteria isolated in several enrichment media and identified by DNA extraction, PCR and sequencing indicated that most isolated bacteria are heterotrophic aerobes or facultative anaerobes commonly isolated from soil and water (such as Dietzia sp., Pseudomonas sp.) and therefore probably contaminants. In parallel, direct DNA extraction from water and PCR-DGGE revealed other contaminant bacteria (such as Staphylococcus sp., Rhizobium sp.). Nevertheless, some species may be indigenous in the Opalinus Clay such as Desulfosporosinus sp. isolated on sulfate-reducing media or Speleomyces sp., identified by PCRDGGE and previously isolated from a medieval mine. Complementary characterizations of these bacteria are required to confirm these first results. The diversity of microorganisms detected shows that both culturing and molecular approaches are essential to study this type of environment. (authors)

Characterization of Serpentine Samples from the Coast Range Ophiolite Microbial Observatory with μ-FTIR and XRD. ­­

Science.gov (United States)

Sousa, A.; Cardace, D.

2017-12-01

Serpentinizing systems hold much promise as potentially habitable environments in diverse planetary settings. They involve abundant and simple ingredients (i.e., the mineral olivine, liquid water), support subsurface microbial communities on Earth (Crespo-Medina et al. 2014; Suzuki et al. 2014; Kelley et al. 2005) and are thought to occur elsewhere in our solar system such as Mars (Schulte et al. 2006; Ehlmann et al. 2010)and possibly ocean worlds (Waite et al. 2017; Vance 2009). Although geochemical and microbial data collection continues in serpentinizing systems, the identification and resolution of potential biosignatures in serpentinites are not yet clear. Specifically, the micro-scale mineralogical contexts in which cell fragments or biofilm residues may be formed and preserved is lacking. Here we report preliminary transmission and reflection mode μ-FTIR spectral maps and XRD diffractograms, obtained with instruments relevant to robotic exploration missions (Blake et al. 2012; Igisu et al. 2009; Leroi et al. 2009). Samples analyzed include ultramafic rock and constituent mineral standards (e.g., olivine) and rocks collected from near surface sites associated with the NASA Astrobiology Institute-funded initiative, the Coast Range Ophiolite Microbial Observatory (CROMO), in Lower Lake, CA (Cardace et al. 2013). These new results provide co-registered, complementary data on astrobiologically important rock and mineral phases related to serpentinization (Crespo-Medina et al. 2014; Twing et al. 2017). Future work will leverage this data set in microbial colonization experiments aimed at parsing background organic loads in serpentinites from surficial/fracture-localized modern biofilm signatures.

Preliminary biological sampling of GT3 and BT1 cores and the microbial community dynamics of existing subsurface wells

Science.gov (United States)

Kraus, E. A.; Stamps, B. W.; Rempfert, K. R.; Ellison, E. T.; Nothaft, D. B.; Boyd, E. S.; Templeton, A. S.; Spear, J. R.

2017-12-01

Subsurface microbial life is poorly understood but potentially very important to the search for life on other planets as well as increasing our understanding of Earth's geobiological processes. Fluids and rocks of actively serpentinizing subsurface environments are a recent target of biological study due to their apparent ubiquity across the solar system. Areas of serpentinization can contain high concentrations of molecular hydrogen, H2, that can serve as the dominant fuel source for subsurface microbiota. Working with the Oman Drilling Project, DNA and RNA were extracted from fluids of seven alkaline wells and two rock cores from drill sites GT3 and BT1 within the Samail ophiolite. DNA and cDNA (produced via reverse transcription from the recovered RNA) were sequenced using universal primers to identify microbial life across all three domains. Alkaline subsurface fluids support a microbial community that changes with pH and host-rock type. In peridotite with pH values of >11, wells NSHQ 14 and WAB 71 have high relative abundances of Meiothermus, Methanobacterium, the family Nitrospiraceae, and multiple types of the class Dehalococcoidia. While also hosted in peridotite but at pH 8.5, wells WAB 104 and 105 have a distinct, more diverse microbial community. This increased variance in community make-up is seen in wells that sit near/at the contact of gabbro and peridotite formations as well. Core results indicate both sampled rock types host a very low biomass environment subject to multiple sources of contamination during the drilling process. Suggestions for contaminant reduction, such as having core handlers wear nitrile gloves and flame-sterilizing the outer surfaces of core rounds for biological sampling, would have minimal impact to overall ODP coreflow and maximize the ability to better understand in situ microbiota in this low-biomass serpentinizing subsurface environment. While DNA extraction was successful with gram amounts of crushed rock, much can be

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.

Science.gov (United States)

Yu, Chaowei; Reddy, Amitha P; Simmons, Christopher W; Simmons, Blake A; Singer, Steven W; VanderGheynst, Jean S

2015-01-01

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and

Marine Microbial Systems Ecology: Microbial Networks in the Sea

NARCIS (Netherlands)

Muijzer, G.; Stal, L.J.; Cretoiu, M.S.

2016-01-01

Next-generation sequencing of DNA has revolutionized microbial ecology. Using this technology, it became for the first time possible to analyze hundreds of samples simultaneously and in great detail. 16S rRNA amplicon sequencing, metagenomics and metatranscriptomics became available to determine the

21 CFR 111.83 - What are the requirements for reserve samples?

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 2 2010-04-01 2010-04-01 false What are the requirements for reserve samples? 111..., PACKAGING, LABELING, OR HOLDING OPERATIONS FOR DIETARY SUPPLEMENTS Requirement to Establish a Production and Process Control System § 111.83 What are the requirements for reserve samples? (a) You must collect and...

Flow cytometric analysis of microbial contamination in food industry technological lines – initial study

OpenAIRE

Katarzyna Czaczyk; Wojciech Juzwa

2012-01-01

Background. Flow cytometry constitutes an alternative for traditional methods of microorganisms identifi cation and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a signifi cant reduction of time required for analysis allowing monitoring of production process...

Rapid filtration separation-based sample preparation method for Bacillus spores in powdery and environmental matrices.

Science.gov (United States)

Isabel, Sandra; Boissinot, Maurice; Charlebois, Isabelle; Fauvel, Chantal M; Shi, Lu-E; Lévesque, Julie-Christine; Paquin, Amélie T; Bastien, Martine; Stewart, Gale; Leblanc, Eric; Sato, Sachiko; Bergeron, Michel G

2012-03-01

Authorities frequently need to analyze suspicious powders and other samples for biothreat agents in order to assess environmental safety. Numerous nucleic acid detection technologies have been developed to detect and identify biowarfare agents in a timely fashion. The extraction of microbial nucleic acids from a wide variety of powdery and environmental samples to obtain a quality level adequate for these technologies still remains a technical challenge. We aimed to develop a rapid and versatile method of separating bacteria from these samples and then extracting their microbial DNA. Bacillus atrophaeus subsp. globigii was used as a simulant of Bacillus anthracis. We studied the effects of a broad variety of powdery and environmental samples on PCR detection and the steps required to alleviate their interference. With a benchmark DNA extraction procedure, 17 of the 23 samples investigated interfered with bacterial lysis and/or PCR-based detection. Therefore, we developed the dual-filter method for applied recovery of microbial particles from environmental and powdery samples (DARE). The DARE procedure allows the separation of bacteria from contaminating matrices that interfere with PCR detection. This procedure required only 2 min, while the DNA extraction process lasted 7 min, for a total of sample preparation procedure allowed the recovery of cleaned bacterial spores and relieved detection interference caused by a wide variety of samples. Our procedure was easily completed in a laboratory facility and is amenable to field application and automation.

A Statistical Framework for Microbial Source Attribution

Energy Technology Data Exchange (ETDEWEB)

Velsko, S P; Allen, J E; Cunningham, C T

2009-04-28

This report presents a general approach to inferring transmission and source relationships among microbial isolates from their genetic sequences. The outbreak transmission graph (also called the transmission tree or transmission network) is the fundamental structure which determines the statistical distributions relevant to source attribution. The nodes of this graph are infected individuals or aggregated sub-populations of individuals in which transmitted bacteria or viruses undergo clonal expansion, leading to a genetically heterogeneous population. Each edge of the graph represents a transmission event in which one or a small number of bacteria or virions infects another node thus increasing the size of the transmission network. Recombination and re-assortment events originate in nodes which are common to two distinct networks. In order to calculate the probability that one node was infected by another, given the observed genetic sequences of microbial isolates sampled from them, we require two fundamental probability distributions. The first is the probability of obtaining the observed mutational differences between two isolates given that they are separated by M steps in a transmission network. The second is the probability that two nodes sampled randomly from an outbreak transmission network are separated by M transmission events. We show how these distributions can be obtained from the genetic sequences of isolates obtained by sampling from past outbreaks combined with data from contact tracing studies. Realistic examples are drawn from the SARS outbreak of 2003, the FMDV outbreak in Great Britain in 2001, and HIV transmission cases. The likelihood estimators derived in this report, and the underlying probability distribution functions required to calculate them possess certain compelling general properties in the context of microbial forensics. These include the ability to quantify the significance of a sequence 'match' or &apos

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

Cellular content of biomolecules in sub-seafloor microbial communities

DEFF Research Database (Denmark)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.

2016-01-01

the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density...... content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates......Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than...

Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

Science.gov (United States)

Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

2007-09-01

In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product.

Estimating and comparing microbial diversity in the presence of sequencing errors

Science.gov (United States)

Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants

Science.gov (United States)

Dobbler, Priscila T.; Procianoy, Renato S.; Mai, Volker; Silveira, Rita C.; Corso, Andréa L.; Rojas, Bruna S.; Roesch, Luiz F. W.

2017-01-01

Despite increased efforts, the diverse etiologies of Necrotizing Enterocolitis (NEC) have remained largely elusive. Clinical predictors of NEC remain ill-defined and currently lack sufficient specificity. The development of a thorough understanding of initial gut microbiota colonization pattern in preterm infants might help to improve early detection or prediction of NEC and its associated morbidities. Here we compared the fecal microbiota successions, microbial diversity, abundance and structure of newborns that developed NEC with preterm controls. A 16S rRNA based microbiota analysis was conducted in a total of 132 fecal samples that included the first stool (meconium) up until the 5th week of life or NEC diagnosis from 40 preterm babies (29 controls and 11 NEC cases). A single phylotype matching closest to the Enterobacteriaceae family correlated strongly with NEC. In DNA from the sample with the greatest abundance of this phylotype additional shotgun metagenomic sequencing revealed Citrobacter koseri and Klebsiella pneumoniae as the dominating taxa. These two taxa might represent suitable microbial biomarker targets for early diagnosis of NEC. In NEC cases, we further detected lower microbial diversity and an abnormal succession of the microbial community before NEC diagnosis. Finally, we also detected a disruption in anaerobic microorganisms in the co-occurrence network of meconium samples from NEC cases. Our data suggest that a strong dominance of Citrobacter koseri and/or Klebsiella pneumoniae, low diversity, low abundance of Lactobacillus, as well as an altered microbial-network structure during the first days of life, correlate with NEC risk in preterm infants. Confirmation of these findings in other hospitals might facilitate the development of a microbiota based screening approach for early detection of NEC. PMID:29187842

Estimates of microbial quality and concentration of copper in distributed drinking water are highly dependent on sampling strategy.

Science.gov (United States)

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

2007-12-01

The numbers of bacteria generally increase in distributed water. Often household pipelines or water fittings (e.g., taps) represent the most critical location for microbial growth in water distribution systems. According to the European Union drinking water directive, there should not be abnormal changes in the colony counts in water. We used a pilot distribution system to study the effects of water stagnation on drinking water microbial quality, concentration of copper and formation of biofilms with two commonly used pipeline materials in households; copper and plastic (polyethylene). Water stagnation for more than 4h significantly increased both the copper concentration and the number of bacteria in water. Heterotrophic plate counts were six times higher in PE pipes and ten times higher in copper pipes after 16 h of stagnation than after only 40 min stagnation. The increase in the heterotrophic plate counts was linear with time in both copper and plastic pipelines. In the distribution system, bacteria originated mainly from biofilms, because in laboratory tests with water, there was only minor growth of bacteria after 16 h stagnation. Our study indicates that water stagnation in the distribution system clearly affects microbial numbers and the concentration of copper in water, and should be considered when planning the sampling strategy for drinking water quality control in distribution systems.

Evaluation of the Adequacy of GMP to Control Microbial Hazards in Dairy Factories in Fars Province

Directory of Open Access Journals (Sweden)

Sajjad Abdi no

2016-07-01

Full Text Available Background and Objectives: Pre-requisite programs (PRPs are “primary conditions and requirements essential for HACCP operations, which are crucial in food safety programs”. The present study was conducted to evaluate the impact of implementation of PRPs on the microbial parameters of pasteurized milk (according to the National Standard of Iran. Effectiveness of HACCP operation requirements and efficiency of Good Laboratory Practice (GLP were also evaluated in control of the above-mentioned microbial parameters. Materials and Methods: According to the approved checklist of the Vice-chancellor in Food and Drug affairs, PRPs of 26 factories were evaluated from March 2014 to March 2015 in two-month intervals, and their total and component scores were obtained along with the microbial parameters of pasteurized milk. Generalized Estimating Equations (GEEs were used to determine the significance of total score and the impact of its components on controlling microbial hazards. Results: There was a reverse significant relation between the total scores of the PRPs and microbial hygiene indices (total and coliform count which approves the effectiveness of operating the programs in controlling the mentioned microorganisms. Efficiency of each pre-requisite program was different in controlling the microbial parameters. Good Laboratory Practice (GLP had a prominent effect on controlling of the index microorganisms of hygienic operations. Overall, the results showed a little probability of contamination with E. coli in the pasteurized milk samples of Fars Province for which the statistical analysis was ignored. Conclusions: The exact operation of PRPs resulted in reduction of microbial parameters in a way that increasing the total score of PRPs led to decrease in microbial parameters of total count (TC, coliforms, molds and yeasts. The findings further suggest the application of this checklist in evaluation and prediction of microbial parameters. Keywords

Microbial biosensors for environmental monitoring

Directory of Open Access Journals (Sweden)

David VOGRINC

2015-12-01

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

Microbial transformation of uranium in wastes

International Nuclear Information System (INIS)

Francis, A.J.; Dodge, C.J.; Gillow, J.B.; Cline, J.E.

1989-01-01

Contamination of soils, water, and sediments by radionuclides and toxic metals from the disposal of uranium processing wastes is a major national concern. Although much is known about the physico- chemical aspects of U, we have little information on the effects of aerobic and anaerobic microbial activities on the mobilization or immobilization of U and other toxic metals in mixed wastes. In order to understand the mechanisms of microbial transformations of uranium, we examined a contaminated pond sediment and a sludge sample from the uranium processing facility at Y-12 Plant, Oak Ridge, TN. The uranium concentration in the sediment and sludge samples was 923 and 3080 ug/g dry wt, respectively. In addition to U, the sediment and sludge samples contained high levels of toxic metals such as Cd, Cr, Cu, Hg, Pb, Ni, and Zn. The association of uranium with the various mineral fractions of the sediment and sludge was determined by selective chemical extraction techniques. Uranium was associated to varying degrees with the exchangeable carbonate, iron oxide, organic, and inert fractions in both samples. Initial results in samples amended with carbon and nitrogen indicate immobilization of U due to enhanced indigenous microbial activity under anaerobic conditions. 23 refs., 4 figs., 5 tabs

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

KAUST Repository

Bayer, Kristina

2015-01-08

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

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

KAUST Repository

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

2015-01-01

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

The ocean sampling day consortium

DEFF Research Database (Denmark)

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo

2015-01-01

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate...... the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our...

Global microbialization of coral reefs.

Science.gov (United States)

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

2016-04-25

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

Shifts in microbial populations in Rusitec fermenters as affected by the type of diet and impact of the method for estimating microbial growth (15N v. microbial DNA).

Science.gov (United States)

Mateos, I; Ranilla, M J; Saro, C; Carro, M D

2017-11-01

Rusitec fermenters are in vitro systems widely used to study ruminal fermentation, but little is known about the microbial populations establishing in them. This study was designed to assess the time evolution of microbial populations in fermenters fed medium- (MC; 50% alfalfa hay : concentrate) and high-concentrate diets (HC; 15 : 85 barley straw : concentrate). Samples from solid (SOL) and liquid (LIQ) content of fermenters were taken immediately before feeding on days 3, 8 and 14 of incubation for quantitative polymerase chain reaction and automated ribosomal intergenic spacer analysis analyses. In SOL, total bacterial DNA concentration and relative abundance of Ruminococcus flavefaciens remained unchanged over the incubation period, but protozoal DNA concentration and abundance of Fibrobacter succinogenes, Ruminococcus albus and fungi decreased and abundance of methanogenic archaea increased. In LIQ, total bacterial DNA concentration increased with time, whereas concentration of protozoal DNA and abundance of methanogens and fungi decreased. Diet×time interactions were observed for bacterial and protozoal DNA and relative abundance of F. succinogenes and R. albus in SOL, as well as for protozoal DNA in LIQ. Bacterial diversity in SOL increased with time, but no changes were observed in LIQ. The incubated diet influenced all microbial populations, with the exception of total bacteria and fungi abundance in LIQ. Bacterial diversity was higher in MC-fed than in HC-fed fermenters in SOL, but no differences were detected in LIQ. Values of pH, daily production of volatile fatty acids and CH4 and isobutyrate proportions remained stable over the incubation period, but other fermentation parameters varied with time. The relationships among microbial populations and fermentation parameters were in well agreement with those previously reported in in vivo studies. Using 15N as a microbial marker or quantifying total microbial DNA for estimating microbial protein synthesis

Dynamics of culturable soil microbial communities during ...

African Journals Online (AJOL)

Ecological zones impacted significantly (P < 0.05) on bacterial proliferation, but not on fungal growth. Sampling period significantly (P < 0.05) affected microbial density and the semi-arid agroecozone was more supportive of microbial proliferation than the arid zone. A total of nine predominant fungal species belonging to ...

Investigations to determine whether viable microorganisms are required during intestinal lactose hydrolysis of fermented milk products by microbial ß-galactosidase using gnotobiotic Göttingen minipigs

OpenAIRE

Winchenbach, Andrea

2010-01-01

The most common reason worldwide for the indigestibility of milk is the lack of ß-galactosidases in the small intestine, leading to the malabsorbtion of lactose. Fermented dairy products are very often much better tolerated than raw (not fermented) milk, because of the microbial ß-galactosidases they contain. The aim of this thesis was to elucidate the question as to weather lactose hydrolysis in the small intestine requires the presence of living bacteria (with their microbial ß-galac...

Seasonality in ocean microbial communities.

Science.gov (United States)

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

Biodiversity of the microbial mat of the Garga hot spring.

Science.gov (United States)

Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

2017-12-28

Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that

Evaluation of microbially-influenced degradation of massive concrete structures

International Nuclear Information System (INIS)

Hamilton, M.A.; Rogers, R.D.; Zolynski, M.; Veeh, R.

1996-01-01

Many low level waste disposal vaults, both above and below ground, are constructed of concrete. One potential contributing agent to the destruction of concrete structures is microbially-influenced degradation (MID). Three groups of bacteria are known to create conditions that are conducive to destroying concrete integrity. They are sulfur oxidizing bacteria, nitrifying bacteria, and heterotrophic bacteria. Research is being conducted at the Idaho National Engineering Laboratory to assess the extent of naturally occurring microbially influenced degradation (MID) and its contribution to the deterioration of massive concrete structures. The preliminary steps to understanding the extent of MID, require assessing the microbial communities present on degrading concrete surfaces. Ultimately such information can be used to develop guidelines for preventive or corrective treatments for MID and aid in formulation of new materials to resist corrosion. An environmental study was conducted to determine the presence and activity of potential MID bacteria on degrading concrete surfaces of massive concrete structures. Scanning electron microscopy detected bacteria on the surfaces of concrete structures such as bridges and dams, where corrosion was evident. Enumeration of sulfur oxidizing thiobacilli and nitrogen oxidizing Nitrosomonas sp. and Nitrobacter sp. from surface samples was conducted. Bacterial community composition varied between sampling locations, and generally the presence of either sulfur oxidizers or nitrifiers dominated, although instances of both types of bacteria occurring together were encountered. No clear correlation between bacterial numbers and degree of degradation was exhibited

[Microbial Community Structure on the Root Surface of Patients with Periodontitis.

Science.gov (United States)

Zhang, Ju-Mei; Zhou, Jian-Ye; Bo, Lei; Hu, Xiao-Pan; Jiao, Kang-Li; Li, Zhi-Jie; Li, Yue-Hong; Li, Zhi-Qiang

2016-11-01

To study the microbial community structure on the root surface of patients with periodontitis. Bacterial plaque and tissues from the root neck (RN group),root middle (RM group) and root tine (RT group) of six teeth with mobility 3 in one patient with periodontitis were sampled.The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform.The microbial community structure was analyzed by Mothur,Qiime and SPSS software. The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples,which was significant different from that of the RN samples.Thirteen phyla were detected in the three groups of samples,which included 7 dominant phyla.29 dominant genera were detected in 184 genera.The abundance of Bacteroidetes _[G-6] and Peptostre ptococcaceae _[XI][G-4] had a positive correlation with the depth of the collection site of samples ( P microbial community structure on the root surface of patients with periodontitis.

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

Science.gov (United States)

Parks, Donovan H; Beiko, Robert G

2013-01-01

High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.

Using pseudoalignment and base quality to accurately quantify microbial community composition.

Directory of Open Access Journals (Sweden)

Mark Reppell

2018-04-01

Full Text Available Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies.

Evaluation of the Level of air Microbial Contamination in some ...

African Journals Online (AJOL)

The level of air microbial contamination in some teaching hospitals waste dump site in South Eastern Nigeria was evaluated using the standard microbiological techniques. Passive air sampling was performed using settle plates. The microbial load of the air around the hospitals waste dumpsite, showed high microbial load ...

Microbial contamination of soft contact lenses & accessories in asymptomatic contact lens users

Directory of Open Access Journals (Sweden)

Deeksha V Thakur

2014-01-01

Full Text Available Background & objectives: With increasing use of soft contact lenses the incidence of contact lens induced infections is also increasing. This study was aimed to assess the knowledge of new and existing contact lens users about the risk of microbial contamination associated with improper use and maintenance of contact lenses, type of microbial flora involved and their potential to cause ophthalmic infections. Methods: Four samples each from 50 participants (n=200 were collected from the lenses, lens care solutions, lens care solution bottles and lens cases along with a questionnaire regarding their lens use. The samples were inoculated onto sheep blood agar, Mac Conkey′s agar and Sabouraud′s dextrose agar. Organisms were identified using standard laboratory protocols. Results: Overall rate of microbial contamination among the total samples was 52 per cent. The most and the least contaminated samples were found to be lens cases (62% and lens care solution (42%, respectively. The most frequently isolated contaminant was Staphylococcus aureus (21% followed by Pseudomonas species (19.5%. Majority (64% of the participants showed medium grade of compliance to lens cleaning practices. Rate of contamination was 100 and 93.75 per cent respectively in those participants who showed low and medium compliance to lens care practices as compared to those who had high level of compliance (43.75% ( p0 <0.05. Interpretation & conclusions: Lens care practices amongst the participants were not optimum which resulted into high level contamination. Hence, creating awareness among the users about the lens care practices and regular cleaning and replacements of lens cases are required.

The role of ecological theory in microbial ecology.

Science.gov (United States)

Prosser, James I; Bohannan, Brendan J M; Curtis, Tom P; Ellis, Richard J; Firestone, Mary K; Freckleton, Rob P; Green, Jessica L; Green, Laura E; Killham, Ken; Lennon, Jack J; Osborn, A Mark; Solan, Martin; van der Gast, Christopher J; Young, J Peter W

2007-05-01

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Radiochemically-Supported Microbial Communities: A Potential Mechanism for Biocolloid Production of Importance to Actinide Transport

Energy Technology Data Exchange (ETDEWEB)

Moser, Duane P. [Desert Research Inst., Nevada University, Reno, NV (United States); Hamilton-Brehm, Scott D. [Desert Research Inst., Nevada University, Reno, NV (United States); Fisher, Jenny C. [Desert Research Inst., Nevada University, Reno, NV (United States); Bruckner, James C. [Desert Research Inst., Nevada University, Reno, NV (United States); Kruger, Brittany [Desert Research Inst., Nevada University, Reno, NV (United States); Sackett, Joshua [Desert Research Inst., Nevada University, Reno, NV (United States); Russell, Charles E. [Desert Research Inst., Nevada University, Reno, NV (United States); Onstott, Tullis C. [Princeton Univ., NJ (United States); Czerwinski, Ken [Univ. of Nevada, Las Vegas, NV (United States); Zavarin, Mavrik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Campbell, James H. [Northwest Missouri State Univ., Maryville, MO (United States)

2014-06-01

Due to the legacy of Cold War nuclear weapons testing, the Nevada National Security Site (NNSS, formerly known as the Nevada Test Site (NTS)) contains millions of Curies of radioactive contamination. Presented here is a summary of the results of the first comprehensive study of subsurface microbial communities of radioactive and nonradioactive aquifers at this site. To achieve the objectives of this project, cooperative actions between the Desert Research Institute (DRI), the Nevada Field Office of the National Nuclear Security Administration (NNSA), the Underground Test Area Activity (UGTA), and contractors such as Navarro-Interra (NI), were required. Ultimately, fluids from 17 boreholes and two water-filled tunnels were sampled (sometimes on multiple occasions and from multiple depths) from the NNSS, the adjacent Nevada Test and Training Range (NTTR), and a reference hole in the Amargosa Valley near Death Valley. The sites sampled ranged from highly-radioactive nuclear device test cavities to uncontaminated perched and regional aquifers. Specific areas sampled included recharge, intermediate, and discharge zones of a 100,000-km2 internally-draining province, known as the Death Valley Regional Flow System (DVRFS), which encompasses the entirety of the NNSS/NTTR and surrounding areas. Specific geological features sampled included: West Pahute and Ranier Mesas (recharge zone), Yucca and Frenchman Flats (transitional zone), and the Western edge of the Amargosa Valley near Death Valley (discharge zone). The original overarching question underlying the proposal supporting this work was stated as: Can radiochemically-produced substrates support indigenous microbial communities and subsequently stimulate biocolloid formation that can affect radionuclides in NNSS subsurface nuclear test/detonation sites? Radioactive and non-radioactive groundwater samples were thus characterized for physical parameters, aqueous geochemistry, and microbial communities using both DNA- and

Microbial quality of agricultural water in Central Florida

Science.gov (United States)

Topalcengiz, Zeynal; Strawn, Laura K.

