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Sample records for commercial microbial culture

  1. Microbial community analysis of food-spoilage bacteria in commercial custard creams using culture-dependent and independent methods.

    PubMed

    Arakawa, K; Kawai, Y; Iioka, H; Tanioka, M; Nishimura, J; Kitazawa, H; Tsurumi, K; Saito, T

    2008-08-01

    Custard cream is made from highly nutritive raw materials such as milk and sugar and is easily spoiled by the multiplication of specific microbial contaminants or residents. However, this spoilage microbial community has not been studied. We determined the spoilage microbiota in commercial custard creams using culture-dependent and independent methods. Using the culture-dependent analysis with various agar media, 185 bacterial colonies and 43 eukaryal colonies were isolated from 7 commercial custard cream products. All bacterial isolates were morphologically, physiologically, and genetically identified as bacilli, staphylococci, lactic acid bacteria, and psychrotrophic gram-negative rods. Using culture-independent molecular analysis, the PCR-denaturing gradient gel electrophoresis technique, spoilage of the commercial custard creams was found to be caused by bacilli, staphylococci, lactic acid bacteria, psychrotrophic gram-negative rods, Anoxybacillus sp., Caurobacter sp., and Streptococcus sp. bacteria. The detected spoilage bacteria were the same species as previously detected in spoiled milk products and shown in other reports, suggesting that spoilage bacteria in a raw material easily grow in processed foods made from milk. We determined the spoilage microbial communities in commercial custard creams, and these are the first data concerning spoilage microbiota in nonfermented processed foods using a culture-independent analysis. Our study will be useful for the manufacture and safe preservation of dairy products because the first step toward safe food preservation by food manufacturers is to understand the spoilage microbiota in a target food to select optimal preservatives and to reduce the use of food additives.

  2. Commercial production of microbial enzymes

    SciTech Connect

    Munro, I.G.

    1985-01-01

    The advantages and uses of industrially produced microbial enzymes are described. The processes involved in the production of these enzymes, cultivation techniques, enzyme extraction, enzyme purification and immobilization are outlined. Both the history of enzyme technology and its future development are discussed.

  3. Microbial assessment of cabin air quality on commercial airliners

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  4. Towards commercial production of microbial surfactants.

    PubMed

    Mukherjee, Soumen; Das, Palashpriya; Sen, Ramkrishna

    2006-11-01

    Biosurfactants or microbial surfactants are surface-active biomolecules that are produced by a variety of microorganisms. Biosurfactants have gained importance in the fields of enhanced oil recovery, environmental bioremediation, food processing and pharmaceuticals owing to their unique properties--higher biodegradability, lower toxicity, and effectiveness at extremes of temperature, pH and salinity. However, large-scale production of these molecules has not been realized because of low yields in production processes and high recovery and purification costs. This article describes some practical approaches that have been adopted to make the biosurfactant production process economically attractive: these include the use of cheaper raw materials, optimized and efficient bioprocesses and overproducing mutant and recombinant strains for obtaining maximum productivity. The application of these strategies in biosurfactant production processes, particularly those using hyper-producing recombinant strains in the optimally controlled environment of a bioreactor, might lead towards the successful commercial production of these valuable and versatile biomolecules in near future.

  5. The DOE Subsurface Microbial Culture Collection (SMCC)

    SciTech Connect

    Balkwill, David L.

    2006-05-23

    The primary activities associated with maintenance of the Subsurface Microbial Culture Collection (SMCC) were designed to ensure that the collection served as a valuable resource to DOE-funded and other scientists, especially DOE-funded scientists associated with the NABIR Program. These activities were carried out throughout the period covered by this report and in-cluded: (1) assistance in the selection of cultures for research, (2) distribution of cultures and/or data on request, (3) incorporation of newly isolated microbial strains, (4) preservation of newly isolated strains, (5) partial characterization of newly isolated strains, (6) development and main-tenance of representative subsets of cultures, (6) screening of SMCC strains for specific charac-teristics, (7) phylogenetic characterization of SMCC strains, (8) development and maintenance of a SMCC website, (9) maintenance of the SMCC databases, (10) archiving of SMCC records, and (11) quality assurance/quality control (QA/QC) activities. We describe in the Final Technical Report our accomplishments related to these activities during the period covered by this report.