2017-01-01

The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR) sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL) from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds). Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci) were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity) measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001). The invA gene (Salmonella) was detected in 26/540 (4.8%) samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%), fliC (51.8%), eaeA (17.4%), rfbE (17.4%), stx-I (32.6%), stx-II (9.4%). While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8%) or STEC (stx-I-32.6%, stx-II-9.4%) was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural surface

Microbial quality of agricultural water in Central Florida.

Directory of Open Access Journals (Sweden)

Zeynal Topalcengiz

Full Text Available The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds. Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001. The invA gene (Salmonella was detected in 26/540 (4.8% samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%, fliC (51.8%, eaeA (17.4%, rfbE (17.4%, stx-I (32.6%, stx-II (9.4%. While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8% or STEC (stx-I-32.6%, stx-II-9.4% was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural

Microbial quality of agricultural water in Central Florida.

Science.gov (United States)

Topalcengiz, Zeynal; Strawn, Laura K; Danyluk, Michelle D

2017-01-01

The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR) sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL) from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds). Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci) were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity) measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001). The invA gene (Salmonella) was detected in 26/540 (4.8%) samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%), fliC (51.8%), eaeA (17.4%), rfbE (17.4%), stx-I (32.6%), stx-II (9.4%). While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8%) or STEC (stx-I-32.6%, stx-II-9.4%) was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural surface

Studies about behavior of microbial degradation of organic compounds

International Nuclear Information System (INIS)

Ohtsuka, Makiko

2003-02-01

Some of TRU waste include organic compounds, thus these organic compounds might be nutrients for microbial growth at disposal site. This disposal system might be exposed to high alkali condition by cement compounds as engineering barrier material. In the former experimental studies, it has been supposed that microbial exist under pH = 12 and the microbial activity acclimated to high alkali condition are able to degrade asphalt under anaerobic condition. Microbes are called extremophile that exist in cruel habitat as high alkali or reductive condition. We know less information about the activity of extremophile, though any recent studies reveal them. In this study, the first investigation is metabolic pathway as microbial activity, the second is microbial degradation of aromatic compounds in anaerobic condition, and the third is microbial activity under high alkali. Microbial metabolic pathway consist of two systems that fulfill their function each other. One system is to generate energy for microbial activities and the other is to convert substances for syntheses of organisms' structure materials. As these systems are based on redox reaction between substances, it is made chart of the microbial activity region using pH, Eh, and depth as parameter, There is much report that microbe is able to degrade aromatic compounds under aerobic or molecular O 2 utilizing condition. For degradation of aromatic compounds in anaerobic condition, supplying electron acceptor is required. Co-metabolism and microbial consortia has important role, too. Alcalophile has individual transporting system depending Na + and acidic compounds contained in cell wall. Generating energy is key for survival and growth under high alkali condition. Co-metabolism and microbial consortia are effective for microbial degradation of aromatic compounds under high alkali and reductive condition, and utilizable electron acceptor and degradable organic compounds are required for keeping microbial activity and

Comparison of sampling methods for the assessment of indoor microbial exposure

DEFF Research Database (Denmark)

Frankel, M; Timm, Michael; Hansen, E W

2012-01-01

revealed. This study thus facilitates comparison between methods and may therefore be used as a frame of reference when studying the literature or when conducting further studies on indoor microbial exposure. Results also imply that the relatively simple EDC method for the collection of settled dust may...

Microbial diversity and community structure in an antimony-rich tailings dump.

Science.gov (United States)

Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

2016-09-01

To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

Methodological approaches for studying the microbial ecology of drinking water distribution systems

OpenAIRE

Douterelo, Isabel; Boxall, Joby B.; Deines, Peter; Sekar, Raju; Fish, Katherine E.; Biggs, Catherine A.

2014-01-01

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for chara...

Microbial communities in acid water environments of two mines, China

Energy Technology Data Exchange (ETDEWEB)

Shengmu, Xiao; Xuehui, Xie [College of Environmental Science and Engineering, Donghua University, Shanghai (China); Jianshe, Liu [College of Environmental Science and Engineering, Donghua University, Shanghai (China); School of Resources Processing and Bioengineering, Central South University, Changsha (China)], E-mail: xiaoshengmu@gmail.com

2009-03-15

To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were {alpha}-Proteobacteria, {beta}-Proteobacteria, {gamma}-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were. - Microbial community compositions in acid-aqueous environments from Chinese mines were studied, and the relationship with geochemical properties was obtained.

Microbial communities in acid water environments of two mines, China

International Nuclear Information System (INIS)

Xiao Shengmu; Xie Xuehui; Liu Jianshe

2009-01-01

To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were. - Microbial community compositions in acid-aqueous environments from Chinese mines were studied, and the relationship with geochemical properties was obtained

Stay connected: Electrical conductivity of microbial aggregates.

Science.gov (United States)

Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

2017-11-01

The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers. Copyright © 2017 Elsevier Inc. All rights reserved.

21 CFR 203.32 - Drug sample storage and handling requirements.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Drug sample storage and handling requirements. 203.32 Section 203.32 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... contamination, deterioration, and adulteration. (b) Compliance with compendial and labeling requirements...

The behaviour of Zy-4 tubes in microbial media

International Nuclear Information System (INIS)

Tunaru, M.; Velciu, L.; Popa, L.; Stancu, M.

2013-01-01

Despite of the high purity of the demineralised water used in spent fuel storage pools, some microbial activity developed ( more accelerated during the summer months) , causing fouling and clogging of filters and ion exchange resins. In this context, the paper presents an assessment (by experimental tests) of the behaviour of Zircaloy- 4 (the material of Candu nuclear fuel) samples in certain microbiological media. Samples of Zircaloy- 4 used in the tests were initially oxidized under the NPP primary circuit (by autoclaving for 110 days in lithium water, ph 10.5, at a temperature of 310 0 C). Some of samples were immersed in microbial environment in order microbiological analysis of their surface and another part was used to perform accelerated electrochemical tests to determine electrochemical parameters for the system Zircaloy- 4 / microbial medium (corrosion rate, the polarization resistance of the surface, susceptibility to pitting corrosion). At the end of the tests, the surface of samples was analyzed by metallographic and microbiologically techniques. (authors)

Antimicrobial Materials for Advanced Microbial Control in Spacecraft Water Systems

Science.gov (United States)

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

2012-01-01

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

Predicting sample size required for classification performance

Directory of Open Access Journals (Sweden)

Figueroa Rosa L

2012-02-01

Full Text Available Abstract Background Supervised learning methods need annotated data in order to generate efficient models. Annotated data, however, is a relatively scarce resource and can be expensive to obtain. For both passive and active learning methods, there is a need to estimate the size of the annotated sample required to reach a performance target. Methods We designed and implemented a method that fits an inverse power law model to points of a given learning curve created using a small annotated training set. Fitting is carried out using nonlinear weighted least squares optimization. The fitted model is then used to predict the classifier's performance and confidence interval for larger sample sizes. For evaluation, the nonlinear weighted curve fitting method was applied to a set of learning curves generated using clinical text and waveform classification tasks with active and passive sampling methods, and predictions were validated using standard goodness of fit measures. As control we used an un-weighted fitting method. Results A total of 568 models were fitted and the model predictions were compared with the observed performances. Depending on the data set and sampling method, it took between 80 to 560 annotated samples to achieve mean average and root mean squared error below 0.01. Results also show that our weighted fitting method outperformed the baseline un-weighted method (p Conclusions This paper describes a simple and effective sample size prediction algorithm that conducts weighted fitting of learning curves. The algorithm outperformed an un-weighted algorithm described in previous literature. It can help researchers determine annotation sample size for supervised machine learning.

Analysis of parallel optical sampling rate and ADC requirements in digital coherent receivers

DEFF Research Database (Denmark)

Lorences Riesgo, Abel; Galili, Michael; Peucheret, Christophe

2012-01-01

We comprehensively assess analog-to-digital converter requirements in coherent digital receiver schemes with parallel optical sampling. We determine the electronic requirements in accordance with the properties of the free running local oscillator.......We comprehensively assess analog-to-digital converter requirements in coherent digital receiver schemes with parallel optical sampling. We determine the electronic requirements in accordance with the properties of the free running local oscillator....

Genome-scale biological models for industrial microbial systems.

Science.gov (United States)

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

Science.gov (United States)

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.

Microbial Communities in the Vertical Atmosphere: Effects of Urbanization and the Natural Environment in Four North American Ecosystems

Science.gov (United States)

Docherty, K. M.; Lemmer, K. M.; Domingue, K. D.; Spring, A.; Kerber, T. V.; Mooney, M. M.

2017-12-01

Airborne transport of microbial communities is a key component of the global ecosystem because it serves as a mechanism for dispersing microbial life between all surface habitats on the planet. However, most of our understanding of airborne microbial distribution is derived from samples collected near the ground. Little is understood about how the vertical layers of the air may act as a habitat filter or how local terrestrial ecosystems contribute to a vast airborne microbial seedbank. Specifically, urbanization may fundamentally alter the terrestrial sources of airborne microbial biodiversity. To address this question, we conducted airborne sampling at minimally disturbed natural sites and paired urban sites in 4 different North American ecosystems: shortgrass steppe, desert scrub, eastern deciduous forest, and northern mesic forest. All natural area sites were co-located with NEON/Ameriflux tower sites collecting atmospheric data. We developed an airborne sampling platform that uses tethered helikites at 3 replicate locations within each ecosystem to launch remote-controlled sampler payloads. We designed sampler payloads to collect airborne bacteria and fungi from 150, 30 and 2 m above the ground. Payload requirements included: ability to be disinfected and remain contaminant-free during transport, remote open/close functionality, payload weight under 6 lbs and automated collection of weather data. After sampling for 6 hours at each location, we extracted DNA collected by the samplers. We also extracted DNA from soil and plant samples collected from each location, and characterized ground vegetation. We conducted bacterial 16S amplicon-based sequencing using Mi-Seq and sequence analysis using QIIME. We used ArcGIS to determine percent land use coverage. Our results demonstrate that terrestrial ecosystem type is the most important factor contributing to differences in airborne bacterial community composition, and that communities differed by ecosystem. The

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.

Science.gov (United States)

Jacobs, Jonathan P; Goudarzi, Maryam; Singh, Namita; Tong, Maomeng; McHardy, Ian H; Ruegger, Paul; Asadourian, Miro; Moon, Bo-Hyun; Ayson, Allyson; Borneman, James; McGovern, Dermot P B; Fornace, Albert J; Braun, Jonathan; Dubinsky, Marla

2016-11-01

Microbes may increase susceptibility to inflammatory bowel disease (IBD) by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives. Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn's disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing, untargeted liquid chromatography-mass spectrometry metabolomics, and calprotectin measurement. Individuals were grouped into microbial and metabolomics states using Dirichlet multinomial models. Multivariate models were used to identify microbes and metabolites associated with these states. Individuals were classified into 2 microbial community types. One was associated with IBD but irrespective of disease status, had lower microbial diversity, and characteristic shifts in microbial composition including increased Enterobacteriaceae, consistent with dysbiosis. This microbial community type was associated similarly with IBD and reduced microbial diversity in an independent pediatric cohort. Individuals also clustered bioinformatically into 2 subsets with shared fecal metabolomics signatures. One metabotype was associated with IBD and was characterized by increased bile acids, taurine, and tryptophan. The IBD-associated microbial and metabolomics states were highly correlated, suggesting that they represented an integrated ecosystem. Healthy relatives with the IBD-associated microbial community type had an increased incidence of elevated fecal calprotectin. Healthy first-degree relatives can have dysbiosis associated with an altered intestinal metabolome that may signify a predisease microbial susceptibility state or subclinical inflammation. Longitudinal prospective

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

Science.gov (United States)

Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T

2012-01-01

Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions.

Science.gov (United States)

Schellenberg, John J; Oh, Angela Yena; Hill, Janet E

2017-05-01

The vaginal microbiome is increasingly characterized by deep sequencing of universal genes. However, there are relatively few studies of how different specimen collection and sample storage and processing influence these molecular profiles. Here, we evaluate molecular microbial community profiles of samples collected using the HerSwab™ self-sampling device, compared to nylon swabs and under different storage conditions. In order to minimize technical variation, mixtures of 11 common vaginal bacteria in simulated vaginal fluid medium were sampled and DNA extracts prepared for massively parallel sequencing of the cpn60 universal target (UT). Three artificial mixtures imitating commonly observed vaginal microbiome profiles were easily distinguished and proportion of sequence reads correlated with the estimated proportion of the organism added to the artificial mixtures. Our results indicate that cpn60 UT amplicon sequencing quantifies the proportional abundance of member organisms in these artificial communities regardless of swab type or storage conditions, although some significant differences were observed between samples that were stored frozen and thawed prior to DNA extraction, compared to extractions from samples stored at room temperature for up to 7days. Our results indicate that an on-the-market device developed for infectious disease diagnostics may be appropriate for vaginal microbiome profiling, an approach that is increasingly facilitated by rapidly dropping deep sequencing costs. Copyright © 2017 Elsevier B.V. All rights reserved.

Deep subsurface microbial processes

Science.gov (United States)

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

Soil microbial diversity in the vicinity of desert shrubs.

Science.gov (United States)

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

Science.gov (United States)

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

Directory of Open Access Journals (Sweden)

Zarraz M.-P. Lee

2017-05-01

Full Text Available Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic. The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P regimes (P only, N:P = 16 and N:P = 75 by atoms. In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

Microbial quality of bagged baby spinach and romaine lettuce: effects of top versus bottom sampling.

Science.gov (United States)

Kase, Julie A; Borenstein, Stacey; Blodgett, Robert J; Feng, Peter C H

2012-01-01

Contamination with Escherichia coli O157:H7 and Salmonella have called into question the safety and microbial quality of bagged ready-to-eat leafy greens. This study expands on previous findings that these goods have high total bacteria counts (TBC) and coliform counts, variation in counts among different lots, that Escherichia coli is present, and disparities in counts when bags are top or bottom sampled. Nearly 100 bags of baby spinach and hearts of romaine lettuce from a single brand were subjected to both top and bottom sampling. Product was blended, and a portion serially diluted and plated to obtain TBC. Total coliform and E. coli levels were estimated by the most-probable-number (MPN) technique with ColiComplete discs. Top-sampled TBC from bags of baby spinach (48 bags, 13 different lots) ranged from 3.9 to 8.1 log CFU/g and bottom-sampled TBC ranged from 4.0 to 8.2 log CFU/g, with 52% of the bags (or 39% of the lots) producing TBC higher in bottom samples. For hearts of romaine (47 bags from 19 different lots), top-sampled bags had TBC ranging from 2.4 to 7.0 log, and bottom-sampled bags had TBC from 3.3 to 7.3 log, with 64% of the bags (or 63% of the lots) showing higher TBC in bottom samples. However, we are unable to reject the hypothesis that the top and bottom samples from either commodity contain the same TBC (P ≥ 0.08). No E. coli was detected and total coliform bacteria counts were, with few exceptions, ≥210 MPN/g, irrespective of TBC. In general, lots with the most number of days before the printed "use-by" date had lower TBC. However, the R(2) values for either baby spinach (0.4085) or hearts of romaine (0.2946) suggest that age might not be a very good predictor of higher TBC. TBC varied widely between lots and even more so within same-lot samples, as indicated by the sum of squares results. This finding, along with higher TBC in bottom samples, suggests further consideration when a microbiological sampling scheme of bagged produce is

Comparison of DNA preservation methods for environmental bacterial community samples.

Science.gov (United States)

Gray, Michael A; Pratte, Zoe A; Kellogg, Christina A

2013-02-01

Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial enhanced oil recovery: Entering the log phase

Energy Technology Data Exchange (ETDEWEB)

Bryant, R.S.

1995-12-31

Microbial enhanced oil recovery (MEOR) technology has advanced internationally since 1980 from a laboratory-based evaluation of microbial processes to field applications. In order to adequately support the decline in oil production in certain areas, research on cost-effective technologies such as microbial enhanced oil recovery processes must focus on both near-term and long-term applications. Many marginal wells are desperately in need of an inexpensive improved oil recovery technology today that can assist producers in order to prevent their abandonment. Microbial enhanced waterflooding technology has also been shown to be an economically feasible technology in the United States. Complementary environmental research and development will also be required to address any potential environmental impacts of microbial processes. In 1995 at this conference, the goal is to further document and promote microbial processes for improved oil recovery and related technology for solving environmental problems.

Microbial Hazards of Street-Vended Grilled Chicken Intestine

Directory of Open Access Journals (Sweden)

Ma. Patricia Azanza

1998-12-01

Full Text Available Microbial hazards associated with street-vended grilled chicken intestine (isaw were studied. Grilling of isaw effected ≥89.00% decrease in the total microbial load of the sample. Cooked isaw contained about 105-106 cfu/g aerobic plate counts and 103-104 MPN/g coliform counts. Salmonella per 25 g sample was isolated from cooked isaw samples. Grilling eliminated Staphylococcus aureus and Listeria monocytogenes cells initially present in pre-cooked samples. Different sauces of isaw showed increasing numbers of total aerobic microorganisms and coliform during vending operations. The total plate counts and coliform counts of the sour sauce, which ranged from 103-105 cfu/g and 101 MPN/g, respectively, were observed to be lower than those found in the sweet sauce. Sources of microbial contaminants of grilled chicken isaw included the natural flora of the raw materials, contaminations from food-contact surfaces, bamboo skewers, and the hands of the food handlers. Among the critical control points identified in the street-vending operation of chicken isaw were the control of time and temperature during cooking and hold-on periods during vending operations.

Design of a microbial fuel cell and its transition to microbial electrolytic cell for hydrogen production by electrohydrogenesis.

Science.gov (United States)

Gupta, Pratima; Parkhey, Piyush; Joshi, Komal; Mahilkar, Anjali

2013-10-01

Anaerobic bacteria were isolated from industrial wastewater and soil samples and tested for exoelectrogenic activity by current production in double chambered microbial fuel cell (MFC), which was further transitioned into a single chambered microbial electrolytic cell to test hydrogen production by electrohydrogenesis. Of all the cultures, the isolate from industrial water sample showed the maximum values for current = 0.161 mA, current density = 108.57 mA/m2 and power density = 48.85 mW/m2 with graphite electrode. Maximum voltage across the cell, however, was reported by the isolate from sewage water sample (506 mv) with copper as electrode. Tap water with KMnO4 was the best cathodic electrolyte as the highest values for all the measured MFC parameters were reported with it. Once the exoelectrogenic activity of the isolates was confirmed by current production, these were tested for hydrogen production in a single chambered microbial electrolytic cell (MEC) modified from the MFC. Hydrogen production was reported positive from co-culture of isolates of both the water samples and co-culture of one soil and one water sample. The maximum rate and yield of hydrogen production was 0.18 m3H2/m3/d and 3.2 mol H2/mol glucose respectively with total hydrogen production of 42.4 mL and energy recovery of 57.4%. Cumulative hydrogen production for a five day cycle of MEC operation was 0.16 m3H2/m3/d.

Fiscal Year 2001 Tank Characterization Technical Sampling Basis and Waste Information Requirements Document

International Nuclear Information System (INIS)

ADAMS, M.R.

2000-01-01

The Fiscal Year 2001 Tank Characterization Technical Sampling Basis and Waste Information Requirements Document (TSB-WIRD) has the following purposes: (1) To identify and integrate sampling and analysis needs for fiscal year (FY) 2001 and beyond. (2) To describe the overall drivers that require characterization information and to document their source. (3) To describe the process for identifying, prioritizing, and weighting issues that require characterization information to resolve. (4) To define the method for determining sampling priorities and to present the sampling priorities on a tank-by-tank basis. (5) To define how the characterization program is going to satisfy the drivers, close issues, and report progress. (6)To describe deliverables and acceptance criteria for characterization deliverables

Hydrodynamics of microbial filter feeding.

Science.gov (United States)

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

Comparison of Microbial Community Compositions of Injection and Production Well Samples in a Long-Term Water-Flooded Petroleum Reservoir

Science.gov (United States)

Ren, Hong-Yan; Zhang, Xiao-Jun; Song, Zhi-yong; Rupert, Wieger; Gao, Guang-Jun; Guo, Sheng-xue; Zhao, Li-Ping

2011-01-01

Water flooding plays an important role in recovering oil from depleted petroleum reservoirs. Exactly how the microbial communities of production wells are affected by microorganisms introduced with injected water has previously not been adequately studied. Using denaturing gradient gel electrophoresis (DGGE) approach and 16S rRNA gene clone library analysis, the comparison of microbial communities is carried out between one injection water and two production waters collected from a working block of the water-flooded Gudao petroleum reservoir located in the Yellow River Delta. DGGE fingerprints showed that the similarities of the bacterial communities between the injection water and production waters were lower than between the two production waters. It was also observed that the archaeal composition among these three samples showed no significant difference. Analysis of the 16S rRNA gene clone libraries showed that the dominant groups within the injection water were Betaproteobacteria, Gammaproteobacteria and Methanomicrobia, while the dominant groups in the production waters were Gammaproteobacteria and Methanobacteria. Only 2 out of 54 bacterial operational taxonomic units (OTUs) and 5 out of 17 archaeal OTUs in the injection water were detected in the production waters, indicating that most of the microorganisms introduced by the injection water may not survive to be detected in the production waters. Additionally, there were 55.6% and 82.6% unique OTUs in the two production waters respectively, suggesting that each production well has its specific microbial composition, despite both wells being flooded with the same injection water. PMID:21858049

Models of microbiome evolution incorporating host and microbial selection.

Science.gov (United States)

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

40 CFR 80.1348 - What gasoline sample retention requirements apply to refiners and importers?

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 16 2010-07-01 2010-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Benzene Sampling, Testing and Retention Requirements § 80.1348 What gasoline sample retention requirements...

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology.

Directory of Open Access Journals (Sweden)

Łukasz Jałowiecki

Full Text Available The aim of the study was to determine the potential of community-level physiological profiles (CLPPs methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A, trickling filter/biofilter system (technology B, and aerated filter system (the fluidized bed reactor, technology C. High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs, as shown by the diversity indices. Principal components analysis (PCA showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters.

A preliminary assessment of the chemical and microbial water ...

African Journals Online (AJOL)

A preliminary assessment of the chemical and microbial water quality of the Chunies River - Limpopo: short communication. ... For this purpose sampling was undertaken on 25 and 26 May 2002, and a range of chemical (macro-elements, micro-elements and heavy metals) and microbial variables (HPC, total coliforms and ...

ATP measurements for monitoring microbial drinking water quality

DEFF Research Database (Denmark)

Vang, Óluva Karin

Current standard methods for surveillance of microbial drinking water quality are culture based, which are laborious and time-consuming, where results not are available before one to three days after sampling. This means that the water may have been consumed before results on deteriorated water....... The overall aim of this PhD study was to investigate various methodological features of the ATP assay for a potential implementation on a sensor platform as a real-time parameter for continuous on-line monitoring of microbial drinking water quality. Commercial reagents are commonly used to determine ATP......, microbial quality in distributed water, detection of aftergrowth, biofilm formation etc. This PhD project demonstrated that ATP levels are relatively low and fairly stable in drinking water without chlorine residual despite different sampling locations, different drinking water systems and time of year...

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities.

Science.gov (United States)

Oldham, Athenia L; Drilling, Heather S; Stamps, Blake W; Stevenson, Bradley S; Duncan, Kathleen E

2012-11-20

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.

Microbial Life in an Underground Gas Storage Reservoir

Science.gov (United States)

Bombach, Petra; van Almsick, Tobias; Richnow, Hans H.; Zenner, Matthias; Krüger, Martin

2015-04-01

While underground gas storage is technically well established for decades, the presence and activity of microorganisms in underground gas reservoirs have still hardly been explored today. Microbial life in underground gas reservoirs is controlled by moderate to high temperatures, elevated pressures, the availability of essential inorganic nutrients, and the availability of appropriate chemical energy sources. Microbial activity may affect the geochemical conditions and the gas composition in an underground reservoir by selective removal of anorganic and organic components from the stored gas and the formation water as well as by generation of metabolic products. From an economic point of view, microbial activities can lead to a loss of stored gas accompanied by a pressure decline in the reservoir, damage of technical equipment by biocorrosion, clogging processes through precipitates and biomass accumulation, and reservoir souring due to a deterioration of the gas quality. We present here results from molecular and cultivation-based methods to characterize microbial communities inhabiting a porous rock gas storage reservoir located in Southern Germany. Four reservoir water samples were obtained from three different geological horizons characterized by an ambient reservoir temperature of about 45 °C and an ambient reservoir pressure of about 92 bar at the time of sampling. A complementary water sample was taken at a water production well completed in a respective horizon but located outside the gas storage reservoir. Microbial community analysis by Illumina Sequencing of bacterial and archaeal 16S rRNA genes indicated the presence of phylogenetically diverse microbial communities of high compositional heterogeneity. In three out of four samples originating from the reservoir, the majority of bacterial sequences affiliated with members of the genera Eubacterium, Acetobacterium and Sporobacterium within Clostridiales, known for their fermenting capabilities. In

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

Directory of Open Access Journals (Sweden)

Chengwei Luo

Full Text Available Next-generation sequencing (NGS is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage correlated highly between the two platforms (R(2>0.9. Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

Directory of Open Access Journals (Sweden)

Ana Beatriz Fernandez

2016-08-01

Full Text Available We combined nucleic acid-based molecular methods, biogeochemical measurements and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea in bulk samples and, in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

Detection of microbial concentration in ice-cream using the impedance technique.

Science.gov (United States)

Grossi, M; Lanzoni, M; Pompei, A; Lazzarini, R; Matteuzzi, D; Riccò, B

2008-06-15

The detection of microbial concentration, essential for safe and high quality food products, is traditionally made with the plate count technique, that is reliable, but also slow and not easily realized in the automatic form, as required for direct use in industrial machines. To this purpose, the method based on impedance measurements represents an attractive alternative since it can produce results in about 10h, instead of the 24-48h needed by standard plate counts and can be easily realized in automatic form. In this paper such a method has been experimentally studied in the case of ice-cream products. In particular, all main ice-cream compositions of real interest have been considered and no nutrient media has been used to dilute the samples. A measurement set-up has been realized using benchtop instruments for impedance measurements on samples whose bacteria concentration was independently measured by means of standard plate counts. The obtained results clearly indicate that impedance measurement represents a feasible and reliable technique to detect total microbial concentration in ice-cream, suitable to be implemented as an embedded system for industrial machines.

Innovative Microbial Surface Sampler, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The QS Team will develop an Innovative Microbial Surface Sampling (IMSS) device design and provide prototype kits for use in the International Space Station (ISS)....

Copepod carcasses as microbial hot spots for pelagic denitrification

DEFF Research Database (Denmark)

Glud, Ronnie N.; Grossart, Hans-Peter; Larsen, Morten

2015-01-01

Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non...... investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in 15NO2 3 amended seawater demonstrated denitrification, of which...

Continuous exposure of pesticides in an aquifer changes microbial biomass, diversity and degradation potential

DEFF Research Database (Denmark)

de Lipthay, J. R.; Johnsen, K.; Aamand, J.

2000-01-01

We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential ...... towards phenoxyalcanoic acid herbicides as well as impact on microbial diversity was observed. Furthermore, bacterial biomass was changed, e.g. increased numbers of phenoxyalcanoic acid degraders in pesticide exposed sediment.......We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential...

Characterization of indigenous oil field microorganisms for microbially enhanced oil recovery (MEOR)

Energy Technology Data Exchange (ETDEWEB)

Sitte, J.; Krueger, M. [Bundesanstalt fuer Geowissenschaften und Rohstoffe (BGR), Hannover (Germany); Biegel, E.; Herold, A. [BASF SE, Ludwigshafen (Germany); Alkan, H. [Wintershall Holding GmbH, Kassel (Germany)

2013-08-01

Microbial activities and their resulting metabolites became a focus of attention for enhanced oil recovery (MEOR, microbial enhanced oil recovery) in the recent years. In order to develop a strategy for a MEOR application in a German oil field operated by Wintershall experiments were performed to investigate different sampling strategies and the microbial communities found in these samples. The objectives of this study were (1) to characterize the indigenous microbial communities, (2) to investigate the dependency of microbial activity/diversity on the different sampling strategies, and (3) to study the influence of the in situ pressure on bacterial growth and metabolite production. Fluids were sampled at the well head (surface) and in situ in approx. 785 m depth to collect uncontaminated production water directly from the reservoir horizon and under the in situ pressure of 31 bar (subsurface). In the lab the pressure was either released quickly or slowly to assess the sensitivity of microorganisms to rapid pressure changes. Quantitative PCR resulted in higher microbial cell numbers in the subsurface than in the surface sample. Biogenic CO{sub 2} and CH{sub 4} formation rates were determined under atmospheric and high pressure conditions in the original fluids, with highest rates found in the surface fluid. Interestingly, no methane was formed in the native fluid samples. While nitrate reduction was exclusively detected in the surface samples, sulfide formation also occurred in the subsurface fluids. Increased CO{sub 2} formation was measured after addition of a variety of substrates in the surface fluids, while only fructose and glucose showed a stimulating effect on CO{sub 2} production for the subsurface sample. Stable enrichment cultures were obtained in complex medium inoculated with the subsurface fluid, both under atmospheric and in situ pressure. Growth experiments with constant or changing pressure, and subsequent DGGE analysis of bacterial 16S rRNA genes

Technical note: Could benzalkonium chloride be a suitable alternative to mercuric chloride for preservation of seawater samples?

Science.gov (United States)

Gloël, J.; Robinson, C.; Tilstone, G. H.; Tarran, G.; Kaiser, J.

2015-12-01

Instrumental equipment unsuitable or unavailable for fieldwork as well as lack of ship space can necessitate the preservation of seawater samples prior to analysis in a shore-based laboratory. Mercuric chloride (HgCl2) is routinely used for such preservation, but its handling and subsequent disposal incur environmental risks and significant expense. There is therefore a strong motivation to find less hazardous alternatives. Benzalkonium chloride (BAC) has been used previously as microbial inhibitor for freshwater samples. Here, we assess the use of BAC for marine samples prior to the measurement of oxygen-to-argon (O2 / Ar) ratios, as used for the determination of biological net community production. BAC at a concentration of 50 mg dm-3 inhibited microbial activity for at least 3 days in samples tested with chlorophyll a (Chl a) concentrations up to 1 mg m-3. BAC concentrations of 100 and 200 mg dm-3 were no more effective than 50 mg dm-3. With fewer risks to human health and the environment, and no requirement for expensive waste disposal, BAC could be a viable alternative to HgCl2 for short-term preservation of seawater samples, but is not a replacement for HgCl2 in the case of oxygen triple isotope analysis, which requires storage over weeks to months. In any event, further tests on a case-by-case basis should be undertaken if use of BAC was considered, since its inhibitory activity may depend on concentration and composition of the microbial community.

Microbial profiling of dental plaque from mechanically ventilated patients.

Science.gov (United States)

Sands, Kirsty M; Twigg, Joshua A; Lewis, Michael A O; Wise, Matt P; Marchesi, Julian R; Smith, Ann; Wilson, Melanie J; Williams, David W

2016-02-01

Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97% gene similarity cut-off for bacterial species level identifications. A significant 'microbial shift' occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

21 CFR 111.465 - What requirements apply to holding reserve samples of dietary supplements?

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 2 2010-04-01 2010-04-01 false What requirements apply to holding reserve samples... Distributing § 111.465 What requirements apply to holding reserve samples of dietary supplements? (a) You must hold reserve samples of dietary supplements in a manner that protects against contamination and...

Microbial and Sensory Quality of Freshly Processed and ...

African Journals Online (AJOL)

The samples were also evaluated for difference and preference. The study showed that the reconstituted beverage had better microbiological quality with detectable difference between the two samples with the fresh sample being preferred. Key words: Millet grains, Kununzaki, microbial quality, sensory quality. J Food Tech ...

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

Science.gov (United States)

Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Microbial Degradation of Forensic Samples of Biological Origin: Potential Threat to Human DNA Typing.

Science.gov (United States)

Dash, Hirak Ranjan; Das, Surajit

2018-02-01

Forensic biology is a sub-discipline of biological science with an amalgam of other branches of science used in the criminal justice system. Any nucleated cell/tissue harbouring DNA, either live or dead, can be used as forensic exhibits, a source of investigation through DNA typing. These biological materials of human origin are rich source of proteins, carbohydrates, lipids, trace elements as well as water and, thus, provide a virtuous milieu for the growth of microbes. The obstinate microbial growth augments the degradation process and is amplified with the passage of time and improper storage of the biological materials. Degradation of these biological materials carriages a huge challenge in the downstream processes of forensic DNA typing technique, such as short tandem repeats (STR) DNA typing. Microbial degradation yields improper or no PCR amplification, heterozygous peak imbalance, DNA contamination from non-human sources, degradation of DNA by microbial by-products, etc. Consequently, the most precise STR DNA typing technique is nullified and definite opinion can be hardly given with degraded forensic exhibits. Thus, suitable precautionary measures should be taken for proper storage and processing of the biological exhibits to minimize their decaying process by micro-organisms.

16S rRNA targeted DGGE fingerprinting of microbial communities

NARCIS (Netherlands)

Tzeneva, V.A.; Heilig, G.H.J.; Vliet, van W.M.; Akkermans, A.D.L.; Vos, de W.M.; Smidt, H.

2008-01-01

The past decades have seen the staggering development of molecular microbial ecology as a discipline that uses the detection of so-called biomarkers to monitor microbial communities in environment samples. A variety of molecules can be used as biomarkers, including cell-wall components, proteins,

Reduction of date microbial load with ozone

Science.gov (United States)

Farajzadeh, Davood; Qorbanpoor, Ali; Rafati, Hasan; Isfeedvajani, Mohsen Saberi

2013-01-01

Background: Date is one of the foodstuffs that are produced in tropical areas and used worldwide. Conventionally, methyl bromide and phosphine are used for date disinfection. The toxic side effects of these usual disinfectants have led food scientists to consider safer agents such as ozone for disinfection, because food safety is a top priority. The present study was performed to investigate the possibility of replacing common conventional disinfectants with ozone for date disinfection and microbial load reduction. Materials and Methods: In this experimental study, date samples were ozonized for 3 and 5 hours with 5 and 10 g/h concentrations and packed. Ozonized samples were divided into two groups and kept in an incubator which was maintained at 25°C and 40°C for 9 months. During this period, every 3 month, microbial load (bacteria, mold, and yeast) were examined in ozonized and non-ozonized samples. Results: This study showed that ozonization with 5 g/h for 3 hours, 5 g/h for 5 hours, 10 g/h for 3 hours, and 10 g/h for 5 hours leads to about 25%, 25%, 53%, and 46% reduction in date mold and yeast load and about 6%, 9%, 76%, and 74.7% reduction in date bacterial load at baseline phase, respectively. Appropriate concentration and duration of ozonization for microbial load reduction were 10 g/h and 3 hours. Conclusion: Date ozonization is an appropriate method for microbial load reduction and leads to an increase in the shelf life of dates. PMID:24124432

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children

OpenAIRE

Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

2017-01-01

Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease. Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints. Methods: In five 10-year-old children, biofilm was collected from th...

Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

Science.gov (United States)

Radhakrishnan, Srinivasan; Varadharajan, Mohan

2016-06-01

Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methodological approaches for studying the microbial ecology of drinking water distribution systems.

Science.gov (United States)

Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Microbial population analysis improves the evidential value of faecal traces in forensic investigations.

Science.gov (United States)

Quaak, Frederike C A; de Graaf, Mei-Lan M; Weterings, Rob; Kuiper, Irene

2017-01-01

The forensic science community has a growing interest in microbial population analysis, especially the microbial populations found inside and on the human body. Both their high abundance, microbes outnumber human cells by a factor 10, and their diversity, different sites of the human body harbour different microbial communities, make them an interesting tool for forensics. Faecal material is a type of trace evidence which can be found in a variety of criminal cases, but is often being ignored in forensic investigations. Deriving a human short tandem repeat (STR) profile from a faecal sample can be challenging. However, the microbial communities within faecal material can be of additional criminalistic value in linking a faecal trace to the possible donor. We present a microarray technique in which the faecal microbial community is used to differentiate between faecal samples and developed a decision model to predict the possible common origin of questioned samples. The results show that this technique may be a useful additional tool when no or only partial human STR profiles can be generated.

Boom clay pore water, home of a diverse microbial community

International Nuclear Information System (INIS)

Wouters, Katinka; Moors, Hugo; Leys, Natalie

2012-01-01

Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

Boom clay pore water, home of a diverse microbial community

Energy Technology Data Exchange (ETDEWEB)

Wouters, Katinka; Moors, Hugo; Leys, Natalie [SCK.CEN, Environment, Health and Safety Institute, B-2400 Mol (Belgium)

2012-10-15

Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

The importance of virulence prediction and gene networks in microbial risk assessment

DEFF Research Database (Denmark)

Wassenaar, Gertrude Maria; Gamieldien, Junaid; Shatkin, JoAnne

2007-01-01

For microbial risk assessment, it is necessary to recognize and predict Virulence of bacterial pathogens, including their ability to contaminate foods. Hazard characterization requires data on strain variability regarding virulence and survival during food processing. Moreover, information...... and characterization of microbial hazards, including emerging pathogens, in the context of microbial risk assessment....

Shotgun microbial profiling of fossil remains

DEFF Research Database (Denmark)

Der Sarkissian, Clio; Ermini, Luca; Jónsson, Hákon

2014-01-01

the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach...... to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial...... community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using...

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

Science.gov (United States)

Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

Directory of Open Access Journals (Sweden)

Xiaohui Wang

Full Text Available BACKGROUND: Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. AIMS: To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs and to understand the effects of environmental factors on their structure. METHODS: 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. RESULTS: High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO, ammonia concentrations and loading rate of chemical oxygen demand (COD. Based on the variance partitioning analyses (VPA, a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25% and operational parameters (23%, respectively. CONCLUSIONS: This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Active microbial community structure of deep subsurface sediments within Baltic Sea Basin

Science.gov (United States)

Reese, B. K.; Zinke, L.; Carvalho, G.; Lloyd, K. G.; Marshall, I.; Shumaker, A.; Amend, J.

2014-12-01

The Baltic Sea Basin (BSB) is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of climatic fluctuations over past tens of thousands of years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates make this an ideal setting to understand the microbial structure of a deep biosphere community in a relatively high carbon, and thus high-energy environment, compared to other deep subsurface sites. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The active microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further refine our understanding of the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease PatientsSummary

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Jonathan P. Jacobs

2016-11-01

Full Text Available Background & Aims: Microbes may increase susceptibility to inflammatory bowel disease (IBD by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives. Methods: Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn’s disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing, untargeted liquid chromatography–mass spectrometry metabolomics, and calprotectin measurement. Individuals were grouped into microbial and metabolomics states using Dirichlet multinomial models. Multivariate models were used to identify microbes and metabolites associated with these states. Results: Individuals were classified into 2 microbial community types. One was associated with IBD but irrespective of disease status, had lower microbial diversity, and characteristic shifts in microbial composition including increased Enterobacteriaceae, consistent with dysbiosis. This microbial community type was associated similarly with IBD and reduced microbial diversity in an independent pediatric cohort. Individuals also clustered bioinformatically into 2 subsets with shared fecal metabolomics signatures. One metabotype was associated with IBD and was characterized by increased bile acids, taurine, and tryptophan. The IBD-associated microbial and metabolomics states were highly correlated, suggesting that they represented an integrated ecosystem. Healthy relatives with the IBD-associated microbial community type had an increased incidence of elevated fecal calprotectin. Conclusions: Healthy first-degree relatives can have dysbiosis associated with an altered intestinal metabolome that may signify a predisease microbial

Microbial processes in radioactive waste repository

International Nuclear Information System (INIS)

Gazso, L.; Farkas-Galgoczi, G.; Diosi, G.

2002-01-01

Microbial processes could potentially affect the performance of a radioactive waste disposal system and related factors that could have an influence on the mobility of radionuclides are outlined. Analytical methods, including sampling of water, rock and surface swabs from a potential disposal site, are described and the quantitative as well as qualitative experimental results obtained are given. Although the results contribute to an understanding of the impact of microbial processes on deep geological disposal of nuclear waste, there is not yet sufficient information for a model which will predict the consequences of these processes. (author)

Microbial Load of Some Medicinal Plants Sold in Some Local ...

African Journals Online (AJOL)

Microbial Load of Some Medicinal Plants Sold in Some Local Markets in Abeokuta, Nigeria. I MacDonald, S Omonigho, J Erhabor, H Efijuemue. Abstract. Purpose: To evaluate the microbial load on 17 randomly selected plant samples from 60 ethnobotanically collected medicinal plants from five local markets in Abeokuta, ...

Effects of Microbial Transglutaminase on Physicochemical, Microbial and Sensorial Properties of Kefir Produced by Using Mixture Cow's and Soymilk.

Science.gov (United States)

Temiz, Hasan; Dağyıldız, Kübra

2017-01-01

The objective of this research was to investigate the effects microbial transglutaminase (m-TGs) on the physicochemical, microbial and sensory properties of kefir produced by using mix cow and soymilk. Kefir batches were prepared using 0, 0.5, 1 and 1.5 Units m-TGs for per g of milk protein. Adding m-TGs to milk caused an increase in the pH and viscosity and caused a decrease in titratable acidity and syneresis in the kefir samples. Total bacteria, lactobacilli and streptococci counts decreased, while yeast counts increased in all the samples during storage. Alcohols and acids compounds have increased in all the samples except in the control samples, while carbonyl compounds have decreased in all the samples during storage (1-30 d). The differences in the percentage of alcohols, carbonyl compounds and acids in total volatiles on the 1st and the 30th d of storage were observed at 8.47-23.52%, 6.94-25.46% and 59.64-63.69%, respectively. The consumer evaluation of the kefir samples showed that greater levels of acceptability were found for samples which had been added 1.5 U m-TGs for per g of milk protein.

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

DEFF Research Database (Denmark)

Zhang, Yifeng; Angelidaki, Irini

2011-01-01

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

Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

Science.gov (United States)

Yu, Ping; Chen, Xingge; Li, Peng

2017-09-01

Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

High-resolution phylogenetic microbial community profiling

Energy Technology Data Exchange (ETDEWEB)

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

Microbial proteomics: a mass spectrometry primer for biologists

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Graham Ciaren

2007-08-01

Full Text Available Abstract It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level. In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.

MICROBIAL QUALITY OF HONEY MIXTURE WITH POLLEN

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Ján Mareček

2011-02-01

Full Text Available Normal 0 21 MicrosoftInternetExplorer4 The aim of this study was evaluation of microbial quality in raw materials (honey, pollen and evaluation of microbial quality in honey mixture with pollen (2.91 % and 3.85 % and also dynamics of microbial groups in honey mixtures with pollen after 14 days storage at the room temperature (approximately 25 °C and in cold store (8 °C. We used dilution plating method for testing of samples. Detections of total plate microbial count (aerobic and anaerobic microorganisms, sporulating bacteria, coliform bacteria, Bifidobacterium sp., Lactobacillus sp. and microscopic fungi were performed. In general, counts of microorganisms decreased in honey mixture with pollen compared to raw pollen and these counts increased compared to natural honey. Total plate count was 5.37 log KTJ.g-1 in pollen; 1.36 log KTJ.g-1 in honey; 2.97 log KTJ.g-1 in honey mixture with 2.91 % pollen and 2.04 log KTJ.g-1 in honey mixture with 3.85 % pollen. Coliform bacteria were detected in pollen (1.77 log KTJ.g-1. Then, we found coliform bacteria in one sample of honey mixtures with pollen (2.91 % - 1.00 log KTJ.g-1.Bifidobacterium species were detected only in raw pollen. We did not findLactobacillus sp. in any of the samples. Microscopic fungi were detected on two cultivating media. Yeasts were present in pollen sample (average 5.39 log KTJ.g-1, honey mixture with 2.91 % pollen (average 2.51 log KTJ.g-1 and honey mixture with 3.85 % pollen (average 1.58 log KTJ.g-1. Filamentous microscopic fungi were detectable in pollen (average 3.38 log KTJ.g-1, in honey (only on one medium: 1.00 log KTJ.g-1, in honey mixture with 2.91 % pollen (average 1.15 log KTJ.g-1 and in honey mixture with 3.85 % pollen (1.71 %. Raw pollen contained microscopic fungi as Absidiasp., Mucor sp., Alternaria sp. andEmericella nidulans. Honey mixture with 2.91 % pollen after storage (14 days contained lower microbial counts when compared with the sample

Microbial analysis of the buffer/container experiment at AECL's Underground Research Laboratory

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Hamon, C.J.; Haveman, S.A.; Delaney, T.L.

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs

Impact of long-term diesel contamination on soil microbial community structure

DEFF Research Database (Denmark)

Sutton, Nora; Maphosa, Farai; Morillo, Jose

2013-01-01

Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical...... properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean...... observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific...

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

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Kevin W. Hager

2017-08-01

Full Text Available The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity.

Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments.

Science.gov (United States)

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-11-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

Science.gov (United States)

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Evaluating Monitoring Strategies to Detect Precipitation-Induced Microbial Contamination Events in Karstic Springs Used for Drinking Water

Directory of Open Access Journals (Sweden)

Michael D. Besmer

2017-11-01

Full Text Available Monitoring of microbial drinking water quality is a key component for ensuring safety and understanding risk, but conventional monitoring strategies are typically based on low sampling frequencies (e.g., quarterly or monthly. This is of concern because many drinking water sources, such as karstic springs are often subject to changes in bacterial concentrations on much shorter time scales (e.g., hours to days, for example after precipitation events. Microbial contamination events are crucial from a risk assessment perspective and should therefore be targeted by monitoring strategies to establish both the frequency of their occurrence and the magnitude of bacterial peak concentrations. In this study we used monitoring data from two specific karstic springs. We assessed the performance of conventional monitoring based on historical records and tested a number of alternative strategies based on a high-resolution data set of bacterial concentrations in spring water collected with online flow cytometry (FCM. We quantified the effect of increasing sampling frequency and found that for the specific case studied, at least bi-weekly sampling would be needed to detect precipitation events with a probability of >90%. We then proposed an optimized monitoring strategy with three targeted samples per event, triggered by precipitation measurements. This approach is more effective and efficient than simply increasing overall sampling frequency. It would enable the water utility to (1 analyze any relevant event and (2 limit median underestimation of peak concentrations to approximately 10%. We conclude with a generalized perspective on sampling optimization and argue that the assessment of short-term dynamics causing microbial peak loads initially requires increased sampling/analysis efforts, but can be optimized subsequently to account for limited resources. This offers water utilities and public health authorities systematic ways to evaluate and optimize their

Mars Sample Return: Mars Ascent Vehicle Mission and Technology Requirements

Science.gov (United States)

Bowles, Jeffrey V.; Huynh, Loc C.; Hawke, Veronica M.; Jiang, Xun J.

2013-01-01

A Mars Sample Return mission is the highest priority science mission for the next decade recommended by the recent Decadal Survey of Planetary Science, the key community input process that guides NASAs science missions. A feasibility study was conducted of a potentially simple and low cost approach to Mars Sample Return mission enabled by the use of developing commercial capabilities. Previous studies of MSR have shown that landing an all up sample return mission with a high mass capacity lander is a cost effective approach. The approach proposed is the use of an emerging commercially available capsule to land the launch vehicle system that would return samples to Earth. This paper describes the mission and technology requirements impact on the launch vehicle system design, referred to as the Mars Ascent Vehicle (MAV).

GC and GC-MS characterization of crude oil transformation in sediments and microbial mat samples after the 1991 oil spill in the Saudi Arabian Gulf coast

International Nuclear Information System (INIS)

Garcia de Oteyza, T.; Grimalt, J.O.

2006-01-01

The massive oil discharge in the Saudi Arabian coast at the end of the 1991 Gulf War is used here as a natural experiment to study the ability of microbial mats to transform oil residues after major spills. The degree of oil transformation has been evaluated from the analysis of the aliphatic and aromatic hydrocarbons by gas chromatography (GC) and GC coupled to mass spectrometry (GC-MS). The oil-polluted microbial mat samples from coastal environments exhibited an intermediate degree of transformation between that observed in superficial and deep sediments. Evaporation, photo-oxidation and water-washing seemed to lead to more effective and rapid elimination of hydrocarbons than cyanobacteria and its associated microorganisms. Furthermore, comparison of some compounds (e.g. regular isoprenoid hydrocarbons or alkylnaphthalenes) in the oil collected in the area after the spill or in the mixtures retained by cyanobacterial growth gave rise to an apparent effect of hydrocarbon preservation in the microbial mat ecosystems. - Cyanobacterial mats inhibit degradation of oil by reducing exposure to the atmosphere and seawater

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers.

Science.gov (United States)

Zhang, Xi Mei; Zhang, Zheng Yu; Zhang, Chen Huan; Wu, Jing; Wang, You Xin; Zhang, Guo Xin

2018-01-01

A case control study including 45 acute pancreatitis and 44 healthy volunteers was performed to investigate the association between intestinal microbial community and acute pancreatitis. High-throughput 16S rRNA gene amplicon sequencing was used to profile the microbiological composition of the samples. In total, 27 microbial phyla were detected and the samples of pancreatitis patients contained fewer phyla. Samples from acute pancreatitis patients contained more Bacteroidetes and Proteobacteria and fewer Firmicutes and Actinobacteria than those from healthy volunteers. PCoA analyses distinguished the fecal microbial communities of acute pancreatitis patients from those of healthy volunteers. The intestinal microbes of acute pancreatitis patients are different from those of healthy volunteers. Modulation of the intestinal microbiome may serve as an alternative strategy for treating acute pancreatitis. Copyright © 2018 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

Science.gov (United States)

Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

2016-01-01

Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

Soil Microbial Activity in Conventional and Organic Agricultural Systems

Directory of Open Access Journals (Sweden)

Romero F.V. Carneiro

2009-06-01

Full Text Available The aim of this study was to evaluate microbial activity in soils under conventional and organic agricultural system management regimes. Soil samples were collected from plots under conventional management (CNV, organic management (ORG and native vegetation (AVN. Soil microbial activity and biomass was significantly greater in ORG compared with CNV. Soil bulk density decreased three years after adoption of organic system. Soil organic carbon (SOC was higher in the ORG than in the CNV. The soil under organic agricultural system presents higher microbial activity and biomass and lower bulk density than the conventional agricultural system.

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

Science.gov (United States)

Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

2017-12-28

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

Studies of the effects of gamma irradiation on the microbial load and physicochemical properties of Ghanaian honey from the Ashanti, Brong Ahafo and Greater Accra regions

International Nuclear Information System (INIS)

Ansah Larbi, D.

2015-01-01

, Apparent Sucrose and Ash content) of honey. The honey samples were analyzed for the presence of Total Viable Counts, Faecal sp., Clostridium sp., Staphylococcus sp., and Salmonella sp. The Plate Count Method of microbial analyses was used to determine the microbes. For the Total Viable Count, Plate Count Agar was the media used; Eosin Methylene Blue agar for Faecal sp., Perfringens Agar for Clostridium sp., Xylose Lysine Deoxycholate Agar for Salmonella sp., and Baird Parker Agar for Staphylococcus sp. The samples were also analyzed for Reducing Sugar and Apparent Sucrose using Titrimetry. pH was determined with a pH meter and Ash Content was determined by Gravimetry. The pH values obtained for the Honey Comb samples were in the range (3.6 – 3.9), and the pH for the Retail samples were in the range (4.9 – 5.6). Microorganisms were not detected in about 70% of the honey sampled directly from the honey comb and the mean microbial count in the remaining 30% were within the range 30% - 35% whereas all the honey sampled from the retailers were contaminated with microbes. The mean microbial counts in the retailer samples were 148 CFU/g, 183 CFU/g and 271 CFU /g for Ashanti, Brong Ahafo and Greater Accra Regions respectively. These values were significantly higher than the required maximum relative to the MERCOSUR (Mercado Comun del SUR) standard (≤ 100 CFU/g). The low level of microbial detection in the Honey Comb samples (30 – 35 CFU/g) could be due to their relatively low pH levels (3.6 – 3.9) compared to the retailer samples with pH within 4.9 – 5.6. The ash content of all the honey sampled and analyzed were within the required standard with an average of 0.16% in the honey comb samples and average of 0.62% for the retail samples. The apparent sucrose concentration (in percentage) in honey sampled from the retailers were within the range 22% - 33% which is beyond the required maximum as stipulated by the CODEX Alimentarius Commission (≤ 10%). From the study, it

Advancing analytical algorithms and pipelines for billions of microbial sequences.