  6. Film forming microbial biopolymers for commercial applications--a review.

    PubMed

    Vijayendra, S V N; Shamala, T R

    2014-12-01

    Microorganisms synthesize intracellular, structural and extracellular polymers also referred to as biopolymers for their function and survival. These biopolymers play specific roles as energy reserve materials, protective agents, aid in cell functioning, the establishment of symbiosis, osmotic adaptation and support the microbial genera to function, adapt, multiply and survive efficiently under changing environmental conditions. Viscosifying, gelling and film forming properties of these have been exploited for specific significant applications in food and allied industries. Intensive research activities and recent achievements in relevant and important research fields of global interest regarding film forming microbial biopolymers is the subject of this review. Microbial polymers such as pullulan, kefiran, bacterial cellulose (BC), gellan and levan are placed under the category of exopolysaccharides (EPS) and have several other functional properties including film formation, which can be used for various applications in food and allied industries. In addition to EPS, innumerable bacterial genera are found to synthesis carbon energy reserves in their cells known as polyhydroxyalkanoates (PHAs), microbial polyesters, which can be extruded into films with excellent moisture and oxygen barrier properties. Blow moldable biopolymers like PHA along with polylactic acid (PLA) synthesized chemically in vitro using lactic acid (LA), which is produced by LA bacteria through fermentation, are projected as biodegradable polymers of the future for packaging applications. Designing and creating of new property based on requirements through controlled synthesis can lead to improvement in properties of existing polysaccharides and create novel biopolymers of great commercial interest and value for wider applications. Incorporation of antimicrobials such as bacteriocins or silver and copper nanoparticles can enhance the functionality of polymer films especially in food packaging

  7. Film forming microbial biopolymers for commercial applications--a review.

    PubMed

    Vijayendra, S V N; Shamala, T R

    2014-12-01

    Microorganisms synthesize intracellular, structural and extracellular polymers also referred to as biopolymers for their function and survival. These biopolymers play specific roles as energy reserve materials, protective agents, aid in cell functioning, the establishment of symbiosis, osmotic adaptation and support the microbial genera to function, adapt, multiply and survive efficiently under changing environmental conditions. Viscosifying, gelling and film forming properties of these have been exploited for specific significant applications in food and allied industries. Intensive research activities and recent achievements in relevant and important research fields of global interest regarding film forming microbial biopolymers is the subject of this review. Microbial polymers such as pullulan, kefiran, bacterial cellulose (BC), gellan and levan are placed under the category of exopolysaccharides (EPS) and have several other functional properties including film formation, which can be used for various applications in food and allied industries. In addition to EPS, innumerable bacterial genera are found to synthesis carbon energy reserves in their cells known as polyhydroxyalkanoates (PHAs), microbial polyesters, which can be extruded into films with excellent moisture and oxygen barrier properties. Blow moldable biopolymers like PHA along with polylactic acid (PLA) synthesized chemically in vitro using lactic acid (LA), which is produced by LA bacteria through fermentation, are projected as biodegradable polymers of the future for packaging applications. Designing and creating of new property based on requirements through controlled synthesis can lead to improvement in properties of existing polysaccharides and create novel biopolymers of great commercial interest and value for wider applications. Incorporation of antimicrobials such as bacteriocins or silver and copper nanoparticles can enhance the functionality of polymer films especially in food packaging

  8. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell.

    PubMed

    Miceli, Joseph F; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I; Krajmalnik-Brown, Rosa

    2014-10-01

    Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways.

  9. Over-pressurized bioreactors: application to microbial cell cultures.

    PubMed

    Lopes, Marlene; Belo, Isabel; Mota, Manuel

    2014-01-01

    In industrial biotechnology, microbial cultures are exposed to different local pressures inside bioreactors. Depending on the microbial species and strains, the increased pressure may have detrimental or beneficial effects on cellular growth and product formation. In this review, the effects of increased air pressure on various microbial cultures growing in bioreactors under moderate total pressure conditions (maximum, 15 bar) will be discussed. Recent data illustrating the diversity of increased air pressure effects at different levels in microbial cells cultivation will be presented, with particular attention to the effects of oxygen and carbon dioxide partial pressures on cellular growth and product formation, and the concomitant effect of oxygen pressure on antioxidant cellular defense mechanisms.