Science.gov (United States)

Gonzalez, Antonio; Knight, Rob

2012-02-01

The vast number of microbial sequences resulting from sequencing efforts using new technologies require us to re-assess currently available analysis methodologies and tools. Here we describe trends in the development and distribution of software for analyzing microbial sequence data. We then focus on one widely used set of methods, dimensionality reduction techniques, which allow users to summarize and compare these vast datasets. We conclude by emphasizing the utility of formal software engineering methods for the development of computational biology tools, and the need for new algorithms for comparing microbial communities. Such large-scale comparisons will allow us to fulfill the dream of rapid integration and comparison of microbial sequence data sets, in a replicable analytical environment, in order to describe the microbial world we inhabit. Copyright © 2011 Elsevier Ltd. All rights reserved.

Limiting Factors for Microbial Fe(III)-Reduction In a Landfill Leachate Polluted Aquifer (Vejen, Denmark)

DEFF Research Database (Denmark)

Albrechtsen, Hans-Jørgen; Heron, Gorm; Christensen, Thomas Højlund

1995-01-01

Aquifer sediment samples from two locations within the anaerobic leachate plume of a municipal landfill were compared with respect to microbiology (especially Fe(III)-reduction) and geochemistry. The samples close to the landfill were characterized by low contents of Fe(III), whereas samples from...... the more distant cluster were rich in Fe(III)-oxides. The active microbial population seemed to be less dense in samples more distant from the landfill (measured by ATP and phospholipid fatty acids (PLFA)), but the microbial communities were very similar in the two sample clusters according...... to the composition of PLFA. Very little, if any, Fe(III)-reduction was observed close to the landfill, but all the more distant samples showed evident microbially mediated Fe(III)-reduction. After amendment with both acetate and Fe(III), all the samples showed a potential for Fe(III)-reduction, and the in situ Fe...

Global Microbial Identifier

DEFF Research Database (Denmark)

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

2017-01-01

) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source...... of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global...... microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require...

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

The use of microarrays in microbial ecology

Energy Technology Data Exchange (ETDEWEB)

Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

2009-09-15

Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

Science.gov (United States)

Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

2014-01-01

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

Directory of Open Access Journals (Sweden)

Thomas H A Haverkamp

Full Text Available Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm sediment communities are affected by local conditions within the sediment.

Simultaneous amplification of two bacterial genes: more reliable method of Helicobacter pylori detection in microbial rich dental plaque samples.

Science.gov (United States)

Chaudhry, Saima; Idrees, Muhammad; Izhar, Mateen; Butt, Arshad Kamal; Khan, Ayyaz Ali

2011-01-01

Polymerase Chain reaction (PCR) assay is considered superior to other methods for detection of Helicobacter pylori (H. pylori) in oral cavity; however, it also has limitations when sample under study is microbial rich dental plaque. The type of gene targeted and number of primers used for bacterial detection in dental plaque samples can have a significant effect on the results obtained as there are a number of closely related bacterial species residing in plaque biofilm. Also due to high recombination rate of H. pylori some of the genes might be down regulated or absent. The present study was conducted to determine the frequency of H. pylori colonization of dental plaque by simultaneously amplifying two genes of the bacterium. One hundred dental plaque specimens were collected from dyspeptic patients before their upper gastrointestinal endoscopy and presence of H. pylori was determined through PCR assay using primers targeting two different genes of the bacterium. Eighty-nine of the 100 samples were included in final analysis. With simultaneous amplification of two bacterial genes 51.6% of the dental plaque samples were positive for H. pylori while this prevalence increased to 73% when only one gene amplification was used for bacterial identification. Detection of H. pylori in dental plaque samples is more reliable when two genes of the bacterium are simultaneously amplified as compared to one gene amplification only.

Stable, geochemically mediated biospheres in the Deep Mine Microbial Observatory, SD, USA

Science.gov (United States)

Osburn, M. R.; Casar, C. P.; Kruger, B.; Flynn, T. M.

2017-12-01

The terrestrial subsurface is a vast reservoir of life, hosting diverse microbial ecosystems with varying levels of connectivity to surface inputs. Understanding long term ecosystem dynamics within the subsurface biosphere is very challenging due to limitations in accessibility, sample availability, and slow microbial growth rates. The establishment of the Deep Mine Microbial Observatory (DeMMO) at the Sanford Underground Research Facility, SD, USA has allowed for bimonthly sampling for nearly two years at six sites spanning 250 to 1500 m below the surface. Here we present a time-resolved analysis of the geomicrobiology of the six DeMMO sites, which have been created from legacy mine boreholes modified to allow for controlled sampling. Our interdisciplinary approach includes analysis of passively draining fracture fluid for aqueous and gas geochemistry, DNA sequencing, microscopy, and isotopic measurements of organic and inorganic substrates. Fluid geochemistry varies significantly between sites, but is relatively stable over time for a given site, even through significant external perturbations such as drilling and installation of permanent sampling devices into the boreholes. The fluid-hosted microbial diversity follows these trends, with consistent populations present at each site through time, even through drilling events. For instance, the shallowest site (DeMMO 1) consistently hosts >30% uncharacterized phyla and >25% Omnitrophica whereas the deepest site (DeMMO 6) is dominated by Firmicutes and Bacterioidetes. Microbial diversity appears to respond to the availability of energy sources such as organic carbon, sulfate, sulfide, hydrogen, and iron. Carbon isotopic measurements reveal closed system behavior with significant recycling of organic carbon into the DIC pool. Together these observations suggest DeMMO hosts isolated subsurface microbial populations adapted to local geochemistry that are stable on yearlong timescales.

Genome-reconstruction for eukaryotes from complex natural microbial communities.

Science.gov (United States)

West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

2018-04-01

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

Potential microbial risk factors related to soil amendments and irrigation water of potato crops.

Science.gov (United States)

Selma, M V; Allende, A; López-Gálvez, F; Elizaquível, P; Aznar, R; Gil, M I

2007-12-01

This study assesses the potential microbial risk factors related to the use of soil amendments and irrigation water on potato crops, cultivated in one traditional and two intensive farms during two harvest seasons. The natural microbiota and potentially pathogenic micro-organisms were evaluated in the soil amendment, irrigation water, soil and produce. Uncomposted amendments and residual and creek water samples showed the highest microbial counts. The microbial load of potatoes harvested in spring was similar among the tested farms despite the diverse microbial levels of Listeria spp. and faecal coliforms in the potential risk sources. However, differences in total coliform load of potato were found between farms cultivated in the autumn. Immunochromatographic rapid tests and the BAM's reference method (Bacteriological Analytical Manual; AOAC International) were used to detect Escherichia coli O157:H7 from the potential risk sources and produce. Confirmation of the positive results by polymerase chain reaction procedures showed that the immunochromatographic assay was not reliable as it led to false-positive results. The potentially pathogenic micro-organisms of soil amendment, irrigation water and soil samples changed with the harvest seasons and the use of different agricultural practices. However, the microbial load of the produce was not always influenced by these risk sources. Improvements in environmental sample preparation are needed to avoid interferences in the use of immunochromatographic rapid tests. The potential microbial risk sources of fresh produce should be regularly controlled using reliable detection methods to guarantee their microbial safety.

Quantitative monitoring of microbial species during bioleaching of a copper concentrate

Directory of Open Access Journals (Sweden)

Sabrina Hedrich

2016-12-01

Full Text Available 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.

Science.gov (United States)

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.

Microbial analysis of the buffer/container experiment at AECL`s Underground Research Laboratory

Energy Technology Data Exchange (ETDEWEB)

Stroes-Gascoyne, S; Hamon, C J; Haveman, S A; Delaney, T L [Atomic Energy of Canada Ltd., Pinawa, MB (Canada). Whiteshell Labs; Pedersen, K; Ekendahl, S; Jahromi, N; Arlinger, J; Hallbeck, L [Univ. of Goeteborg, (Sweden). Dept. of General and Marine Microbiology; Daumas, S; Dekeyser, K [Guiges Recherche Appliquee en Microbiologie, Aix-en-Provence, (France)

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs.

A communal catalogue reveals Earth's multiscale microbial diversity.

Science.gov (United States)

Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

2017-11-23

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

DNA metabarcoding of microbial communities for healthcare

Directory of Open Access Journals (Sweden)

Zaets I. Ye.

2016-02-01

Full Text Available High-throughput sequencing allows obtaining DNA barcodes of multiple species of microorganisms from single environmental samples. Next Generation Sequencing (NGS-based profiling provides new opportunities to evaluate the human health effect of microbial community members affiliated to probiotics. The DNA metabarcoding may serve to a quality control of microbial communities, comprising complex probiotics and other fermented foods. A detailed inventory of complex communities is a pre-requisite of understanding their functionality as whole entities that makes it possible to design more effective bio-products by precise replacement of one community member by others. The present paper illustrates how the NGS-based DNA metabarcoding aims at the profiling of both wild and hybrid multi-microbial communities with the example of kombucha probiotic beverage fermented by yeast-bacterial partners.

MICROBIAL STATUS OF DONKEY’S MILK: FIRST RESULTS

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L. Alberghini

2012-08-01

Full Text Available For its chemical and nutritional composition donkey milk is an excellent substitute for human breast milk. In fact, woman’s milk and donkey one are quite similar for their composition and for certain intrinsic properties. Based on these considerations, we performed a study on the microbiological characteristics of 86 jannet’s milk in 10 farms. Special attention was given to the aspects of health quality of the milk samples examined, referring to the analysis of total microbial count and pH, the possible presence of potentially pathogenic micro-organisms, especially by seeking the bacteria Escherichia coli O157, Salmonella spp., Listeria monocytogenes and Campylobacter spp. The samples of milk were picked up from January to March 2010. Our research showed a situation quite positive in terms of sanitation, finding levels of total microbial count (on average 1,8·104 cfu/ml and pH (mean 7,02 entirely in line with data found in previous investigations of other Authors and with values reassuring in terms of healthiness of the product. Regarding the detection of potentially pathogenic microorganisms, only a milk sample of 86 tested was positive for E. coli O157; in an other sample low charges of Campylobacter spp. have been measured. Salmonella spp. and Listeria monocytogenes were not found in all samples. Total microbial count confirm the good quality of the donkey milk. However, occasional isolation of E. coli O157 and Campylobacter spp. suggests careful attention is to be done to the correct procedures of milking hygiene.

Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

DEFF Research Database (Denmark)

Damgaard, Ida; Bjerg, Poul Løgstrup; Bælum, Jacob

2013-01-01

subsampling of the clay till cores. The study demonstrates that an integrated approach combining chemical analysis, molecular microbial tools and compound specific isotope analysis (CSIA) was required in order to document biotic and abiotic degradations in the clay till system. © 2013 Elsevier B.V.......The degradation of chlorinated ethenes and ethanes in clay till was investigated at a contaminated site (Vadsby, Denmark) by high resolution sampling of intact cores combined with groundwater sampling. Over decades of contamination, bioactive zones with degradation of trichloroethene (TCE) and 1...

Microbial quality of some medicinal herbal products in Kashan, Iran

Directory of Open Access Journals (Sweden)

Mazroi Arani Navid

2014-04-01

Full Text Available Introduction: The use of medicinal plants has risen worldwide. In Iran, herbal waters and rose waters are of traditional medicinal products and as a result, they are widespreadly consumed. Therefore, diagnosis of microbial quality of these products is important. The aim of this study was to evaluate microbial quality of herbal extracts distributed in Kashan, Iran. Methods: In this descriptive study, 256 samples of herbal waters and 191 samples of rose waters (total samples of 447 distributed in Kashan during 2012 to 2013 were purchased and transferred to laboratory. Then microbial tests such as total aerobic bacterial count, mold and yeast count, total coliforms, and detection of Enterococcus, Pseudomonas and sulphite-reducing Clostridia were evaluated based on national standard of Iran. Results: Contamination with Pseudomonas and Enterococcus was observed in the herbal water samples. 196 cases (43.84% of the total samples, 113 cases (44.15% of the herbal waters and 83 cases (43.45% of the rose waters were usable based on the national standard of Iran. Neither herbal waters nor rosewater samples were contaminated by E.Coli and Sulphite-reducing clostridia. Additionally, none of the rosewater samples was contaminated by Coliforms and Pseudomonas. Conclusion: Based on the findings and due to the fact that these products are contaminated with aerobic mesophilic bacteria, mold and yeast, to minimize the risks we recommend to apply pasteurized temperature, high-quality packaging material and hygiene observance in processing time of herbal waters and rose waters.

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania.

Directory of Open Access Journals (Sweden)

Timothy R Julian

Full Text Available Diarrheal diseases are a leading cause of under-five mortality and morbidity in sub-Saharan Africa. Quantitative exposure modeling provides opportunities to investigate the relative importance of fecal-oral transmission routes (e.g. hands, water, food responsible for diarrheal disease. Modeling, however, requires accurate descriptions of individuals' interactions with the environment (i.e., activity data. Such activity data are largely lacking for people in low-income settings. In the present study, we collected activity data and microbiological sampling data to develop a quantitative microbial exposure model for two female caretakers in peri-urban Tanzania. Activity data were combined with microbiological data of contacted surfaces and fomites (e.g. broom handle, soil, clothing to develop example exposure profiles describing second-by-second estimates of fecal indicator bacteria (E. coli and enterococci concentrations on the caretaker's hands. The study demonstrates the application and utility of video activity data to quantify exposure factors for people in low-income countries and apply these factors to understand fecal contamination exposure pathways. This study provides both a methodological approach for the design and implementation of larger studies, and preliminary data suggesting contacts with dirt and sand may be important mechanisms of hand contamination. Increasing the scale of activity data collection and modeling to investigate individual-level exposure profiles within target populations for specific exposure scenarios would provide opportunities to identify the relative importance of fecal-oral disease transmission routes.

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania.

Science.gov (United States)

Julian, Timothy R; Pickering, Amy J

2015-01-01

Diarrheal diseases are a leading cause of under-five mortality and morbidity in sub-Saharan Africa. Quantitative exposure modeling provides opportunities to investigate the relative importance of fecal-oral transmission routes (e.g. hands, water, food) responsible for diarrheal disease. Modeling, however, requires accurate descriptions of individuals' interactions with the environment (i.e., activity data). Such activity data are largely lacking for people in low-income settings. In the present study, we collected activity data and microbiological sampling data to develop a quantitative microbial exposure model for two female caretakers in peri-urban Tanzania. Activity data were combined with microbiological data of contacted surfaces and fomites (e.g. broom handle, soil, clothing) to develop example exposure profiles describing second-by-second estimates of fecal indicator bacteria (E. coli and enterococci) concentrations on the caretaker's hands. The study demonstrates the application and utility of video activity data to quantify exposure factors for people in low-income countries and apply these factors to understand fecal contamination exposure pathways. This study provides both a methodological approach for the design and implementation of larger studies, and preliminary data suggesting contacts with dirt and sand may be important mechanisms of hand contamination. Increasing the scale of activity data collection and modeling to investigate individual-level exposure profiles within target populations for specific exposure scenarios would provide opportunities to identify the relative importance of fecal-oral disease transmission routes.

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

Science.gov (United States)

Shade, Ashley; Carey, Cayelan C; Kara, Emily; Bertilsson, Stefan; McMahon, Katherine D; Smith, Matthew C

2009-08-01

Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

OpenAIRE

Stewart, Frank J.; Ulloa, Osvaldo; DeLong, Edward

2010-01-01

Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycl...

Enrichment and isolation of microbial strains degrading bioplastic ...

African Journals Online (AJOL)

acer

2015-07-08

Jul 8, 2015 ... The sea sediments and sea water samples were collected from sites highly polluted with plastic waste from one of the beaches of Mumbai, India. Polymer sample. PVA (M.W. 125000) in powdered form was purchased from S. D.. Fine Chemicals, Mumbai, India. Enrichment of PVA degrading microbial stains.

Technical assessment of compliance with work place air sampling requirements at T Plant. Revision No. 1

International Nuclear Information System (INIS)

Hackworth, M.F.

1995-01-01

The US DOE requires its contractors to conduct air sampling to detect and evaluate airborne radioactive material in the workplace. Hanford Reservation T Plant compliance with workplace air sampling requirements has been assessed. Requirements, basis for determining compliance and recommendations are included

Distribution of the dominant microbial communities in marine sediments containing high concentrations of gas hydrates

Energy Technology Data Exchange (ETDEWEB)

Briggs, B.; Colwell, F.; Carini, P.; Torres, M. [Oregon State Univ., Corvallis, OR (United States); Hangsterfer, A.; Kastner, M. [California Univ., San Diego, CA (United States). Scripps Inst. of Oceanography; Brodie, E. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Center for Environmental Biotechnology; Daly, R. [California Univ., Berkeley, CA (United States); Holland, M. [GeoTek, Daventry, Northants (United Kingdom); Long, P.; Schaef, H. [Pacific Northwest National Laboratory, Richland, WA (United States). Environmental Technology; Delwiche, M. [Idaho National Laboratory, Idaho Falls, ID (United States). Biotechnology; Winters, W. [United States Geological Survey, Woods Hole, MA (United States). Woods Hole Science Center; Riedel, M. [McGill Univ., Montreal, PQ (Canada). Dept. of Earth and Planetary Sciences

2008-07-01

Methane produced by microorganisms represents a large portion of the methane that occurs in marine sediments where gas hydrates are present. The diverse communities that populate these formations have been documented by cultures or through molecular traces. Previous studies have explored the biogeography of hydrate-bearing systems by comparing clone libraries developed from sediments where hydrates are abundant with those developed from sediments that lack hydrates. There is a distinct microbial community present in sediments that have methane hydrates. This paper presented an investigation into finer-scale biogeography, in order to determine how factors such as the presence or absence of hydrates, grain size, and the depositional environment in marine sediments may control the number, type and distribution of microbial communities in sediments. The purpose of the study was to understand the controls on the distribution and activity of all microbes that contribute to the conversion of organic matter to methane. To this aim, DNA was extracted from deep marine sediments cored from continental slope locations including offshore India and the Cascadia Margin. The data from the study was used to refine computational models that require biological rate terms that are consistent with sediment conditions in order to accurately describe the dynamics of this large methane reservoir. The paper discussed the materials and methods used for the study, including the sample site, sample collection and microbiological analysis. Results were presented in terms of DNA extractions; microbial diversity; and biofilm analyses. It was concluded that the findings from the study complemented previously reported studies which indicated the presence of diverse microbial communities in sediments containing methane hydrates. 9 refs., 5 figs.

Effects of Microbial Transglutaminase on Physicochemical, Microbial and Sensorial Properties of Kefir Produced by Using Mixture Cow’s and Soymilk

Science.gov (United States)

2017-01-01

The objective of this research was to investigate the effects microbial transglutaminase (m-TGs) on the physicochemical, microbial and sensory properties of kefir produced by using mix cow and soymilk. Kefir batches were prepared using 0, 0.5, 1 and 1.5 Units m-TGs for per g of milk protein. Adding m-TGs to milk caused an increase in the pH and viscosity and caused a decrease in titratable acidity and syneresis in the kefir samples. Total bacteria, lactobacilli and streptococci counts decreased, while yeast counts increased in all the samples during storage. Alcohols and acids compounds have increased in all the samples except in the control samples, while carbonyl compounds have decreased in all the samples during storage (1-30 d). The differences in the percentage of alcohols, carbonyl compounds and acids in total volatiles on the 1st and the 30th d of storage were observed at 8.47-23.52%, 6.94-25.46% and 59.64-63.69%, respectively. The consumer evaluation of the kefir samples showed that greater levels of acceptability were found for samples which had been added 1.5 U m-TGs for per g of milk protein. PMID:28943774

Technical assessment of compliance with workplace air sampling requirements in the 300 Area

International Nuclear Information System (INIS)

Olsen, P.A.

1995-01-01

The purpose of this Technical Work Document is to satisfy HSRCM-1, the ''Hanford Site Radiological Control Manual.'' Article 551.4 of that manual states a requirement for a documented study of facility workplace air sampling programs (WPAS). This first revision of the original Supporting Document covers the period from January 1, 1995 to December 31, 1995. HSRCM-1 is the primary guidance for radiological control at Westinghouse Hanford Company (WHC). It was written to implement DOE/EH-0256T ''US Department of Energy Radiological Control Manual'' as it applies to programs at Hanford. As such, it complies with Title 10, Part 835 of the Code of Federal Regulations. There are also several Department of Energy (DOE) Orders, national consensus standards, and reports that provide criteria, standards, and requirements for workplace air sampling programs. This document provides a summary of these, as they apply to WHC facility workplace air sampling programs. This document also provides an evaluation of the compliance of 300 Areas' workplace air sampling program to the criteria, standards, and requirements and documents compliance with the requirements where appropriate. Where necessary, it also indicates changes needed to bring specific locations into compliance. The areas evaluated were the 340 Facility, the Advanced Reactor Operations Division Facilities, the N Reactor Fuels Supply Facility, and The Geotechnical Engineering Laboratory

Soil fertilization leads to a decline in between-samples variability of microbial community δ13C profiles in a grassland fertilization experiment.

Directory of Open Access Journals (Sweden)

Stavros D Veresoglou

Full Text Available Gas chromatography combustion isotope ratio mass spectrometry (GC-C-IRMS was used to measure the (13C/(12C ratios of PLFAs at natural abundance levels from a temperate grassland nitrogen (N and phosphorus (P factorial fertilization experiment in northern Greece. In each plot two rhizosphere samples were derived centred around individual Agrostis capillaris and Prunella vulgaris plants. It was hypothesized that the isotopic signal of microbes that preferentially feed on recalcitrant litter such as fungi would be modified by fertilization more strongly than that of opportunistic microbes using labile C. Microbial community δ(13C was affected by both P and N fertilization regime and plant species identity. However, we have been unable to detect significant nutrient effects on individual groups of microbes when analyzed separately in contrast to our original hypothesis. Intra-treatment variability, as evaluated from Hartley's F(max tests in the five first PCA components axes as well as the size of the convex hulls in PCA scoreplots and Mahalanobis distances, was considerably higher in the non-fertilized controls. Moreover, a significant relationship was established between the change in PLFA abundances and their respective changes in δ(13C for the aggregate of samples and those simultaneously fertilized with N and P. We conclude that use of compound specific isotope analysis in the absence of labelling represents a valuable and overlooked tool in obtaining an insight of microbial community functioning.

Method Verification Requirements for an Advanced Imaging System for Microbial Plate Count Enumeration.

Science.gov (United States)

Jones, David; Cundell, Tony

2018-01-01

The Growth Direct™ System that automates the incubation and reading of membrane filtration microbial counts on soybean-casein digest, Sabouraud dextrose, and R2A agar differs only from the traditional method in that micro-colonies on the membrane are counted using an advanced imaging system up to 50% earlier in the incubation. Based on the recommendations in USP Validation of New Microbiological Testing Methods , the system may be implemented in a microbiology laboratory after simple method verification and not a full method validation. LAY ABSTRACT: The Growth Direct™ System that automates the incubation and reading of microbial counts on membranes on solid agar differs only from the traditional method in that micro-colonies on the membrane are counted using an advanced imaging system up to 50% earlier in the incubation time. Based on the recommendations in USP Validation of New Microbiological Testing Methods , the system may be implemented in a microbiology laboratory after simple method verification and not a full method validation. © PDA, Inc. 2018.

Iron oxyhydroxide mineralization on microbial extracellular polysaccharides

Energy Technology Data Exchange (ETDEWEB)

Chan, Clara S.; Fakra, Sirine C.; Edwards, David C.; Emerson, David; Banfield, Jillian F.

2010-06-22

Iron biominerals can form in neutral pH microaerophilic environments where microbes both catalyze iron oxidation and create polymers that localize mineral precipitation. In order to classify the microbial polymers that influence FeOOH mineralogy, we studied the organic and mineral components of biominerals using scanning transmission X-ray microscopy (STXM), micro X-ray fluorescence ({mu}XRF) microscopy, and high-resolution transmission electron microscopy (HRTEM). We focused on iron microbial mat samples from a creek and abandoned mine; these samples are dominated by iron oxyhydroxide-coated structures with sheath, stalk, and filament morphologies. In addition, we characterized the mineralized products of an iron-oxidizing, stalk-forming bacterial culture isolated from the mine. In both natural and cultured samples, microbial polymers were found to be acidic polysaccharides with carboxyl functional groups, strongly spatially correlated with iron oxyhydroxide distribution patterns. Organic fibrils collect FeOOH and control its recrystallization, in some cases resulting in oriented crystals with high aspect ratios. The impact of polymers is particularly pronounced as the materials age. Synthesis experiments designed to mimic the biomineralization processes show that the polysaccharide carboxyl groups bind dissolved iron strongly but release it as mineralization proceeds. Our results suggest that carboxyl groups of acidic polysaccharides are produced by different microorganisms to create a wide range of iron oxyhydroxide biomineral structures. The intimate and potentially long-term association controls the crystal growth, phase, and reactivity of iron oxyhydroxide nanoparticles in natural systems.

Quantitative microbiome profiling links gut community variation to microbial load.

Science.gov (United States)

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).

Selenite reduction by anaerobic microbial aggregates: Microbial community structure, and proteins associated to the produced selenium spheres.

Directory of Open Access Journals (Sweden)

Graciela eGonzalez-Gil

2016-04-01

Full Text Available Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0, insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20 % and Pseudomonadaceae (c.a.10 % were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (~200 m of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres

KAUST Repository

Gonzalez-Gil, Graciela

2016-04-26

Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0), insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20%) and Pseudomonadaceae (c.a.10%) were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (∼200 μm) of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano)spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Microbial Quality of Traditional Alcoholic Beverages Consumed in ...

African Journals Online (AJOL)

mbege', 'mnazi' and 'komoni' were subjected to microbiological assessments in order to determine their microbial quality and possible resistance to antibiotics among the isolated microorganisms. Twenty-seven samples were randomly ...

Carbon and nitrogen assimilation in deep subseafloor microbial cells

OpenAIRE

Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

2011-01-01

Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individua...

Technical assessment of workplace air sampling requirements at tank farm facilities. Revision 1

International Nuclear Information System (INIS)

Olsen, P.A.

1994-01-01

WHC-CM-1-6 is the primary guidance for radiological control at Westinghouse Hanford Company (WHC). It was written to implement DOE N 5480.6 ''US Department of Energy Radiological Control Manual'' as it applies to programs at Hanford which are now overseen by WHC. As such, it complies with Title 10, Part 835 of the Code of Federal Regulations. In addition to WHC-CM-1-6, there is HSRCM-1, the ''Hanford Site Radiological Control Manual'' and several Department of Energy (DOE) Orders, national consensus standards, and reports that provide criteria, standards, and requirements for workplace air sampling programs. This document provides a summary of these, as they apply to WHC facility workplace air sampling programs. This document also provides an evaluation of the compliance of Tank Farms' workplace air sampling program to the criteria, standards, and requirements and documents compliance with the requirements where appropriate. Where necessary, it also indicates changes needed to bring specific locations into compliance

Microbial Signatures of Cadaver Gravesoil During Decomposition.

Science.gov (United States)

Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

2016-04-01

Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

KAUST Repository

Zhang, Weipeng; Bougouffa, Salim; Wang, Yong; Lee, On On; Yang, Jiangke; Chan, Colin; Song, Xingyu; Qian, Pei-Yuan

2014-01-01

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Toward understanding the dynamics of microbial communities in an estuarine system.

Directory of Open Access Journals (Sweden)

Weipeng Zhang

Full Text Available Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE. The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

KAUST Repository

Zhang, Weipeng

2014-04-14

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.

Microbial ecology-based engineering of Microbial Electrochemical Technologies.

Science.gov (United States)

Koch, Christin; Korth, Benjamin; Harnisch, Falk

2018-01-01

Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Physicochemical and microbial assessment of spring water quality for drinking supply in Piedmont of Béni-Mellal Atlas (Morocco)

Science.gov (United States)

Barakat, Ahmed; Meddah, Redouane; Afdali, Mustapha; Touhami, Fatima

2018-04-01

The present study was conducted to examine the water quality of karst springs located along the Piedmont of Béni-Mellal Atlas (Morocco) for drinking purposes. Twenty-five water samples were collected from seven springs in June, July, August and September 2013, and May 2016 have been analyzed for their physicochemical and microbial characteristics. The analytical data of temperature, pH, DO, TAC, TH, oxidizability and NH4+ showed that all sampled springs are suitable as drinking water according to Moroccan and the World Health Organization (WHO) standards. Nevertheless, EC, turbidity, and NO3- were sometimes noted higher than the allowable limits, what would be ascribed to erosion and leaching of soil and karstic rocks. The microbial analysis revealed the presence of fecal contamination (total coliforms, E. coli, and intestinal enterococci) in all springs at various times. The water quality index (WQI) calculated based on physicochemical and microbial data reveled that water quality categorization for all sampling springs was found to be 'medium' to 'good' for drinking uses in the National Sanitation Foundation WQI (NSF-WQI), and ''necessary treatment becoming more extensive'' to ''purification not necessary'' in the Dinius' Second Index (D-WQI). The Aine Asserdoune and Foum el Anceur springs showed the good quality of drinking water. According to Moroccan standards for water used for drinking purposes, the waters belong to category A1 that requires becoming drinkable a simple physical treatment and disinfection. From the type of parameters present in quantities exceeding drinking water limits, it is very obvious that these water resources are under the influence of anthropogenic activities such as sewage, waste disposal, deforestation and agricultural activities, caused land degradation and nonpoint pollution sources. Environmental attention, such as systematic quality control and adequate treatment before being used for drinking use and access to sewage

Microbial respiration per unit microbial biomass increases with carbon-to-nutrient ratios in soils

Science.gov (United States)

Spohn, Marie; Chodak, Marcin

2015-04-01

The ratio of carbon-to-nutrient in forest floors is usually much higher than the ratio of carbon-to-nutrient that soil microorganisms require for their nutrition. In order to understand how this mismatch affects carbon cycling, the respiration rate per unit soil microbial biomass carbon - the metabolic quotient (qCO2) - was studied. This was done in a field study (Spohn and Chodak, 2015) and in a meta-analysis of published data (Spohn, 2014). Cores of beech, spruce, and mixed spruce-beech forest soils were cut into slices of 1 cm from the top of the litter layer down to 5 cm in the mineral soil, and the relationship between the qCO2 and the soil carbon-to-nitrogen (C:N) and the soil carbon-to-phosphorus (C:P) ratio was analyzed. We found that the qCO2 was positively correlated with soil C:N ratio in spruce soils (R = 0.72), and with the soil C:P ratio in beech (R = 0.93), spruce (R = 0.80) and mixed forest soils (R = 0.96). We also observed a close correlation between the qCO2 and the soil C concentration in all three forest types. Yet, the qCO2 decreased less with depth than the C concentration in all three forest types, suggesting that the change in qCO2 is not only controlled by the soil C concentration. We conclude that microorganisms increase their respiration rate per unit biomass with increasing soil C:P ratio and C concentration, which adjusts the substrate to their nutritional demands in terms of stoichiometry. In an analysis of literature data, I tested the effect of the C:N ratio of soil litter layers on microbial respiration in absolute terms and per unit microbial biomass C. For this purpose, a global dataset on the microbial respiration rate per unit microbial biomass C - termed the metabolic quotient (qCO2) - was compiled form literature data. It was found that the qCO2 in the soil litter layers was positively correlated with the litter C:N ratio and negatively related with the litter nitrogen (N) concentration. The positive relation between the qCO2

The worm has turned--microbial virulence modeled in Caenorhabditis elegans.

Science.gov (United States)

Sifri, Costi D; Begun, Jakob; Ausubel, Frederick M

2005-03-01

The nematode Caenorhabditis elegans is emerging as a facile and economical model host for the study of evolutionarily conserved mechanisms of microbial pathogenesis and innate immunity. A rapidly growing number of human and animal microbial pathogens have been shown to injure and kill nematodes. In many cases, microbial genes known to be important for full virulence in mammalian models have been shown to be similarly required for maximum pathogenicity in nematodes. C. elegans has been used in mutation-based screening systems to identify novel virulence-related microbial genes and immune-related host genes, many of which have been validated in mammalian models of disease. C. elegans-based pathogenesis systems hold the potential to simultaneously explore the molecular genetic determinants of both pathogen virulence and host defense.

Microbial effects on high-level waste disposal. Research review and perspective

Energy Technology Data Exchange (ETDEWEB)

Ohnuki, Toshihiko [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

2002-09-01

Various microorganisms have been observed in deep geologic formation. The effects of such microorganisms on the performance of HLW disposal are still unknown. This paper reviews the studies of microbial effects on the long-term containment of HLW disposal, and discusses the future work to be carried out. Microbial reduction and oxidation and byproducts derived from microbial activities affect performance of HLW repository and have a potential to enhance actinides migration in geologic formation (degradation of the materials of repository, complex-formation, dissolution of actinides precipitates and occurrence of nm scale colloid formation). Potential microbial perturbation of performance of the barriers may enhance confinement of actinides by biomineralization, bioadsorption, bioaccumulation and precipitation. These studies indicate that further experiments are required to elucidate microbial effects on the performance of HLW disposal. (author)

Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

Science.gov (United States)

di Meo, C. A.; Giovannoni, S.; Fisk, M.

2002-12-01

Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the

Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens.

Science.gov (United States)

Peltoniemi, Krista; Laiho, Raija; Juottonen, Heli; Kiikkilä, Oili; Mäkiranta, Päivi; Minkkinen, Kari; Pennanen, Taina; Penttilä, Timo; Sarjala, Tytti; Tuittila, Eeva-Stiina; Tuomivirta, Tero; Fritze, Hannu

2015-07-01

Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial community analysis of fouled reverse osmosis membranes used in water recycling

KAUST Repository

Ayache, C.; Manes, Carmem Lara De O; Pidou, Marc; Croue, Jean-Philippe; Gernjak, Wolfgang

2013-01-01

Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

Microbial community analysis of fouled reverse osmosis membranes used in water recycling

KAUST Repository

Ayache, C.

2013-06-01

Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

Science.gov (United States)

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

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

Science.gov (United States)

Larsen, Peter; Gilbert, Jack

2013-01-01

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

Measures of Microbial Biomass for Soil Carbon Decomposition Models

Science.gov (United States)

Mayes, M. A.; Dabbs, J.; Steinweg, J. M.; Schadt, C. W.; Kluber, L. A.; Wang, G.; Jagadamma, S.

2014-12-01

Explicit parameterization of the decomposition of plant inputs and soil organic matter by microbes is becoming more widely accepted in models of various complexity, ranging from detailed process models to global-scale earth system models. While there are multiple ways to measure microbial biomass, chloroform fumigation-extraction (CFE) is commonly used to parameterize models.. However CFE is labor- and time-intensive, requires toxic chemicals, and it provides no specific information about the composition or function of the microbial community. We investigated correlations between measures of: CFE; DNA extraction yield; QPCR base-gene copy numbers for Bacteria, Fungi and Archaea; phospholipid fatty acid analysis; and direct cell counts to determine the potential for use as proxies for microbial biomass. As our ultimate goal is to develop a reliable, more informative, and faster methods to predict microbial biomass for use in models, we also examined basic soil physiochemical characteristics including texture, organic matter content, pH, etc. to identify multi-factor predictive correlations with one or more measures of the microbial community. Our work will have application to both microbial ecology studies and the next generation of process and earth system models.

Studies of heavy metal contents and microbial composition of ...

African Journals Online (AJOL)

This study investigated the heavy metal content and microbial composition of rhizosphere of Panicum maximum obtained from some auto mechanic workshops in Benin City, Nigeria. The grass was uprooted and soil sample was taken from its rhizosphere. The sample were labeled appropriately and immediately transported ...

Effects of hydraulic frac fluids and formation waters on groundwater microbial communities

Science.gov (United States)

Krueger, Martin; Jimenez, Nuria

2017-04-01

Shale gas is being considered as a complementary energy resource to other fossil fuels. Its exploitation requires using advanced drilling techniques and hydraulic stimulation (fracking). During fracking operations, large amounts of fluids (fresh water, proppants and chemicals) are injected at high pressures into the formations, to create fractures and fissures, and thus to release gas from the source rock into the wellbore. The injected fluid partly remains in the formation, while up to 40% flows back to the surface, together with reservoir waters, sometimes containing dissolved hydrocarbons, high salt concentrations, etc. The aim of our study was to investigate the potential impacts of frac or geogenic chemicals, frac fluid, formation water or flowback on groudnwater microbial communities. Laboratory experiments under in situ conditions (i.e. at in situ temperature, high pressure) were conducted using groundwater samples from three different locations. Series of microcosms containing R2 broth medium or groundwater spiked with either single frac chemicals (including biocides), frac fluids, artificial reservoir water, NaCl, or different mixtures of reservoir water and frac fluid (to simulate flowback) were incubated in the dark. Controls included non-amended and non-inoculated microcosms. Classical microbiological methods and molecular analyses were used to assess changes in the microbial abundance, community structure and function in response to the different treatments. Microbial communities were quite halotolerant and their growth benefited from low concentrations of reservoir waters or salt, but they were negatively affected by higher concentrations of formation waters, salt, biocides or frac fluids. Changes on the microbial community structure could be detected by T-RFLP. Single frac components like guar gum or choline chloride were used as substrates, while others like triethanolamine or light oil distillate hydrogenated prevented microbial growth in

Agroforestry management in vineyards: effects on soil microbial communities

Science.gov (United States)

Montagne, Virginie; Nowak, Virginie; Guilland, Charles; Gontier, Laure; Dufourcq, Thierry; Guenser, Josépha; Grimaldi, Juliette; Bourgade, Emilie; Ranjard, Lionel

2017-04-01

Some vineyard practices (tillage, chemical weeding or pest management) are generally known to impact the environment with particular negative effects on the diversity and the abundance of soil microorganisms, and cause water and soil pollutions. In an agro-ecological context, innovative cropping systems have been developed to improve ecosystem services. Among them, agroforestry offers strategies of sustainable land management practices. It consists in intercropping trees with annual/perennial/fodder crop on the same plot but it is weakly referenced with grapevine. The present study assesses the effects of intercropped and neighbouring trees on the soil of three agroforestry vineyards, in south-western France regions. More precisely soils of the different plots were sampled and the impact of the distance to the tree or to the neighbouring trees (forest) on soil microbial community has been considered. Indigenous soil microbial communities were characterized by a metagenomic approach that consisted in extracting the molecular microbial biomass, then in calculating the soil fungi/bacteria ratio - obtained by qPCR - and then in characterizing the soil microbial diversity - through Illumina sequencing of 16S and 18S regions. Our results showed a significant difference between the soil of agroforestry vineyards and the soil sampled in the neighbouring forest in terms of microbial abundance and diversity. However, only structure and composition of bacterial community seem to be influenced by the implanted trees in the vine plots. In addition, the comparison of microbial co-occurrence networks between vine and forest plots as well as inside vine plots according to distance to the tree allow revealing a more sensitive impact of agroforestry practices. Altogether, the results we obtained build up the first references for concerning the soil of agroforestry vineyards which will be interpreted in terms of soil quality, functioning and sustainability.

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium.

Science.gov (United States)

Vardanyan, Narine; Sevoyan, Garegin; Navasardyan, Taron; Vardanyan, Arevik

2018-05-28

Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.

Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food.

Science.gov (United States)

Zhang, Jiachao; Wang, Xiaoru; Huo, Dongxue; Li, Wu; Hu, Qisong; Xu, Chuanbiao; Liu, Sixin; Li, Congfa

2016-08-31

Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample.

Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

Science.gov (United States)

Gómez-Brandón, María; Aira, Manuel; Lores, Marta; Domínguez, Jorge

2011-01-01

Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. To address these questions we determined the microbial community structure (phospholipid fatty acid profiles) and microbial activity (fluorescein diacetate hydrolysis) in the earthworm casts derived from three types of animal manure (cow, horse and pig manure), which differed in microbial composition. The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions within the decomposer food web influence on nutrient cycling.

Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

Directory of Open Access Journals (Sweden)

María Gómez-Brandón

Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

[Fibers as carriers of microbial particles].

Science.gov (United States)

Górny, Rafał L; Ławniczek-Wałczyk, Anna; Stobnicka, Agata; Gołofit-Szymczak, Małgorzata; Cyprowski, Marcin

2015-01-01

The aim of the study was to assess the ability of natural, synthetic and semi-synthetic fibers to transport microbial particles. The simultaneously settled dust and aerosol sampling was carried out in 3 industrial facilities processing natural (cotton, silk, flax, hemp), synthetic (polyamide, polyester, polyacrylonitrile, polypropylene) and semi-synthetic (viscose) fibrous materials; 2 stables where horses and sheep were bred; 4 homes where dogs or cats were kept and 1 zoo lion pavilion. All samples were laboratory analyzed for their microbiological purity. The isolated strains were qualitatively identified. To identify the structure and arrangement of fibers that may support transport of microbial particles, a scanning electron microscopy analysis was performed. Both settled and airborne fibers transported analogous microorganisms. All synthetic, semi-synthetic and silk fibers, present as separated threads with smooth surface, were free from microbial contamination. Natural fibers with loose packing and rough surface (e.g., wool, horse hair), sheaf packing and septated surface (e.g., flax, hemp) or present as twisted ribbons with corrugated surface (cotton) were able to carry up to 9×10(5) cfu/g aerobic bacteria, 3.4×10(4) cfu/g anaerobic bacteria and 6.3×10(4) cfu/g of fungi, including pathogenic strains classified by Directive 2000/54/EC in hazard group 2. As plant and animal fibers are contaminated with a significant number of microorganisms, including pathogens, all of them should be mechanically eliminated from the environment. In factories, if the manufacturing process allows, they should be replaced by synthetic or semi-synthetic fibers. To avoid unwanted exposure to harmful microbial agents on fibers, the containment measures that efficiently limit their presence and dissemination in both occupational and non-occupational environments should be introduced. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Fibers as carriers of microbial particles

Directory of Open Access Journals (Sweden)

Rafał L. Górny

2015-08-01

Full Text Available Background: The aim of the study was to assess the ability of natural, synthetic and semi-synthetic fibers to transport microbial particles. Material and Methods: The simultaneously settled dust and aerosol sampling was carried out in 3 industrial facilities processing natural (cotton, silk, flax, hemp, synthetic (polyamide, polyester, polyacrylonitrile, polypropylene and semi-synthetic (viscose fibrous materials; 2 stables where horses and sheep were bred; 4 homes where dogs or cats were kept and 1 zoo lion pavilion. All samples were laboratory analyzed for their microbiological purity. The isolated strains were qualitatively identified. To identify the structure and arrangement of fibers that may support transport of microbial particles, a scanning electron microscopy analysis was performed. Results: Both settled and airborne fibers transported analogous microorganisms. All synthetic, semi-synthetic and silk fibers, present as separated threads with smooth surface, were free from microbial contamination. Natural fibers with loose packing and rough surface (e.g., wool, horse hair, sheaf packing and septated surface (e.g., flax, hemp or present as twisted ribbons with corrugated surface (cotton were able to carry up to 9×105 cfu/g aerobic bacteria, 3.4×104 cfu/g anaerobic bacteria and 6.3×104 cfu/g of fungi, including pathogenic strains classified by Directive 2000/54/EC in hazard group 2. Conclusions: As plant and animal fibers are contaminated with a significant number of microorganisms, including pathogens, all of them should be mechanically eliminated from the environment. In factories, if the manufacturing process allows, they should be replaced by synthetic or semi-synthetic fibers. To avoid unwanted exposure to harmful microbial agents on fibers, the containment measures that efficiently limit their presence and dissemination in both occupational and non-occupational environments should be introduced. Med Pr 2015;66(4:511–523

Recent Advances in Microbial Single Cell Genomics Technology and Applications

Science.gov (United States)

Stepanauskas, R.

2016-02-01

Single cell genomics is increasingly utilized as a powerful tool to decipher the metabolic potential, evolutionary histories and in situ interactions of environmental microorganisms. This transformative technology recovers extensive information from cultivation-unbiased samples of individual, unicellular organisms. Thus, it does not require data binning into arbitrary phylogenetic or functional groups and therefore is highly compatible with agent-based modeling approaches. I will present several technological advances in this field, which significantly improve genomic data recovery from individual cells and provide direct linkages between cell's genomic and phenotypic properties. I will also demonstrate how these new technical capabilities help understanding the metabolic potential and viral infections of the "microbial dark matter" inhabiting aquatic and subsurface environments.

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

DEFF Research Database (Denmark)

Arthur, Emmanuel; Møldrup, Per; Holmstrup, Martin

2012-01-01

years; from background concentrations up to 3837 mg Cu kg–1) on soil microbial enzyme activity, physical properties and resilience to compression. Soil samples and cores were taken from a fallow sandy loam field in Denmark. Microbial activity was quantified using fluorescein diacetate (FDA...

40 CFR 80.335 - What gasoline sample retention requirements apply to refiners and importers?

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 16 2010-07-01 2010-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention Requirements for Refiners and Importers § 80.335 What gasoline sample...

Sorption of radioiodide in an acidic, nutrient-poor boreal bog: insights into the microbial impact

International Nuclear Information System (INIS)

Lusa, M.; Bomberg, M.; Aromaa, H.; Knuutinen, J.; Lehto, J.

2015-01-01

the sorption of iodide on peat. • Sorption is restored by incubating sterilized peat samples with microbial extract. • Viable microbes and oxic conditions are required for I − sorption in an acidic bog

Assessing the Accuracy of Quantitative Molecular Microbial Profiling

Directory of Open Access Journals (Sweden)

Denise M. O'Sullivan

2014-11-01

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

Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration

Directory of Open Access Journals (Sweden)

Jin-Feng eLiu

2015-03-01

Full Text Available Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.

Microbial biogeography of San Francisco Bay sediments

Science.gov (United States)

Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess

Status Report on the Microbial Characterization of Halite and Groundwater Samples from the WIPP

International Nuclear Information System (INIS)

Swanson, Juliet S.; Reed, Donald T.; Ams, David A.; Norden, Diana; Simmons, Karen A.

2012-01-01

This report summarizes the progress made in the ongoing task of characterizing the microbial community structures within the WIPP repository and in surrounding groundwaters. Through cultivation and DNA-based identification, the potential activity of these organisms is being inferred, thus leading to a better understanding of their impact on WIPP performance. Members of the three biological domains - Bacteria, Archaea, and Eukarya (in this case, Fungi) - that are associated with WIPP halite have been identified. Thus far, their activity has been limited to aerobic respiration; anaerobic incubations are underway. WIPP halite constitutes the near-field microbial environment. We expect that microbial activity in this setting will proceed from aerobic respiration, through nitrate reduction to focus on sulfate reduction. This is also the current WIPP performance assessment (PA) position. Sulfate reduction can occur at extremely high ionic strengths, and sulfate is available in WIPP brines and in the anhydrite interbeds. The role of methanogenesis in the WIPP remains unclear, due to both energetic constraints imposed by a high-salt environment and substrate selectivity, and it is no longer considered in PA. Archaea identified in WIPP halite thus far fall exclusively within the family Halobacteriaceae. These include Halobacterium noricense, cultivated from both low- and high-salt media, and a Halorubrum-like species. The former has also been detected in other salt mines worldwide; the latter likely constitutes a new species. Little is known of its function, but it was prevalent in experiments investigating the biodegradation of organic complexing agents in WIPP brines. Bacterial signatures associated with WIPP halite include members of the phylum Proteobacteria - Halomonas, Pelomonas, Limnobacter, and Chromohalobacter - but only the latter has been isolated. Also detected and cultivated were Salinicoccus and Nesterenkonia spp. Fungi were also isolated from halite. Although

Status Report on the Microbial Characterization of Halite and Groundwater Samples from the WIPP

Energy Technology Data Exchange (ETDEWEB)

Swanson, Juliet S. [Los Alamos National Laboratory; Reed, Donald T. [Los Alamos National Laboratory; Ams, David A. [Los Alamos National Laboratory; Norden, Diana [Ohio State University; Simmons, Karen A. [Los Alamos National Laboratory

2012-07-10

This report summarizes the progress made in the ongoing task of characterizing the microbial community structures within the WIPP repository and in surrounding groundwaters. Through cultivation and DNA-based identification, the potential activity of these organisms is being inferred, thus leading to a better understanding of their impact on WIPP performance. Members of the three biological domains - Bacteria, Archaea, and Eukarya (in this case, Fungi) - that are associated with WIPP halite have been identified. Thus far, their activity has been limited to aerobic respiration; anaerobic incubations are underway. WIPP halite constitutes the near-field microbial environment. We expect that microbial activity in this setting will proceed from aerobic respiration, through nitrate reduction to focus on sulfate reduction. This is also the current WIPP performance assessment (PA) position. Sulfate reduction can occur at extremely high ionic strengths, and sulfate is available in WIPP brines and in the anhydrite interbeds. The role of methanogenesis in the WIPP remains unclear, due to both energetic constraints imposed by a high-salt environment and substrate selectivity, and it is no longer considered in PA. Archaea identified in WIPP halite thus far fall exclusively within the family Halobacteriaceae. These include Halobacterium noricense, cultivated from both low- and high-salt media, and a Halorubrum-like species. The former has also been detected in other salt mines worldwide; the latter likely constitutes a new species. Little is known of its function, but it was prevalent in experiments investigating the biodegradation of organic complexing agents in WIPP brines. Bacterial signatures associated with WIPP halite include members of the phylum Proteobacteria - Halomonas, Pelomonas, Limnobacter, and Chromohalobacter - but only the latter has been isolated. Also detected and cultivated were Salinicoccus and Nesterenkonia spp. Fungi were also isolated from halite. Although

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

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Peter Larsen

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

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children

Science.gov (United States)

Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

2017-01-01

Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease. Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints. Methods: In five 10-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper-points inserted into the subgingival sulcus at eight sites. After supragingival cleaning using an electric toothbrush and water, sampling was performed, firstly, excluding (Mode A) and, secondly, including (Mode B) cleansing with sterile cotton pellets. DNA was extracted from the pooled samples, and primers targeting 16S rRNA hypervariable regions V5 and V6 were used for 454-pyrosequencing. Wilcoxon signed rank test and t-test were applied to compare sampling modes. Principal coordinate analysis (PCoA) and average agglomerative hierarchical clustering were calculated with unweighted UniFrac distance matrices. Sample grouping was tested with permutational MANOVA (Adonis). Results: Data filtering and quality control yielded 67,218 sequences with an average sequence length of 243bp (SD 6.52; range 231–255). Actinobacteria (2.8–24.6%), Bacteroidetes (9.2–25.1%), Proteobacteria (4.9–50.6%), Firmicutes (16.5–57.4%), and Fusobacteria (2.2–17.1%) were the five major phyla found in all samples. Differences in microbial abundances between sampling modes were not evident. High sampling numbers are needed to achieve significance for rare bacterial phyla. Samples taken from one individual using different sampling modes were more similar to each other than to other individuals' samples. PCoA and hierarchical clustering showed a grouping of the paired samples. Permutational MANOVA did not reveal sample

Sampling Modification Effects in the Subgingival Microbiome Profile of Healthy Children.

Science.gov (United States)

Santigli, Elisabeth; Trajanoski, Slave; Eberhard, Katharina; Klug, Barbara

2016-01-01

Background: Oral microbiota are considered major players in the development of periodontal diseases. Thorough knowledge of intact subgingival microbiomes is required to elucidate microbial shifts from health to disease. Aims: This comparative study investigated the subgingival microbiome of healthy children, possible inter- and intra-individual effects of modified sampling, and basic comparability of subgingival microprints. Methods: In five 10-year-old children, biofilm was collected from the upper first premolars and first molars using sterilized, UV-treated paper-points inserted into the subgingival sulcus at eight sites. After supragingival cleaning using an electric toothbrush and water, sampling was performed, firstly, excluding (Mode A) and, secondly, including (Mode B) cleansing with sterile cotton pellets. DNA was extracted from the pooled samples, and primers targeting 16S rRNA hypervariable regions V5 and V6 were used for 454-pyrosequencing. Wilcoxon signed rank test and t -test were applied to compare sampling modes. Principal coordinate analysis (PCoA) and average agglomerative hierarchical clustering were calculated with unweighted UniFrac distance matrices. Sample grouping was tested with permutational MANOVA (Adonis). Results: Data filtering and quality control yielded 67,218 sequences with an average sequence length of 243bp (SD 6.52; range 231-255). Actinobacteria (2.8-24.6%), Bacteroidetes (9.2-25.1%), Proteobacteria (4.9-50.6%), Firmicutes (16.5-57.4%), and Fusobacteria (2.2-17.1%) were the five major phyla found in all samples. Differences in microbial abundances between sampling modes were not evident. High sampling numbers are needed to achieve significance for rare bacterial phyla. Samples taken from one individual using different sampling modes were more similar to each other than to other individuals' samples. PCoA and hierarchical clustering showed a grouping of the paired samples. Permutational MANOVA did not reveal sample grouping by

B-Vitamin Competition: Intracellular and Dissolved B-Vitamins Provide Insight into Marine Microbial Community Dynamics

Science.gov (United States)

Suffridge, C.; Gomez-Consarnau, L.; Qu, P.; Tenenbaum, N.; Fu, F.; Hutchins, D. A.; Sanudo-Wilhelmy, S. A.

2016-02-01

The availability of B-vitamins has the ability to directly affect the dynamics of the marine microbial community. Here we show, for the first time, the connection between dissolved and intracellular B-vitamins in a marine environmental community. Two incubation experiments were conducted at a long-term study site (SPOT) in the San Pedro Basin off the coast of Los Angeles, CA. Experiments were conducted in oligotrophic, preupwelling conditions. Due to the 2015 El Niño event, the seasonal upwelling at SPOT did not occur, creating unusually nutrient depleted conditions. Vitamins B1, B7, and B12 were added in addition to macronutrients at concentrations similar to typical SPOT upwelling conditions. Intracellular and dissolved B-vitamin analyses were conducted to determine shifts in cellular B-vitamin requirements as a function of growth rate. We observed a significant bacterioplankton and phytoplankton growth responses with the addition of B-vitamins in a manner that appears to match the enzymatic requirements for these compounds (e.g. B1>B7>B12). Intracellular B-vitamin analysis of T0 samples support this observation, as all four forms of B12 were not detectable within cells, yet multiple forms of B1 and B7 were detected at or near levels previously reported. Treatments with B12 and macronutrients were observed to have the greatest growth rates. This finding, in addition to the apparent lack of intracellular B12 in the initial community, appears to indicate that the initial microbial community was limited by B12. The addition of each vitamin caused a distinct shift in the blooming microbial community. Our results demonstrate that B-vitamins strongly influence not only the growth rate, but also the species composition and species succession of the microbial community as a whole. Large-scale changes to upwelling regimes are predicted in the future ocean; our results indicate that B-vitamins will have a substantial role in controlling microbial community dynamics under

Heavy metal levels, physicochemical properties and microbial ...

African Journals Online (AJOL)

Journal of Applied Sciences and Environmental Management ... out to assess the microbial, physicochemical and heavy metal characteristics of soil samples from five different waste collection sites within the University of Benin, Benin City and evaluated using standard analytical and classical microbiological methods.

Microbial Evaluation of Some Non-sterile Pharmaceutical ...

African Journals Online (AJOL)

Purpose: To determine the type and incidence of predominant microorganisms in certain non-sterile pharmaceuticals immediately after collection and one year later. Methods: All pharmaceutical samples were subjected to the following examinations: total bacterial count and presence of microbial pathogens, using ...

Evaluation of ATP measurements to detect microbial ingress by wastewater and surface water in drinking water.

Science.gov (United States)

Vang, Óluva K; Corfitzen, Charlotte B; Smith, Christian; Albrechtsen, Hans-Jørgen

2014-11-01

Fast and reliable methods are required for monitoring of microbial drinking water quality in order to protect public health. Adenosine triphosphate (ATP) was investigated as a potential real-time parameter for detecting microbial ingress in drinking water contaminated with wastewater or surface water. To investigate the ability of the ATP assay in detecting different contamination types, the contaminant was diluted with non-chlorinated drinking water. Wastewater, diluted at 10(4) in drinking water, was detected with the ATP assay, as well as 10(2) to 10(3) times diluted surface water. To improve the performance of the ATP assay in detecting microbial ingress in drinking water, different approaches were investigated, i.e. quantifying microbial ATP or applying reagents of different sensitivities to reduce measurement variations; however, none of these approaches contributed significantly in this respect. Compared to traditional microbiological methods, the ATP assay could detect wastewater and surface water in drinking water to a higher degree than total direct counts (TDCs), while both heterotrophic plate counts (HPC 22 °C and HPC 37 °C) and Colilert-18 (Escherichia coli and coliforms) were more sensitive than the ATP measurements, though with much longer response times. Continuous sampling combined with ATP measurements displays definite monitoring potential for microbial drinking water quality, since microbial ingress in drinking water can be detected in real-time with ATP measurements. The ability of the ATP assay to detect microbial ingress is influenced by both the ATP load from the contaminant itself and the ATP concentration in the specific drinking water. Consequently, a low ATP concentration of the specific drinking water facilitates a better detection of a potential contamination of the water supply with the ATP assay. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial community of high arsenic groundwater in agricultural irrigation area of Hetao Plain, Inner Mongolia

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Yanhong Wang

2016-12-01

Full Text Available Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina Miseq sequencing approach targeting the V4 region of the 16S rRNA gene. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with NH4+ and TOC. Sequencing results revealed that a total of 329-2823 OTUs were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing As-rich aquifers of Hetao Plain and other high As groundwater aquifers including Bangladesh, West Bengal and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal coordinate analysis and co-inertia analysis. Other geochemical

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.

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Kantor, Rose S; van Zyl, A Wynand; van Hille, Robert P; Thomas, Brian C; Harrison, Susan T L; Banfield, Jillian F

2015-12-01

Gold ore processing uses cyanide (CN(-) ), which often results in large volumes of thiocyanate- (SCN(-) ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN(-) and CN(-) , but little is known about their membership and metabolic potential. Microbial-based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN(-) and CN(-) into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory-scale bioreactors used to study SCN(-) and CN(-) degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN(-) degradation. Genome-based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN(-) degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Improving Microbial Genome Annotations in an Integrated Database Context

Science.gov (United States)

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Improving microbial genome annotations in an integrated database context.

Directory of Open Access Journals (Sweden)

I-Min A Chen

Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

Science.gov (United States)

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

Energy Technology Data Exchange (ETDEWEB)

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Post-Flight Microbial Analysis of Samples from the International Space Station Water Recovery System and Oxygen Generation System

Science.gov (United States)

Birmele, Michele N.

2011-01-01

The Regenerative, Environmental Control and Life Support System (ECLSS) on the International Space Station (ISS) includes the the Water Recovery System (WRS) and the Oxygen Generation System (OGS). The WRS consists of a Urine Processor Assembly (UPA) and Water Processor Assembly (WPA). This report describes microbial characterization of wastewater and surface samples collected from the WRS and OGS subsystems, returned to KSC, JSC, and MSFC on consecutive shuttle flights (STS-129 and STS-130) in 2009-10. STS-129 returned two filters that contained fluid samples from the WPA Waste Tank Orbital Recovery Unit (ORU), one from the waste tank and the other from the ISS humidity condensate. Direct count by microscopic enumeration revealed 8.38 x 104 cells per mL in the humidity condensate sample, but none of those cells were recoverable on solid agar media. In contrast, 3.32 x lOs cells per mL were measured from a surface swab of the WRS waste tank, including viable bacteria and fungi recovered after S12 days of incubation on solid agar media. Based on rDNA sequencing and phenotypic characterization, a fungus recovered from the filter was determined to be Lecythophora mutabilis. The bacterial isolate was identified by rDNA sequence data to be Methylobacterium radiotolerans. Additional UPA subsystem samples were returned on STS-130 for analysis. Both liquid and solid samples were collected from the Russian urine container (EDV), Distillation Assembly (DA) and Recycle Filter Tank Assembly (RFTA) for post-flight analysis. The bacterium Pseudomonas aeruginosa and fungus Chaetomium brasiliense were isolated from the EDV samples. No viable bacteria or fungi were recovered from RFTA brine samples (N= 6), but multiple samples (N = 11) from the DA and RFTA were found to contain fungal and bacterial cells. Many recovered cells have been identified to genus by rDNA sequencing and carbon source utilization profiling (BiOLOG Gen III). The presence of viable bacteria and fungi from WRS

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

Science.gov (United States)

Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

2016-03-22

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Changes of soil organic matter and microbial activity in irrigated and non irrigated olive groves

Science.gov (United States)

Kavvadias, Victor; Papadopoulou, Maria; Theocharopoulos, Sideris; Vavoulidou, Evagelia; Doula, Maria; Reppas, Spiros

2014-05-01

The implementation of olive cultivation techniques in Greece has not been systematically tested under the prevailing Mediterranean conditions. A LIFE+ project was initiated (oLIVE-CLIMA; LIFE 11/ENV/000942) aiming to introduce new management practices in olive tree crops that lead to increased carbon dioxide uptake by plants as well as carbon sequestration from the atmosphere and reverse the trend of soil organic matter decline, erosion and desertification. This paper presents data on soil organic matter and microbial activity from a soil campaign in a pilot region in Greece, and particularly in the area of Chora, prefecture of Messinia, South west Peloponnese. The soil campaign took place during the period December 2012-February 2013. Twelve soil parcels of olive groves were selected (6 irrigated and 6 rainfed) and in each soil parcel six composite soil samples were taken from 0-10 cm depth at equal intervals along a straight line of the trunk of the tree to the middle of the distance from the nearest tree of the next tree series. The first three samples were under olive tree canopy. An additional composite sample was taken at depth of 10-40 cm. Soil samples were analyzed for soil physicochemical and biological properties. In this study results for total organic carbon (TOC), soil basal microbial respiration (BR), microbial biomass C (MB-C) from the region of Messinia, are presented. Organic matter was determined by dichromate oxidation. The microbial activity was measured by the amount of CO2 evolution, while microbial biomass C was determined by substrate-induced respiration, after the addition of glucose. The results showed considerable differences in TOC, BR and MB-C associated with the sampling position and soil depth. The higher TOC, BR and MB-C values, in most cases, were determined in samples taken from points under the canopy, but not close to the tree trunk compared to the sampling points outside the canopy. This indicates the positive effect of

Seasonality and vertical structure of microbial communities in an ocean gyre.

Science.gov (United States)

Treusch, Alexander H; Vergin, Kevin L; Finlay, Liam A; Donatz, Michael G; Burton, Robert M; Carlson, Craig A; Giovannoni, Stephen J

2009-10-01

Vertical, seasonal and geographical patterns in ocean microbial communities have been observed in many studies, but the resolution of community dynamics has been limited by the scope of data sets, which are seldom up to the task of illuminating the highly structured and rhythmic patterns of change found in ocean ecosystems. We studied vertical and temporal patterns in the microbial community composition in a set of 412 samples collected from the upper 300 m of the water column in the northwestern Sargasso Sea, on cruises between 1991 and 2004. The region sampled spans the extent of deep winter mixing and the transition between the euphotic and the upper mesopelagic zones, where most carbon fixation and reoxidation occurs. A bioinformatic pipeline was developed to de-noise, normalize and align terminal restriction fragment length polymorphism (T-RFLP) data from three restriction enzymes and link T-RFLP peaks to microbial clades. Non-metric multidimensional scaling statistics resolved three microbial communities with distinctive composition during seasonal stratification: a surface community in the region of lowest nutrients, a deep chlorophyll maximum community and an upper mesopelagic community. A fourth microbial community was associated with annual spring blooms of eukaryotic phytoplankton that occur in the northwestern Sargasso Sea as a consequence of winter convective mixing that entrains nutrients to the surface. Many bacterial clades bloomed in seasonal patterns that shifted with the progression of stratification. These richly detailed patterns of community change suggest that highly specialized adaptations and interactions govern the success of microbial populations in the oligotrophic ocean.

A microbial trigger for gelled polymers

Energy Technology Data Exchange (ETDEWEB)

Bailey, S.; Bryant, R.; Zhu, T.

1995-12-31

A process using a microbially gelled biopolymer was developed and used to modify permeability in coreflood experiments. Alkaline-soluble curdlan biopolymer was mixed with microbial nutrients and acid-producing alkaliphilic bacteria, and injected into Berea sandstone cores. Concurrent bottle tests with the polymer solution were incubated beside the core. Polymer in the bottle tests formed rigid gel in 2-5 days at 27{degree}C. After 7 days incubation, 25-35 psi fluid pressure was required to begin flow through the cores. Permeability of the cores was decreased from 852 md to 2.99 md and from 904 md to 4.86 md, respectively, giving residual resistance factors of 334 and 186.

Microbial Flora of Partially Processed Periwinkles (Tympantotonus ...

African Journals Online (AJOL)

A survey of microbial flora of partially processed periwinkles (Tympanotonus fuscatus) sold in six markets in Port Harcourt was undertaken for twelve weeks. Results show that all samples of periwinkles were contaminated with Staphylococcus aureus, Bacillus sp., Escherichia coil, Staphepidermidis sp., Micrococcus sp., ...

Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

Science.gov (United States)

Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

2008-12-15

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan

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Satoshi Hiraoka

2017-08-01

Full Text Available The presence of microbes in the atmosphere and their transport over long distances across the Earth's surface was recently shown. Precipitation is likely a major path by which aerial microbes fall to the ground surface, affecting its microbial ecosystems and introducing pathogenic microbes. Understanding microbial communities in precipitation is of multidisciplinary interest from the perspectives of microbial ecology and public health; however, community-wide and seasonal analyses have not been conducted. Here, we carried out 16S rRNA amplicon sequencing of 30 precipitation samples that were aseptically collected over 1 year in the Greater Tokyo Area, Japan. The precipitation microbial communities were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria and were overall consistent with those previously reported in atmospheric aerosols and cloud water. Seasonal variations in composition were observed; specifically, Proteobacteria abundance significantly decreased from summer to winter. Notably, estimated ordinary habitats of precipitation microbes were dominated by animal-associated, soil-related, and marine-related environments, and reasonably consistent with estimated air mass backward trajectories. To our knowledge, this is the first amplicon-sequencing study investigating precipitation microbial communities involving sampling over the duration of a year.

Requirements for modeling airborne microbial contamination in space stations

Science.gov (United States)

Van Houdt, Rob; Kokkonen, Eero; Lehtimäki, Matti; Pasanen, Pertti; Leys, Natalie; Kulmala, Ilpo

2018-03-01

Exposure to bioaerosols is one of the facets that affect indoor air quality, especially for people living in densely populated or confined habitats, and is associated to a wide range of health effects. Good indoor air quality is thus vital and a prerequisite for fully confined environments such as space habitats. Bioaerosols and microbial contamination in these confined space stations can have significant health impacts, considering the unique prevailing conditions and constraints of such habitats. Therefore, biocontamination in space stations is strictly monitored and controlled to ensure crew and mission safety. However, efficient bioaerosol control measures rely on solid understanding and knowledge on how these bioaerosols are created and dispersed, and which factors affect the survivability of the associated microorganisms. Here we review the current knowledge gained from relevant studies in this wide and multidisciplinary area of bioaerosol dispersion modeling and biological indoor air quality control, specifically taking into account the specific space conditions.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

NARCIS (Netherlands)

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

Perspectives of microbial oils for biodiesel production

Energy Technology Data Exchange (ETDEWEB)

Li Qiang; Du Wei; Liu Dehua [Tsinghua Univ., Beijing (China). Dept. of Chemical Engineering

2008-10-15

Biodiesel has become more attractive recently because of its environmental benefits, and the fact that it is made from renewable resources. Generally speaking, biodiesel is prepared through transesterification of vegetable oils or animal fats with short chain alcohols. However, the lack of oil feedstocks limits the large-scale development of biodiesel to some extent. Recently, much attention has been paid to the development of microbial, oils and it has been found that many microorganisms, such as algae, yeast, bacteria, and fungi, have the ability to accumulate oils under some special cultivation conditions. Compared to other plant oils, microbial oils have many advantages, such as short life cycle, less labor required, less affection by venue, season and climate, and easier to scale up. With the rapid expansion of biodiesel, microbial oils might become one of potential oil feedstocks for biodiesel production in the future, though there are many works associated with microorganisms producing oils need to be carried out further. This review is covering the related research about different oleaginous microorganisms producing oils, and the prospects of such microbial oils used for biodiesel production are also discussed. (orig.)

Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

Science.gov (United States)

Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

2012-01-01

During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman's statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

Understanding aquatic microbial processes using EEM's and in-situ fluorescence sensors

Science.gov (United States)

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

2015-04-01

The diverse origin of dissolved organic matter (DOM) in aquatic systems is well documented within the literature. Previous literature indicates that coloured dissolved organic matter (CDOM) is, in part, transformed by aquatic microbial processes, and that dissolved organic material derived from a microbial origin exhibits tryptophan-like fluorescence. However, this phenomenon is not fully understood and very little data is available within the current literature. The overall aim of our work is to reveal the microbial-CDOM interactions that give rise to the observed tryptophan-like fluorescence. The work reported here investigates the microbial processes that occur within freshwater aquatic samples, as defined by the biochemical oxygen demand (BOD) test, as a function of the T1 peak (λex/em 280/330-370 nm). A series of standard water samples were prepared using glucose, glutamic acid, BOD dilution water and a bacterial seed (Cole-Parmer BOD microbe capsules). Samples were spiked with CDOM (derived from an environmental water body) and subjected to time resolved BOD analysis and as excitation-emission fluorescence spectroscopy. All EEM spectral data was interrogated using parallel factor analysis (PARAFAC) in an attempt to determine the presence and dominance (relative intensities) of the CDOM-related and T1-related fluorophores within the samples. In-situ fluorescence sensors (Chelsea Technologies Group Ltd.) were also used to monitor the T1 fluorescence peak (UviLux Tryptophan) and the CDOM fluorescence peak (UviLux CDOM) during experiments. Tryptophan-like fluorescence was observed (albeit transient) in both spiked and un-spiked standard water samples. By furthering our understanding of aquatic organic matter fluorescence, its origin, transformation, fate and interaction with aquatic microbiological processes, we aim to inform the design of a new generation in-situ fluorescence sensor for the monitoring of aquatic ecosystem health.

Building beef cow nutritional programs with the 1996 NRC beef cattle requirements model.

Science.gov (United States)

Lardy, G P; Adams, D C; Klopfenstein, T J; Patterson, H H

2004-01-01

Designing a sound cow-calf nutritional program requires knowledge of nutrient requirements, diet quality, and intake. Effectively using the NRC (1996) beef cattle requirements model (1996NRC) also requires knowledge of dietary degradable intake protein (DIP) and microbial efficiency. Objectives of this paper are to 1) describe a framework in which 1996NRC-applicable data can be generated, 2) describe seasonal changes in nutrients on native range, 3) use the 1996NRC to predict nutrient balance for cattle grazing these forages, and 4) make recommendations for using the 1996NRC for forage-fed cattle. Extrusa samples were collected over 2 yr on native upland range and subirrigated meadow in the Nebraska Sandhills. Samples were analyzed for CP, in vitro OM digestibility (IVOMD), and DIP. Regression equations to predict nutrients were developed from these data. The 1996NRC was used to predict nutrient balances based on the dietary nutrient analyses. Recommendations for model users were also developed. On subirrigated meadow, CP and IVOMD increased rapidly during March and April. On native range, CP and IVOMD increased from April through June but decreased rapidly from August through September. Degradable intake protein (DM basis) followed trends similar to CP for both native range and subirrigated meadow. Predicted nutrient balances for spring- and summer-calving cows agreed with reported values in the literature, provided that IVOMD values were converted to DE before use in the model (1.07 x IVOMD - 8.13). When the IVOMD-to-DE conversion was not used, the model gave unrealistically high NE(m) balances. To effectively use the 1996NRC to estimate protein requirements, users should focus on three key estimates: DIP, microbial efficiency, and TDN intake. Consequently, efforts should be focused on adequately describing seasonal changes in forage nutrient content. In order to increase use of the 1996NRC, research is needed in the following areas: 1) cost-effective and

Effect of gamma irradiation and refrigeration storage on microbial, sensorial and chemical quality of fresh-cut lettuce

International Nuclear Information System (INIS)

Hammad, A. A.; Taha, S. M.; Amal, S. M.; Gebreel, H. M.

2010-01-01

Fresh-cut lettuce samples were collected and examined for their microbial, sensory and chemical qualities. All the examined samples had high level of microbial load. All examined samples contained Escherichia coli (E. coli), Enterococcus faecalis (Ent. faecalis), Staphylococcus aureus (S. aureus) and Aeromonas hydrophila (A. hydrophila), indicating that most these samples were unsatisfactory. Listeria monocytogenes (L monocytogenes) and Salmonella spp were not detected. Irradiation caused a great reduction in all microbial loads. During refrigerated storage, the counts of all microorganisms increased, but the rate of increase was slower in irradiated samples. Irradiation dose of 3 kGy was the optimum dose for preservation of fresh-cut lettuce which extended the refrigeration shelf-life up to 20 days and it was sufficient in eliminating all pathogenic bacteria without adverse effect on sensorial quality and slight effect on chemical quality.

Responses of microbial community from tropical pristine coastal soil to crude oil contamination

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Daniel Morais

2016-02-01

Full Text Available Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg−1, in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

Microbial community analysis of ambient temperature anaerobic digesters

Energy Technology Data Exchange (ETDEWEB)

Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

2010-07-01

This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

Microbial Response to UV Exposure and Nitrogen Limitation in Desert Soil Crusts

Science.gov (United States)

Fulton, J. M.; Van Mooy, B. A.

2016-12-01

Microbiotic soil crusts have diverse biomarker distributions and C and N stable isotopic compositions that covary with soil type. Sparse plant cover and the relative lack of soil disturbance in arid/semi-arid landscapes allows populations of soil cyanobacteria to develop along with fungi and heterotrophic bacteria. Microbial communities in this extreme environment depend in part on the production of scytonemin, a UV protective pigment, by cyanobacteria near the top of the crust. N limitation of microbial growth also affects soil crust population dynamics, increasing the requirement of N2fixation by diazotrophic cyanobacteria. We collected 56 soil crust samples from 27 locations throughout the Great Salt Lake Desert, including four transects spanning high-elevation, erosion-dominated soils to lower elevation soils dominated by silt-accumulation. Erosion-dominated soil surfaces included rounded gravel and cobbles; in the interstices there were poorly-developed microbiotic crusts on sandy loam with low δ15N values near 0‰ that point toward microbial growth dependent on cyanobacterial N2 fixation. Nutrients regenerated by heterotrophic bacteria may have been eroded from the system, providing a positive feedback for N2 fixation. High scytonemin:chlorophyll a ratios suggest that cyanobacteria required enhanced protection from UV damage in these crusts. A similar increase in scytonemin:chlorophyll a ratio during soil crust rehydration experiments also points toward the importance of UV protection. Glycolipid:phospholipid ratios were lowest where N2 fixation was favored, however, suggesting that the cyanobacterial population was relatively small, possibly because of the metabolic cost of N2fixation. Microbiotic crusts on silt loam soils, on the other hand, had higher δ15N values between 3.5 and 7.8‰, consistent with heterotrophic growth and nutrient recycling. Lower scytonemin:chlorophyll a ratios suggest that relatively high photosynthetic activity was supported in

Integrating Microbial Electrochemical Technology with Forward Osmosis and Membrane Bioreactors: Low-Energy Wastewater Treatment, Energy Recovery and Water Reuse

KAUST Repository

Werner, Craig M.

2014-06-01

Wastewater treatment is energy intensive, with modern wastewater treatment processes consuming 0.6 kWh/m3 of water treated, half of which is required for aeration. Considering that wastewater contains approximately 2 kWh/m3 of energy and represents a reliable alternative water resource, capturing part of this energy and reclaiming the water would offset or even eliminate energy requirements for wastewater treatment and provide a means to augment traditional water supplies. Microbial electrochemical technology is a novel technology platform that uses bacteria capable of producing an electric current outside of the cell to recover energy from wastewater. These bacteria do not require oxygen to respire but instead use an insoluble electrode as their terminal electron acceptor. Two types of microbial electrochemical technologies were investigated in this dissertation: 1) a microbial fuel cell that produces electricity; and 2) a microbial electrolysis cell that produces hydrogen with the addition of external power. On their own, microbial electrochemical technologies do not achieve sufficiently high treatment levels. Innovative approaches that integrate microbial electrochemical technologies with emerging and established membrane-based treatment processes may improve the overall extent of wastewater treatment and reclaim treated water. Forward osmosis is an emerging low-energy membrane-based technology for seawater desalination. In forward osmosis water is transported across a semipermeable membrane driven by an osmotic gradient. The microbial osmotic fuel cell described in this dissertation integrates a microbial fuel cell with forward osmosis to achieve wastewater treatment, energy recovery and partial desalination. This system required no aeration and generated more power than conventional microbial fuel cells using ion exchange membranes by minimizing electrochemical losses. Membrane bioreactors incorporate semipermeable membranes within a biological wastewater

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

Science.gov (United States)

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

Directory of Open Access Journals (Sweden)

Ping Li

Full Text Available A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs. Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-, SO4(2-/total sulfur ratio, and Fe(2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

Science.gov (United States)

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

Science.gov (United States)

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

NARCIS (Netherlands)

Kraigher, Barbara; Stres, Blaz; Hacin, Janez; Ausec, Luka; Mahne, Ivan; van Elsas, Jan D.; Mandic-Mulec, Ines

Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

Science.gov (United States)

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pPCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

Microbial Rechargeable Battery

NARCIS (Netherlands)

Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

2016-01-01

Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

The Validation of Vapor Phase Hydrogen Peroxide Microbial Reduction for Planetary Protection and a Proposed Vacuum Process Specification

Science.gov (United States)

Chung, Shirley; Barengoltz, Jack; Kern, Roger; Koukol, Robert; Cash, Howard

2006-01-01

The Jet Propulsion Laboratory, in conjunction with the NASA Planetary Protection Officer, has selected the vapor phase hydrogen peroxide sterilization process for continued development as a NASA approved sterilization technique for spacecraft subsystems and systems. The goal is to include this technique, with an appropriate specification, in NPR 8020.12C as a low temperature complementary technique to the dry heat sterilization process.To meet microbial reduction requirements for all Mars in-situ life detection and sample return missions, various planetary spacecraft subsystems will have to be exposed to a qualified sterilization process. This process could be the elevated temperature dry heat sterilization process (115 C for 40 hours) which was used to sterilize the Viking lander spacecraft. However, with utilization of such elements as highly sophisticated electronics and sensors in modern spacecraft, this process presents significant materials challenges and is thus an undesirable bioburden reduction method to design engineers. The objective of this work is to introduce vapor hydrogen peroxide (VHP) as an alternative to dry heat microbial reduction to meet planetary protection requirements.The VHP process is widely used by the medical industry to sterilize surgical instruments and biomedical devices, but high doses of VHP may degrade the performance of flight hardware, or compromise material properties. Our goal for this study was to determine the minimum VHP process conditions to achieve microbial reduction levels acceptable for planetary protection.

40 CFR 158.2100 - Microbial pesticides definition and applicability.

Science.gov (United States)

2010-07-01

... to which the organism has been genetically modified. (4) Pest control organisms such as insect... and supported by data required in this subpart. (3) Genetically modified microbial pesticides may be...

Comparison of microbial contamination at various sites along the ...

African Journals Online (AJOL)

This study was aimed at investigating and comparing the microbial contamination levels at various sites in the Plankenburg and Diep Rivers in the Western Cape, South Africa. Sampling of sites along the Plankenburg River started in June 2004 and continued for a period of 1 year until June 2005. Sampling of the Diep ...

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock

Directory of Open Access Journals (Sweden)

Dhiraj ePaul

2016-01-01

Full Text Available Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world created in the basalt rocks. Although culture-dependent studies have been reported, the comprehensive understanding of microbial community composition and structure of Lonar Lake remain obscure. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet near consistent community composition. The predominance of bacterial phyla Proteobacteria (30% followed by Actinobacteria (24%, Firmicutes (11% and Cyanobacteria (5% was observed. Bacterial phylum Bacteroidetes (1.12%, BD1-5 (0.5%, Nitrospirae (0.41% and Verrucomicrobia (0.28% were detected as relatively minor populations in Lonar Lake ecosystem. Within Proteobacteria, Gammaproteobacteria represented the most abundant population (21-47% among all the sediments and as a minor population in water samples. Bacterial members Proteobacteria and Firmicutes were present significantly higher (p≥0.05 in sediment samples, whereas members of Actinobacteria, Candidate_division_TM7 and Cyanobacteria (p≥0.05 were significantly abundant in water samples. It was noted that compared to other hypersaline soda lakes, Lonar Lake samples formed one distinct cluster, suggesting a different microbial community composition and structure. The present study reports for the first time the different composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. Having better insight of community structure of this Lake ecosystem could be useful in understanding the microbial role in the geochemical cycle for future functional exploration of the unique hypersaline Lonar Lake.

A fermented meat model system for studies of microbial aroma formation

DEFF Research Database (Denmark)

Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

2003-01-01

A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starte......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage.......A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... cultures Pediococcus pentosaceus and Staphylococcus xylosus. Volatiles were collected and analysed by dynamic headspace sampling and GC MS. The analysis was primarily focused on volatiles arising from amino acid degradation and a total of 24 compounds, of which 19 were quantified, were used...

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

Directory of Open Access Journals (Sweden)

Masanori Fujimoto

Full Text Available The impact of NaOH as a ballast water treatment (BWT on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12 treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001. UniFrac distance based principal coordinate analysis (PCoA plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new

Characterization of microbial communities in heavy crude oil from Saudi Arabia.

Science.gov (United States)

Albokari, Majed; Mashhour, Ibrahim; Alshehri, Mohammed; Boothman, Chris; Al-Enezi, Mousa

The complete mineralization of crude oil into carbon dioxide, water, inorganic compounds and cellular constituents can be carried out as part of a bioremediation strategy. This involves the transformation of complex organic contaminants into simpler organic compounds by microbial communities, mainly bacteria. A crude oil sample and an oil sludge sample were obtained from Saudi ARAMCO Oil Company and investigated to identify the microbial communities present using PCR-based culture-independent techniques. In total, analysis of 177 clones yielded 30 distinct bacterial sequences. Clone library analysis of the oil sample was found to contain Bacillus , Clostridia and Gammaproteobacteria species while the sludge sample revealed the presence of members of the Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Clostridia , Spingobacteria and Flavobacteria . The dominant bacterial class identified in oil and sludge samples was found to be Bacilli and Flavobacteria , respectively. Phylogenetic analysis showed that the dominant bacterium in the oil sample has the closest sequence identity to Enterococcus aquimarinus and the dominant bacterium in the sludge sample is most closely related to the uncultured Bacteroidetes bacterium designated AH.KK.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

Science.gov (United States)

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Microbial consortia in Oman oil fields: a possible use in enhanced oil recovery.

Science.gov (United States)

Al-Bahry, Saif N; Elshafie, Abdulkader E; Al-Wahaibi, Yahya M; Al-Bemani, Ali S; Joshi, Sanket J; Al-Maaini, Ratiba A; Al-Alawi, Wafa J; Sugai, Yuichi; Al-Mandhari, Mussalam

2013-01-01

Microbial enhanced oil recovery (MEOR) is one of the most economical and efficient methods for extending the life of production wells in a declining reservoir. Microbial consortia from Wafra oil wells and Suwaihat production water, Al-Wusta region, Oman were screened. Microbial consortia in brine samples were identified using denaturing gradient gel electrophoresis and 16S rRNA gene sequences. The detected microbial consortia of Wafra oil wells were completely different from microbial consortia of Suwaihat formation water. A total of 33 genera and 58 species were identified in Wafra oil wells and Suwaihat production water. All of the identified microbial genera were first reported in Oman, with Caminicella sporogenes for the first time reported from oil fields. Most of the identified microorganisms were found to be anaerobic, thermophilic, and halophilic, and produced biogases, biosolvants, and biosurfactants as by-products, which may be good candidates for MEOR.

Microbial Photoelectrosynthesis for Self-Sustaining Hydrogen Generation.

Science.gov (United States)

Lu, Lu; Williams, Nicholas B; Turner, John A; Maness, Pin-Ching; Gu, Jing; Ren, Zhiyong Jason

2017-11-21

Current artificial photosynthesis (APS) systems are promising for the storage of solar energy via transportable and storable fuels, but the anodic half-reaction of water oxidation is an energy intensive process which in many cases poorly couples with the cathodic half-reaction. Here we demonstrate a self-sustaining microbial photoelectrosynthesis (MPES) system that pairs microbial electrochemical oxidation with photoelectrochemical water reduction for energy efficient H 2 generation. MPES reduces the overall energy requirements thereby greatly expanding the range of semiconductors that can be utilized in APS. Due to the recovery of chemical energy from waste organics by the mild microbial process and utilization of cost-effective and stable catalyst/electrode materials, our MPES system produced a stable current of 0.4 mA/cm 2 for 24 h without any external bias and ∼10 mA/cm 2 with a modest bias under one sun illumination. This system also showed other merits, such as creating benefits of wastewater treatment and facile preparation and scalability.

Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

Science.gov (United States)

Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

2016-05-01

The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

Screening Microbial Contamination of Smoking Waterpipe (Narghile in Erbil city/ Iraq

Directory of Open Access Journals (Sweden)

Salah Tofik Jalal Balaky

2018-03-01

Full Text Available Tobacco smoking, which is a traditional habit is a major health risk worldwide. However waterpipe (Narghile smoking is an emerging smoking type, specifically among Erbil/ Iraq. In the recent years, smoking of Shisha (Narghile has spread amongst adolescents and young adults in Erbil city. The aims of this study are to examine the prevalence of shisha pipe smoking in Erbil city and to determine the microbial pathogen contaminants present in these Shisha pipes. In this study, we performed a qualitative and quantitative analysis of the microbial contamination of (90 Shisha hose samples in Erbil. Eighteen samples were selected from each cafe and swabs were cultured and identified. Results showed that most Narghile users 82.2 % were male and half of them (50% were in the age group of 20-30 years followed by the age group of 30-40 years. Data showed that 54% of the samples were contaminated, from them most microbial pathogens were G+ve bacteria. Staphylococcus albus and Staphylococcus aureus were among the most isolated pathogens, however E. coli was the most common G-ve bacteria in this study. On the other hand the number of fungi and yeasts identified in this study were 7 isolates, among them Monilia, Paecillomycet spp and Aspergillus niger were most common isolates. In conclusion, data produced from this study showed that Narghile users are exposed to many infectious microbial agents, because many users are unaware of the associated microbial contaminations and smoke narghile as a safe alternative to cigarette smoking. More research, should focus on strategies on how to avoid shisha smoking as the impact of its use is expected to affect the health and life of many people in our local community.

Evaluation of Microbial Contamination and Chemical Qualities of Cream-filled Pastries in Confectioneries of Chaharmahal Va Bakhtiari Province (Southwestern Iran).

Science.gov (United States)

Sharifzadeh, Ali; Hajsharifi-Shahreza, Mohammad; Ghasemi-Dehkordi, Payam

2016-12-01

High consumption of bakery products such as cream-filled pastries may cause serious health risks and food poisoning to humans. Therefore, investigation of the microbial and chemical qualities of bakery products containing cream is necessary. The purpose of the present study was to investigate the chemical qualities and microbial contaminations of cream-filled pastries collected from confectioneries located in six cities in Chaharmahal Va Bakhtiari province (Southwestern Iran). Microbial tests and chemical characteristics (fat and acidity level) were done on 228 cream-filled pastries samples that were collected randomly from various confectioneries. After microbial tests, it was found that 33.33% of all samples were contaminated by microbial agents. The microbial tests showed that Shahrekord (10.09%) and Broujen (9.21%) cities had high levels of contamination and in Koohrang (1.31%) it was low compared with the other four cities. High contamination of coliforms (61.84%), staphylococci (48.68%), and yeast (27.63%) were observed in almost all samples. The chemical analysis showed maximum amounts of fat content and titratable acidity in cream-filled pastry samples obtained from Lordegan and Shahrekord cities, respectively. The findings of the present work demonstrated that the microbial contamination and chemical quality of cream-filled pastries produced in confectionaries of Chaharmahal Va Bakhtiari province were not in acceptable ranges. These problems may be related to fecal contamination of cream samples or lack of hygiene by handlers and it is necessary to observe the standards of hygiene and to develop safe food handling techniques and aseptic pastry manufacturing systems in some confectioneries of Chaharmahal Va Bakhtiari province.

Microbial biosensors

International Nuclear Information System (INIS)

Le Yu; Chen, Wilfred; Mulchandani, Ashok

2006-01-01

A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

Microbial impacts on geothermometry temperature predictions

Energy Technology Data Exchange (ETDEWEB)

Yoshiko Fujita; David W. Reed; Kaitlyn R. Nowak; Vicki S. Thompson; Travis L. McLing; Robert W. Smith

2013-02-01

Conventional geothermometry approaches assume that the composition of a collected water sample originating in a deep geothermal reservoir still reflects chemical equilibration of the water with the deep reservoir rocks. However, for geothermal prospecting samples whose temperatures have dropped to <120°C, temperature predictions may be skewed by the activity of microorganisms; microbial metabolism can drastically and rapidly change the water’s chemistry. We hypothesize that knowledge of microbial impacts on exploration sample geochemistry can be used to constrain input into geothermometry models and thereby improve the reliability of reservoir temperature predictions. To evaluate this hypothesis we have chosen to focus on sulfur cycling, because of the significant changes in redox state and pH associated with sulfur chemistry. Redox and pH are critical factors in defining the mineral-fluid equilibria that form the basis of solute geothermometry approaches. Initially we are developing assays to detect the process of sulfate reduction, using knowledge of genes specific to sulfate reducing microorganisms. The assays rely on a common molecular biological technique known as quantitative polymerase chain reaction (qPCR), which allows estimation of the number of target organisms in a particular sample by enumerating genes specific to the organisms rather than actually retrieving and characterizing the organisms themselves. For quantitation of sulfate reducing genes using qPCR, we constructed a plasmid (a piece of DNA) containing portions of two genes (known as dsrA and dsrB) that are directly involved with sulfate reduction and unique to sulfate reducing microorganisms. Using the plasmid as well as DNA from other microorganisms known to be sulfate reducers or non-sulfate reducers, we developed qPCR protocols and showed the assay’s specificity to sulfate reducers and that a qPCR standard curve using the plasmid was linear over >5 orders of magnitude. As a first test

Microbial dynamics during industrial rearing, processing, and storage of the tropical house cricket (Gryllodes sigillatus) for human consumption.

Science.gov (United States)

Vandeweyer, Dries; Wynants, Enya; Crauwels, Sam; Verreth, Christel; Viaene, Nikolaas; Claes, Johan; Lievens, Bart; Van Campenhout, Leen

2018-04-06

limited. Samples monitored for their microbiota were obtained in this study from an industrial rearing and processing cycle. The results lead in the first place to the identification of process steps which are critical for microbial food safety. Secondly, they can be used in the construction of a HACCP plan and of a Novel Food dossier which is required in Europe for edible insects. Finally, they confirm the shelf life period which was determined by the rearer. Copyright © 2018 American Society for Microbiology.

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.

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James Kaminski

2015-12-01

Full Text Available Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity. We developed ShortBRED (Short, Better Representative Extract Dataset to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i a method that reduces reference proteins of interest to short, highly representative amino acid sequences ("markers" and (ii a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred.

Aligning the Measurement of Microbial Diversity with Macroecological Theory

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James C. Stegen

2016-09-01

Full Text Available The number of microbial operational taxonomic units (OTUs within a community is akin to species richness within plant/animal (‘macrobial’ systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study’s outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we (i propose a new sampling approach that estimates OTU richness per-mass of soil, which results in strong support for species energy theory, (ii use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and (iii show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts, we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness.

Microbial diversity and carbon cycling in San Francisco Bay wetlands

Energy Technology Data Exchange (ETDEWEB)

Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2014-03-21

Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled the diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.

Airborne microbial composition in a high-throughput poultry slaughtering facility.

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Liang, Ruiping; Tian, Jijing; She, Ruiping; Meng, Hua; Xiao, Peng; Chang, Lingling

2013-03-01

A high-throughput chicken slaughtering facility in Beijing was systematically investigated for numbers of airborne microorganisms. Samples were assessed for counts of aerobic bacteria, Staphylococcus aureus, total coliforms, Escherichia coli, Pseudomonas aeruginosa, Listeria monocytogenes, Bacillus cereus, and Salmonella. During a 4-month period (September to December 2011), samples were collected for 10 min three times daily (preproduction, production, and postproduction). Samples were collected for three consecutive days of each month with an FA-1 sampler from six sampling sites: receiving-hanging, soaking-scalding and defeathering, evisceration, precooling, subdividing, and packing. Humidity, temperature, wind velocity, and airborne particulates also were recorded at each sampling site and time. The highest counts of microorganisms were recorded in the initial stages of processing, i.e., the receiving-hanging and defeathering areas, with a definite decline toward the evisceration, prechilling, subdividing, and packing areas; the prechilling area had the lowest microbial counts of 2.4 × 10(3) CFU/m(3). Mean total coliforms counts ranged from 8.4 × 10(3) to 140 CFU/m(3). Maximum E. coli counts were 6.1 × 10(3) CFU/m(3) in the soaking-scalding and defeathering area. B. cereus, P. aeruginosa, and S. aureus represented only a small proportion of the microbial population (1,900 to 20 CFU/m(3)). L. monocytogenes and Salmonella were rarely detected in evisceration, precooling, subdividing, and packing areas. Our study identified the levels of bioaerosols that may affect chicken product quality. This finding could be useful for improved control of microbial contamination to ensure product quality.

Microbial contamination of single-and multiple-dose vials after opening in a pulmonary teaching hospital

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Shadi Baniasadi

Full Text Available OBJECTIVES: Intravenous therapy is a complex procedure usually requiring the preparation of the medication in the clinical area before administration to the patient. Breaches in aseptic technique may result in microbial contaminations of vials which is a potential cause of different avoidable infections. We aimed to investigate the prevalence and pattern of microbial contamination of single- and multiple-dose vials in the largest pulmonary teaching hospital in Iran. METHODS: In a period of 2 months, opened single- and multiple-dose vials from different wards were sampled by a pharmacist. The name of the medication, ward, labeling of the vials, the date of opening, and storing temperature were recorded for each vial. Remained contents of each vial were cultured using appropriate bacterial and fungal growth media. RESULTS: Microbial contamination was identified in 11 of 205 (5.36% of vials. The highest contamination rate was 14.28% for vials used in interventional bronchoscopy unit. The most frequent contaminated medication was insulin. Gram-positive bacteria (81.82% were more significantly involved than gram-negative ones (9.09% and fungi (9.09%, with the highest frequency for Staphylococcus epidermidis . CONCLUSIONS: Our data demonstrate that repeated use of vials especially if basic sterility measures are disobeyed can cause microbial contamination of administered products to the patients. Infection preventionists are responsible to train health care workers regarding aseptic techniques and apply guidelines for aseptic handling of intravenous solutions.

Microbial contamination of single-and multiple-dose vials after opening in a pulmonary teaching hospital

Directory of Open Access Journals (Sweden)

Shadi Baniasadi

2013-02-01

Full Text Available OBJECTIVES: Intravenous therapy is a complex procedure usually requiring the preparation of the medication in the clinical area before administration to the patient. Breaches in aseptic technique may result in microbial contaminations of vials which is a potential cause of different avoidable infections. We aimed to investigate the prevalence and pattern of microbial contamination of single- and multiple-dose vials in the largest pulmonary teaching hospital in Iran. METHODS: In a period of 2 months, opened single- and multiple-dose vials from different wards were sampled by a pharmacist. The name of the medication, ward, labeling of the vials, the date of opening, and storing temperature were recorded for each vial. Remained contents of each vial were cultured using appropriate bacterial and fungal growth media. RESULTS: Microbial contamination was identified in 11 of 205 (5.36% of vials. The highest contamination rate was 14.28% for vials used in interventional bronchoscopy unit. The most frequent contaminated medication was insulin. Gram-positive bacteria (81.82% were more significantly involved than gram-negative ones (9.09% and fungi (9.09%, with the highest frequency for Staphylococcus epidermidis . CONCLUSIONS: Our data demonstrate that repeated use of vials especially if basic sterility measures are disobeyed can cause microbial contamination of administered products to the patients. Infection preventionists are responsible to train health care workers regarding aseptic techniques and apply guidelines for aseptic handling of intravenous solutions.

How Much Will It Cost To Monitor Microbial Drinking Water Quality in Sub-Saharan Africa?

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Delaire, Caroline; Peletz, Rachel; Kumpel, Emily; Kisiangani, Joyce; Bain, Robert; Khush, Ranjiv

2017-06-06

Microbial water quality monitoring is crucial for managing water resources and protecting public health. However, institutional testing activities in sub-Saharan Africa are currently limited. Because the economics of water quality testing are poorly understood, the extent to which cost may be a barrier to monitoring in different settings is unclear. This study used cost data from 18 African monitoring institutions (piped water suppliers and health surveillance agencies in six countries) and estimates of water supply type coverage from 15 countries to assess the annual financial requirements for microbial water testing at both national and regional levels, using World Health Organization recommendations for sampling frequency. We found that a microbial water quality test costs 21.0 ± 11.3 USD, on average, including consumables, equipment, labor, and logistics, which is higher than previously calculated. Our annual cost estimates for microbial monitoring of piped supplies and improved point sources ranged between 8 000 USD for Equatorial Guinea and 1.9 million USD for Ethiopia, depending primarily on the population served but also on the distribution of piped water system sizes. A comparison with current national water and sanitation budgets showed that the cost of implementing prescribed testing levels represents a relatively modest proportion of existing budgets (water sources in sub-Saharan Africa would cost 16.0 million USD per year, which is minimal in comparison to the projected annual capital costs of achieving Sustainable Development Goal 6.1 of safe water for all (14.8 billion USD).

Mapping the ecological networks of microbial communities.

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Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan; Waldor, Matthew K; Weiss, Scott T; Liu, Yang-Yu

2017-12-11

Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka-Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

Opportunistic Pathogens and Microbial Communities and Their Associations with Sediment Physical Parameters in Drinking Water Storage Tank Sediments

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Qin, Ke; Struewing, Ian; Domingo, Jorge Santo; Lytle, Darren

2017-01-01

The occurrence and densities of opportunistic pathogens (OPs), the microbial community structure, and their associations with sediment elements from eight water storage tanks in Ohio, West Virginia, and Texas were investigated. The elemental composition of sediments was measured through X-ray fluorescence (XRF) spectra. The occurrence and densities of OPs and amoeba hosts (i.e., Legionella spp. and L. pneumophila, Mycobacterium spp., P. aeruginosa, V. vermiformis, Acanthamoeba spp.) were determined using genus- or species-specific qPCR assays. Microbial community analysis was performed using next generation sequencing on the Illumina Miseq platform. Mycobacterium spp. were most frequently detected in the sediments and water samples (88% and 88%), followed by Legionella spp. (50% and 50%), Acanthamoeba spp. (63% and 13%), V. vermiformis (50% and 25%), and P. aeruginosa (0 and 50%) by qPCR method. Comamonadaceae (22.8%), Sphingomonadaceae (10.3%), and Oxalobacteraceae (10.1%) were the most dominant families by sequencing method. Microbial communities in water samples were mostly separated with those in sediment samples, suggesting differences of communities between two matrices even in the same location. There were associations of OPs with microbial communities. Both OPs and microbial community structures were positively associated with some elements (Al and K) in sediments mainly from pipe material corrosions. Opportunistic pathogens presented in both water and sediments, and the latter could act as a reservoir of microbial contamination. There appears to be an association between potential opportunistic pathogens and microbial community structures. These microbial communities may be influenced by constituents within storage tank sediments. The results imply that compositions of microbial community and elements may influence and indicate microbial water quality and pipeline corrosion, and that these constituents may be important for optimal storage tank management

The binning of metagenomic contigs for microbial physiology of mixed cultures.

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Strous, Marc; Kraft, Beate; Bisdorf, Regina; Tegetmeyer, Halina E

2012-01-01

So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population. In the present study eight metagenomic samples from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to existing algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a 100 times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt).

The binning of metagenomic contigs for microbial physiology of mixed cultures

Directory of Open Access Journals (Sweden)

Marc eStrous

2012-12-01

Full Text Available So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population.In the present study eight metagenomic samples originating from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to exisiting algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a hunderd times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt.

PanFP: pangenome-based functional profiles for microbial communities.

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Jun, Se-Ran; Robeson, Michael S; Hauser, Loren J; Schadt, Christopher W; Gorin, Andrey A

2015-09-26

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. We present a computational method called pangenome-based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU's taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome's functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8-0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique

Spatial Autocorrelation, Source Water and the Distribution of Total and Viable Microbial Abundances within a Crystalline Formation to a Depth of 800 m

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E. D. Beaton

2017-09-01

Full Text Available Proposed radioactive waste repositories require long residence times within deep geological settings for which we have little knowledge of local or regional subsurface dynamics that could affect the transport of hazardous species over the period of radioactive decay. Given the role of microbial processes on element speciation and transport, knowledge and understanding of local microbial ecology within geological formations being considered as host formations can aid predictions for long term safety. In this relatively unexplored environment, sampling opportunities are few and opportunistic. We combined the data collected for geochemistry and microbial abundances from multiple sampling opportunities from within a proposed host formation and performed multivariate mixing and mass balance (M3 modeling, spatial analysis and generalized linear modeling to address whether recharge can explain how subsurface communities assemble within fracture water obtained from multiple saturated fractures accessed by boreholes drilled into the crystalline formation underlying the Chalk River Laboratories site (Deep River, ON, Canada. We found that three possible source waters, each of meteoric origin, explained 97% of the samples, these are: modern recharge, recharge from the period of the Laurentide ice sheet retreat (ca. ∼12000 years before present and a putative saline source assigned as Champlain Sea (also ca. 12000 years before present. The distributed microbial abundances and geochemistry provide a conceptual model of two distinct regions within the subsurface associated with bicarbonate – used as a proxy for modern recharge – and manganese; these regions occur at depths relevant to a proposed repository within the formation. At the scale of sampling, the associated spatial autocorrelation means that abundances linked with geochemistry were not unambiguously discerned, although fine scale Moran’s eigenvector map (MEM coefficients were correlated with

The role of macrobiota in structuring microbial communities along rocky shores

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Catherine A. Pfister

2014-10-01

Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

Microbial fuel cells and microbial electrolysis cells for the production of bioelectricity and biomaterials.

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Zhou, Minghua; Yang, Jie; Wang, Hongyu; Jin, Tao; Xu, Dake; Gu, Tingyue

2013-01-01

Today's global energy crisis requires a multifaceted solution. Bioenergy is an important part of the solution. The microbial fuel cell (MFC) technology stands out as an attractive potential technology in bioenergy. MFCs can convert energy stored in organic matter directly into bioelectricity. MFCs can also be operated in the electrolysis mode as microbial electrolysis cells to produce bioproducts such as hydrogen and ethanol. Various wastewaters containing low-grade organic carbons that are otherwise unutilized can be used as feed streams for MFCs. Despite major advances in the past decade, further improvements in MFC power output and cost reduction are needed for MFCs to be practical. This paper analysed MFC operating principles using bioenergetics and bioelectrochemistry. Several major issues were explored to improve the MFC performance. An emphasis was placed on the use of catalytic materials for MFC electrodes. Recent advances in the production of various biomaterials using MFCs were also investigated.

Seasonal Development of Microbial Activity in Soils of Northern Norway

Institute of Scientific and Technical Information of China (English)

M. B(O)LTER; N. SOETHE; R. HORN; C. UHLIG

2005-01-01

Seasonal development of soil microbial activity and bacterial biomass in sub-polar regions was investigated to determine the impacts of biotic and abiotic factors, such as organic matter content, temperature and moisture. The study was performed during spring thaw from three cultivated meadows and two non-cultivated forest sites near Alta, in northern Norway. Samples from all five sites showed increasing respiration rates directly after the spring thaw with soil respiration activity best related to soil organic matter content. However, distributions of bacterial biomass showed fewer similarities to these two parameters. This could be explained by variations of litter exploitation through the biomass. Microbial activity started immediately after the thaw while root growth had a longer time lag. An influence of root development on soil microbes was proposed for sites where microorganisms and roots had a tight relationship caused by a more intensive root structure. Also a reduction of microbial activity due to soil compaction in the samples from a wheel track could not be observed under laboratory conditions. New methodological approaches of differential staining for live and dead organisms were applied in order to follow changes within the microbial community. Under laboratory conditions freeze and thaw cycles showed a damaging influence on parts of the soil bacteria. Additionally, different patterns for active vs.non-active bacteria were noticeable after freeze-thaw cycles.

BIOMASS AND MICROBIAL ACTIVITY UNDER DIFFERENT FOREST COVERS

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Rafael Malfitano Braga

2016-06-01

Full Text Available This study evaluated the soil fertility, biomass and microbial activity of the soil under forest cover of Eucalyptus grandis, Eucalyptus pilularis, Eucalyptus cloeziana and Corymbia maculata; Pinus Caribbean var. hondurensis, 40 years old, and a fragment of Semideciduous Forest, located on the campus of the Federal University of Lavras. In soil samples collected in the 0-5 cm layer were determined fertility parameters, basal respiration and microbial biomass carbon. The results showed that for the species E. grandis and E. cloeziana the carbon of biomass microbial content was higher than for any other ecosystem evaluated, and equal to those observed under native forest. In contrast, the ground under Pinus had the lowest microbiological indexes. Under C. maculata and E. pilularis the contents were intermediate for this parameter. The basal respiration of all ecosystems was equal. The fertility level was very low in all types of evaluated vegetation.

Microbial Metabolism in Serpentinite Fluids

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Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

2013-12-01

Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

KAUST Repository

Li, D.; Sharp, J. O.; Saikaly, Pascal; Ali, Shahjahan; Alidina, M.; Alarawi, M. S.; Keller, S.; Hoppe-Jones, C.; Drewes, J. E.

2012-01-01

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

KAUST Repository

Li, D.

2012-07-13

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems.

Science.gov (United States)

Li, Dong; Sharp, Jonathan O; Saikaly, Pascal E; Ali, Shahjahan; Alidina, Mazahirali; Alarawi, Mohammed S; Keller, Stephanie; Hoppe-Jones, Christiane; Drewes, Jörg E

2012-10-01

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation.

Science.gov (United States)

Campeão, Mariana E; Reis, Luciana; Leomil, Luciana; de Oliveira, Louisi; Otsuki, Koko; Gardinali, Piero; Pelz, Oliver; Valle, Rogerio; Thompson, Fabiano L; Thompson, Cristiane C

2017-01-01

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical-chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae , and Alcanivoracaceae ), archaea (e.g., Halobacteriaceae, Desulfurococcaceae , and Methanobacteriaceae ), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

Directory of Open Access Journals (Sweden)

Jenna L Shelton

2016-09-01

Full Text Available Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow up-dip wells was different than the 17 deeper, down-dip wells, and that

Sample Size Requirements for Assessing Statistical Moments of Simulated Crop Yield Distributions

NARCIS (Netherlands)

Lehmann, N.; Finger, R.; Klein, T.; Calanca, P.

2013-01-01

Mechanistic crop growth models are becoming increasingly important in agricultural research and are extensively used in climate change impact assessments. In such studies, statistics of crop yields are usually evaluated without the explicit consideration of sample size requirements. The purpose of

Microbial Activity and Silica Degradation in Rice Straw

Science.gov (United States)

Kim, Esther Jin-kyung

increased. Silicase activity did not change across nitrogen treatments despite a shift in microbial community with varied nitrogen concentration. Samples treated with different nitrogen concentrations had similar levels of diversity, however the microbial community composition differed with added nitrogen. The results demonstrated that adding nitrogen to rice straw during thermophilic decomposition nurtured a more active microbial community and promoted enzyme secretion thus improving the ability to discover enzymes for rice straw deconstruction. These results can inform future experiments for cultivating a unique, thriving compost-derived microbial community that can successfully decompose rice straw. Understanding the silicase activity of microorganisms may alleviate the challenges associated with silica in various feedstocks.

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

Science.gov (United States)

Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

2016-08-01

Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. Copyright © 2016 Elsevier B.V. All rights reserved.

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil.

Science.gov (United States)

Bagi, Andrea; Riiser, Even Sannes; Molland, Hilde Steine; Star, Bastiaan; Haverkamp, Thomas H A; Sydnes, Magne Olav; Pampanin, Daniela Maria

2018-04-02

The expansion of offshore oil exploration increases the risk of marine species being exposed to oil pollution in currently pristine areas. The adverse effects of oil exposure through toxic properties of polycyclic aromatic hydrocarbons (PAHs) have been well studied in Atlantic cod (Gadus morhua). Nevertheless, the fate of conjugated metabolites in the intestinal tract and their effect on the diversity of intestinal microbial community in fish is less understood. Here, we investigated the intestinal microbial community composition of Atlantic cod after 28 days of exposure to crude oil (concentration range 0.0-0.1 mg/L). Analysis of PAH metabolites in bile samples confirmed that uptake and biotransformation of oil compounds occurred as a result of the exposure. Various evidence for altered microbial communities was found in fish exposed to high (0.1 mg/L) and medium (0.05 mg/L) concentrations of oil when compared to fish exposed to low oil concentration (0.01 mg/L) or no oil (control). First, altered banding patterns were observed on denaturing gradient gel electrophoresis for samples pooled from each treatment group. Secondly, based on 16S rRNA sequences, higher levels of oil exposure were associated with a loss of overall diversity of the gut microbial communities. Furthermore, 8 operational taxonomic units (OTUs) were found to have significantly different relative abundances in samples from fishes exposed to high and medium oil concentrations when compared to samples from the control group and low oil concentration. Among these, only one OTU, a Deferribacterales, had increased relative abundance in samples from fish exposed to high oil concentration. The results presented herein contribute to a better understanding of the effects of oil contamination on the gut microbial community changes in fish and highlight the importance of further studies into the area. Our findings suggest that increased relative abundance of bacteria belonging to the order

Down Under – Aspects of Microbial Fuel Cell’s sewer implementation

OpenAIRE

Andrich, Jonas Maximilian Sven

2017-01-01

Increasing energy demand and simultaneous depletion of raw materials requires us to use existing resources more wisely. Microbial Fuel Cells (MFCs) recover energy from waste water while clearing it. The sewage system with its million-kilometer-length is a highly interesting field for its application. The present work is therefore dedicated to aspects of Microbial Fuel Cells’ sewer implementation. Firstly, the wastewater infrastructure was evaluated with respect to suitable implementation s...

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

Science.gov (United States)

Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

2015-01-01

Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

Laser engineering of microbial systems

Science.gov (United States)

Yusupov, V. I.; Gorlenko, M. V.; Cheptsov, V. S.; Minaev, N. V.; Churbanova, E. S.; Zhigarkov, V. S.; Chutko, E. A.; Evlashin, S. A.; Chichkov, B. N.; Bagratashvili, V. N.

2018-06-01

A technology of laser engineering of microbial systems (LEMS) based on the method of laser-induced transfer of heterogeneous mixtures containing microorganisms (laser bioprinting) is described. This technology involves laser printing of soil microparticles by focusing near-infrared laser pulses on a specially prepared gel/soil mixture spread onto a gold-coated glass plate. The optimal range of laser energies from the point of view of the formation of stable jets and droplets with minimal negative impact on living systems of giant accelerations, laser pulse irradiation, and Au nanoparticles was found. Microsamples of soil were printed on glucose-peptone-yeast agar plates to estimate the LEMS process influence on structural and morphological microbial diversity. The obtained results were compared with traditionally treated soil samples. It was shown that LEMS technology allows significantly increasing the biodiversity of printed organisms and is effective for isolating rare or unculturable microorganisms.

Acetaldehyde production and microbial colonization in oral squamous cell carcinoma and oral lichenoid disease.

Science.gov (United States)

Marttila, Emilia; Uittamo, Johanna; Rusanen, Peter; Lindqvist, Christian; Salaspuro, Mikko; Rautemaa, Riina

2013-07-01

The main aim of this prospective study was to explore the ability of the oral microbiome to produce acetaldehyde in ethanol incubation. A total of 90 patients [30 oral squamous cell carcinoma (OSCC); 30 oral lichenoid disease (OLD); 30 healthy controls (CO)] were enrolled in the study. Microbial samples were taken from the mucosa using a filter paper method. The density of microbial colonization was calculated and the spectrum analyzed. Microbial acetaldehyde production was measured by gas chromatography. The majority (68%) of cultures produced carcinogenic levels of acetaldehyde (>100 μM) when incubated with ethanol (22 mM). The mean acetaldehyde production by microbes cultured from smoker samples was significantly higher (213 μM) than from non-smoker samples (141 μM) (P=.0326). The oral microbiota from OSCC, OLD patients and healthy individuals are able to produce carcinogenic levels of acetaldehyde. The present provisional study suggests smoking may increase the production of acetaldehyde. Copyright © 2013 Elsevier Inc. All rights reserved.

Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information

Directory of Open Access Journals (Sweden)

Hannu Myllykallio

2018-05-01

Full Text Available Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin co-factors (FADH2 in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and

Microbial Biomass Changes during Decomposition of Plant Residues in a Lixisol

Directory of Open Access Journals (Sweden)

Kachaka, SK.

2003-01-01

Full Text Available A lixisol was amended with four different alley cropping species: Senna siamea, Leucaena leucocephala, Dactyladenia barteri and Flemingia macrophylla. Soil samples were incubated for 140 days at 25 °C and the soil microbial biomass was determined by the ninhydrin extraction method along the incubation period. The soil microbial biomass values ranged between 80 and 600 mg.kg-1 and followed, in all cases, the decreasing order: Leucaena> Senna> Flemingia> Dactyladenia.

Hydrogen production profiles using furans in microbial electrolysis cells.

Science.gov (United States)

Catal, Tunc; Gover, Tansu; Yaman, Bugra; Droguetti, Jessica; Yilancioglu, Kaan

2017-06-01

Microbial electrochemical cells including microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) are novel biotechnological tools that can convert organic substances in wastewater or biomass into electricity or hydrogen. Electroactive microbial biofilms used in this technology have ability to transfer electrons from organic compounds to anodes. Evaluation of biofilm formation on anode is crucial for enhancing our understanding of hydrogen generation in terms of substrate utilization by microorganisms. In this study, furfural and hydroxymethylfurfural (HMF) were analyzed for hydrogen generation using single chamber membrane-free MECs (17 mL), and anode biofilms were also examined. MECs were inoculated with mixed bacterial culture enriched using chloroethane sulphonate. Hydrogen was succesfully produced in the presence of HMF, but not furfural. MECs generated similar current densities (5.9 and 6 mA/cm 2 furfural and HMF, respectively). Biofilm samples obtained on the 24th and 40th day of cultivation using aromatic compounds were evaluated by using epi-fluorescent microscope. Our results show a correlation between biofilm density and hydrogen generation in single chamber MECs.

Microbial acetate oxidation in horizontal rotating tubular bioreactor

Indian Academy of Sciences (India)

Unknown

shaped partition walls that served as carriers for micro- bial biomass. Mixing ... from soil sample collected from Zagreb mountain. This microbial culture was ... HRTB was made of a plastic tube 1⋅8 m long with an inner diameter of 0⋅25 m.

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

Energy Technology Data Exchange (ETDEWEB)

Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

2009-12-01

Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

Capillary absorption spectrometer and process for isotopic analysis of small samples

Energy Technology Data Exchange (ETDEWEB)

Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.; Moran, James J.; Newburn, Matthew K.; Blake, Thomas A.

2018-04-24

A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The process also permits sampling in vivo permitting real-time ambient studies of microbial communities.

Capillary absorption spectrometer and process for isotopic analysis of small samples

Energy Technology Data Exchange (ETDEWEB)

Alexander, M. Lizabeth; Kelly, James F.; Sams, Robert L.; Moran, James J.; Newburn, Matthew K.; Blake, Thomas A.

2016-03-29

A capillary absorption spectrometer and process are described that provide highly sensitive and accurate stable absorption measurements of analytes in a sample gas that may include isotopologues of carbon and oxygen obtained from gas and biological samples. It further provides isotopic images of microbial communities that allow tracking of nutrients at the single cell level. It further targets naturally occurring variations in carbon and oxygen isotopes that avoids need for expensive isotopically labeled mixtures which allows study of samples taken from the field without modification. The method also permits sampling in vivo permitting real-time ambient studies of microbial communities.

Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples

DEFF Research Database (Denmark)

Belstrøm, Daniel; Holmstrup, Palle; Jensen, Allan Bardow

2016-01-01

BACKGROUND AND OBJECTIVE: The microbial profiles of stimulated saliva samples have been shown to differentiate between patients with periodontitis, patients with dental caries, and orally healthy individuals. Saliva was stimulated to allow for easy and rapid collection; however, microbial...

Response of soil aggregate stability to storage time of soil samples

International Nuclear Information System (INIS)

Gerzabek, M.H.; Roessner, H.

1993-04-01

The aim of the present study was to investigate the well known phenomenon of changing aggregate stability values as result of soil sample storage. In order to evaluate the impact of soil microbial activity, the soil sample was split into three subsamples. Two samples were sterilized by means of chloroform fumigation and gamma irradiation, respectively. However, the aggregate stability measurements at three different dates were not correlated with the microbial activity (dehydrogenase activity). The moisture content of the aggregate samples seems to be of higher significance. Samples with lower moisture content (range: 0.4 to 1.9%) exhibited higher aggregate stabilities. Thus, airdried aggregate samples without further treatment don't seem to be suitable for standardized stability measurements. (authors)

Microbial sensor for drug susceptibility testing of Mycobacterium tuberculosis.

Science.gov (United States)

Zhang, Z-T; Wang, D-B; Li, C-Y; Deng, J-Y; Zhang, J-B; Bi, L-J; Zhang, X-E

2018-01-01

Drug susceptibility testing (DST) of clinical isolates of Mycobacterium tuberculosis is critical in treating tuberculosis. We demonstrate the possibility of using a microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The sensor is made of an oxygen electrode with M. tuberculosis cells attached to its surface. This sensor monitors the residual oxygen consumption of M. tuberculosis cells after treatment with anti-TB drugs with glycerine as a carbon source. In principle, after drug pretreatment for 4-5 days, the response differences between the sensors made of drug-sensitive isolates are distinguishable from the sensors made of drug-resistant isolates. The susceptibility of the M. tuberculosis H37Ra strain, its mutants and 35 clinical isolates to six common anti-TB drugs: rifampicin, isoniazid, streptomycin, ethambutol, levofloxacin and para-aminosalicylic acid were tested using the proposed method. The results agreed well with the gold standard method (LJ) and were determined in significantly less time. The whole procedure takes approximately 11 days and therefore has the potential to inform clinical decisions. To our knowledge, this is the first study that demonstrates the possible application of a dissolved oxygen electrode-based microbial sensor in M. tuberculosis drug resistance testing. This study used the microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The overall detection result of the microbial sensor agreed well with that of the conventional LJ proportion method and takes less time than the existing phenotypic methods. In future studies, we will build an O 2 electrode array microbial sensor reactor to enable a high-throughput drug resistance analysis. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

Exploring Microbial Iron Oxidation in Wetland Soils

Science.gov (United States)

Wang, J.; Muyzer, G.; Bodelier, P. L. E.; den Oudsten, F.; Laanbroek, H. J.

2009-04-01

Iron is one of the most abundant elements on earth and is essential for life. Because of its importance, iron cycling and its interaction with other chemical and microbial processes has been the focus of many studies. Iron-oxidizing bacteria (FeOB) have been detected in a wide variety of environments. Among those is the rhizosphere of wetland plants roots which release oxygen into the soil creating suboxic conditions required by these organisms. It has been reported that in these rhizosphere microbial iron oxidation proceeds up to four orders of magnitude faster than strictly abiotic oxidation. On the roots of these wetland plants iron plaques are formed by microbial iron oxidation which are involved in the sequestering of heavy metals as well organic pollutants, which of great environmental significance.Despite their important role being catalysts of iron-cycling in wetland environments, little is known about the diversity and distribution of iron-oxidizing bacteria in various environments. This study aimed at developing a PCR-DGGE assay enabling the detection of iron oxidizers in wetland habitats. Gradient tubes were used to enrich iron-oxidizing bacteria. From these enrichments, a clone library was established based on the almost complete 16s rRNA gene using the universal bacterial primers 27f and 1492r. This clone library consisted of mainly α- and β-Proteobacteria, among which two major clusters were closely related to Gallionella spp. Specific probes and primers were developed on the basis of this 16S rRNA gene clone library. The newly designed Gallionella-specific 16S rRNA gene primer set 122f/998r was applied to community DNA obtained from three contrasting wetland environments, and the PCR products were used in denaturing gradient gel electrophoresis (DGGE) analysis. A second 16S rRNA gene clone library was constructed using the PCR products from one of our sampling sites amplified with the newly developed primer set 122f/998r. The cloned 16S rRNA gene

Evaluation of microbial and physico-chemical qualities of some cough syrups marketed in Sana’a city, Yemen.

Directory of Open Access Journals (Sweden)

Ali G. Al−Kaf

2015-08-01

Full Text Available Context: Microbial contamination of cough syrups can bring clinical hazards to the users or patients as well as physical and chemical changes in the product. Aims: To evaluate the microbial and physicochemical characteristics of two hundred samples of four different types of cough syrups marketed in Sana’a city, Yemen. Methods: All collected samples were subjected to the following examinations: the total microbial count, type of isolated microorganisms, physical parameters, and concentration of active ingredients were identified and assessed by standard techniques described in US Pharmacopeia. Results: All the cough syrup samples used contained viable microbial load within acceptable limit according Pharmacopeia specifications. Bacillus subtilis, Micrococcus fulvum, and Staphylococcus epidermidis were the most commonly recovered bacteria. However, Aspergillus niger, Aspergillus fumigatus, Penicillium notatum, Mucor sp., and Aspergillus flavus were the most fungi isolated. The physical properties represented in the appearance, density, and pH of the analyzed samples complied with Pharmacopoeia standards. The concentrations of diphenhydramine HCl (92,51 – 108,78%, pseudoephedrine HCl (94,55 – 109,07%, and triprolidine HCl (98,20 – 104,19% were recorded. Conclusions: All cough syrups marketed in Sana’a City had good microbiological and physico-chemical qualities.

Microbial populations in contaminant plumes

Science.gov (United States)

Haack, Sheridan K.; Bekins, Barbara A.

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation. La biodégradation efficace des polluants souterrains requiert deux éléments: des populations microbiennes possédant les aptitudes nécessaires à la dégradation, et des conditions géochimiques et hydrologiques souterraines favorables. Des contraintes pratiques sur la conception et l'interprétation des expériences à la fois en microbiologie et en hydrogéologie ont conduit à une connaissance limitée des interactions entre les

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes.

Science.gov (United States)

Xu, Jiajiong; Tang, Wei; Ma, Jun; Wang, Hong

2017-07-01

Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.

Raman Spectroscopy of Microbial Pigments

Science.gov (United States)

Edwards, Howell G. M.; Oren, Aharon

2014-01-01

Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions. PMID:24682303

Microbial ecology laboratory procedures manual NASA/MSFC

Science.gov (United States)

Huff, Timothy L.

1990-01-01

An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

Magnetic Separation for the Direct Observation of Mineral-Associated Microbial Diversity

Science.gov (United States)

Harrison, B. K.; Orphan, V.

2006-12-01

Previous studies have demonstrated that microorganisms may selectively colonize mineral surfaces in diverse environments. Mineral substrates may serve as an important source of limiting nutrients or provide electron acceptors and donors for dissimilatory reactions. This work presents a new method for characterizing the microbial diversity associated with specific components in environmental samples. Minerals are concentrated from the bulk sample according to magnetic susceptibility, resulting in compositionally distinct partitions. The microbial communities associated with these partitions are subsequently characterized using molecular techniques. Initial testing of samples from active and dormant hydrothermal chimney structures from the Lau and Fiji Basins show that mineral components may be concentrated from bulk samples without concealing pre-existing patterns of selective colonization. 16S gene surveys from environmental clone libraries reveal distinct colonization patterns for thermophilic archaea and bacteria between sulfide mineral partitions. This method offers a unique tool discerning the role of mineral composition in surface-associated diversity.

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

OpenAIRE

Timmers, Ruud A.; Rothballer, Michael; Strik, David P. B. T. B.; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode–rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) w...

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

International Nuclear Information System (INIS)

Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

1995-01-01

Two chronosequence of unsaturated buried loess sediments ranging in age from and lt;10,000 years to and gt;1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was(approx)250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age:(approx)1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments ( and lt;9 m at Washtucna, and lt;12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the

Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Energy Technology Data Exchange (ETDEWEB)

Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

1995-01-05

Two chronosequence of unsaturated buried loess sediments ranging in age from <10,000 years to >1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was {approx}250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: {approx}1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

Science.gov (United States)

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Microbial bioremediation of Uranium: an overview

International Nuclear Information System (INIS)

Acharya, Celin

2015-01-01

Uranium contamination is a worldwide problem. Preventing uranium contamination in the environment is quite challenging and requires a thorough understanding of the microbiological, ecological and biogeochemical features of the contaminated sites. Bioremediation of uranium is largely dependent on reducing its bioavailability in the environment. In situ bioremediation of uranium by microbial processes has been shown to be effective for immobilizing uranium in contaminated sites. Such microbial processes are important components of biogeochemical cycles and regulate the mobility and fate of uranium in the environment. It is therefore vital to advance our understanding of the uranium-microbe interactions to develop suitable bioremediation strategies for uranium contaminated sites. This article focuses on the fundamental mechanisms adopted by various microbes to mitigate uranium toxicity which could be utilized for developing various approaches for uranium bioremediation. (author)

Microbial hotspots and hot moments in soil

Science.gov (United States)

Kuzyakov, Yakov; Blagodatskaya, Evgenia

2015-04-01

increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. Finally, we estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil.

Carbon input increases microbial nitrogen demand, but not microbial nitrogen mining in boreal forest soils

Science.gov (United States)

Wild, Birgit; Alaei, Saeed; Bengtson, Per; Bodé, Samuel; Boeckx, Pascal; Schnecker, Jörg; Mayerhofer, Werner; Rütting, Tobias

2016-04-01

Plant primary production at mid and high latitudes is often limited by low soil N availability. It has been hypothesized that plants can indirectly increase soil N availability via root exudation, i.e., via the release of easily degradable organic compounds such as sugars into the soil. These compounds can stimulate microbial activity and extracellular enzyme synthesis, and thus promote soil organic matter (SOM) decomposition ("priming effect"). Even more, increased C availability in the rhizosphere might specifically stimulate the synthesis of enzymes targeting N-rich polymers such as proteins that store most of the soil N, but are too large for immediate uptake ("N mining"). This effect might be particularly important in boreal forests, where plants often maintain high primary production in spite of low soil N availability. We here tested the hypothesis that increased C availability promotes protein depolymerization, and thus soil N availability. In a laboratory incubation experiment, we added 13C-labeled glucose to a range of soil samples derived from boreal forests across Sweden, and monitored the release of CO2 by C mineralization, distinguishing between CO2 from the added glucose and from the native, unlabeled soil organic C (SOC). Using a set of 15N pool dilution assays, we further measured gross rates of protein depolymerization (the breakdown of proteins into amino acids) and N mineralization (the microbial release of excess N as ammonium). Comparing unamended control samples, we found a high variability in C and N mineralization rates, even when normalized by SOC content. Both C and N mineralization were significantly correlated to SOM C/N ratios, with high C mineralization at high C/N and high N mineralization at low C/N, suggesting that microorganisms adjusted C and N mineralization rates to the C/N ratio of their substrate and released C or N that was in excess. The addition of glucose significantly stimulated the mineralization of native SOC in soils

Microbial biofilm growth on irradiated, spent nuclear fuel cladding

International Nuclear Information System (INIS)

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

2009-01-01

A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 x 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments

Microbial Enzymatic Degradation of Biodegradable Plastics.

Science.gov (United States)

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

2017-01-01

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

An assessment of microbial communities associated with surface mining-disturbed overburden.

Science.gov (United States)

Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

2014-03-01

To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.

Science.gov (United States)

Pernice, Massimo C; Giner, Caterina R; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2016-04-01

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

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

Science.gov (United States)

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

2012-12-01

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

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

Science.gov (United States)

Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

2016-10-01

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities

Recovery of Soil Microbial Community Structure in a Wildfire Impacted Forest Soil

Science.gov (United States)

Tate, Robert, III; Mikita, Robyn

2010-05-01

Wildfires are common disturbances that will increase in frequency and intensity as a result of conditions associated with the changing climate. In turn, forest fires exacerbate climate conditions by increasing carbon and atmospheric aerosols, and changing the surface albedo. Fires have significant economic, environmental, and ecological repercussions; however, we have a limited understanding on the effect of severe wildfires on the composition, diversity, and function of belowground microorganisms. The objective of this research was to examine the shift of the forest soil microbial community as a result of a severe wildfire in the New Jersey Pinelands. Over the span of two years following the fire, soil samples from the organic and mineral layers of the severely burned sites were collected six times. Samples were also collected twice from an unburned control site. It was hypothesized that soil microbial communities from severely burned samples collected shortly after the fire would be significantly different from (1) the unburned samples that serve as controls and (2) the severely burned samples collected more than a year after the fire. Microbial community composition was analyzed by principal component analysis and multivariate analysis of variance of molecular fingerprint data from denaturing gradient gel electrophoresis of bacterial and archaeal-specific amplicons. Bacterial community composition was significantly different among all the organic and mineral layer samples collected 2, 5, 13, and 17 months following the fire. This indicated a shift in the bacterial communities with time following the fire. Common phylotypes from the burned organic layer samples collected 2 months after the fire related closely to members of the phyla Cyanobacteria and Acidobacteria, whereas those from later samples (5, 13, and 17 months following the fire) were closely related to members of the genus Mycobacteria. Canonical correlation analysis was used to determine connections