  10. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell

    PubMed Central

    Miceli, Joseph F.; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I.; Krajmalnik-Brown, Rosa

    2014-01-01

    Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (~11 A/m2) and Coulombic efficiency (~70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ~80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed micro bial cultures containing complementing biochemical pathways. PMID:25048958

  11. Microbial production of surfactants and their commercial potential.

    PubMed Central

    Desai, J D; Banat, I M

    1997-01-01

    Many microorganisms, especially bacteria, produce biosurfactants when grown on water-immiscible substrates. Biosurfactants are more effective, selective, environmentally friendly, and stable than many synthetic surfactants. Most common biosurfactants are glycolipids in which carbohydrates are attached to a long-chain aliphatic acid, while others, like lipopeptides, lipoproteins, and heteropolysaccharides, are more complex. Rapid and reliable methods for screening and selection of biosurfactant-producing microorganisms and evaluation of their activity have been developed. Genes involved in rhamnolipid synthesis (rhlAB) and regulation (rhlI and rhlR) in Pseudomonas aeruginosa are characterized, and expression of rhlAB in heterologous hosts is discussed. Genes for surfactin production (sfp, srfA, and comA) in Bacillus spp. are also characterized. Fermentative production of biosurfactants depends primarily on the microbial strain, source of carbon and nitrogen, pH, temperature, and concentration of oxygen and metal ions. Addition of water-immiscible substrates to media and nitrogen and iron limitations in the media result in an overproduction of some biosurfactants. Other important advances are the use of water-soluble substrates and agroindustrial wastes for production, development of continuous recovery processes, and production through biotransformation. Commercialization of biosurfactants in the cosmetic, food, health care, pulp- and paper-processing, coal, ceramic, and metal industries has been proposed. However, the most promising applications are cleaning of oil-contaminated tankers, oil spill management, transportation of heavy crude oil, enhanced oil recovery, recovery of crude oil from sludge, and bioremediation of sites contaminated with hydrocarbons, heavy metals, and other pollutants. Perspectives for future research and applications are also discussed. PMID:9106364

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

    SciTech Connect

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

    2015-09-01

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

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

    PubMed Central

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

    2015-01-01

    The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. PMID:26092453

  14. Recent advances towards development and commercialization of plant cell culture processes for synthesis of biomolecules

    PubMed Central

    Wilson, Sarah A.; Roberts, Susan C.

    2011-01-01

    (1) Summary Plant cell culture systems were initially explored for use in commercial synthesis of several high value secondary metabolites, allowing for sustainable production that was not limited by the low yields associated with natural harvest or the high cost associated with complex chemical synthesis. Although there have been some commercial successes, most notably paclitaxel production from Taxus sp., process limitations exist with regards to low product yields and inherent production variability. A variety of strategies are being developed to overcome these limitations including elicitation strategies, in situ product removal and metabolic engineering with single genes and transcription factors. Recently, the plant cell culture production platform has been extended to pharmaceutically active heterologous proteins. Plant systems are beneficial because they are able to produce complex proteins that are properly glycosylated, folded and assembled without the risk of contamination by toxins that are associated with mammalian or microbial production systems. Additionally, plant cell culture isolates transgenic material from the environment, allows for more controllable conditions over field grown crops and promotes secretion of proteins to the medium, reducing downstream purification costs. Despite these benefits, the increase in cost of heterologous protein synthesis in plant cell culture as opposed to field grown crops is significant and therefore processes must be optimized with regards to maximizing secretion and enhancing protein stability in the cell culture media. This review discusses recent advancements in plant cell culture processing technology, focusing on progress towards overcoming the problems associated with commercialization of these production systems and highlighting recent commercial successes. PMID:22059985

  15. Effects of inoculation of commercial starter cultures on the quality and histamine accumulation in fermented sausages.

    PubMed

    Wang, Xinhui; Ren, Hongyang; Wang, Wei; Zhang, Yin; Bai, Ting; Li, Junxia; Zhu, Wenyou

    2015-02-01

    To meet the requirements of high-quality safe products, starter cultures are used to produce fermented sausages. The effects of 3 commercial starter cultures, namely SM-194, T-SPX, and SM-181, on histamine accumulation and quality parameters including microbial quality, pH, water activity, and total volatile base nitrogen, as well as the color and texture properties, were evaluated during the fermentation and ripening of fermented sausages. Although initial counts of Escherichia coli, Enterobacteriaceae, and Pseudomonas were similar in the 4 batches, the growth of these microorganisms was significantly inhibited (P < 0.05) in batches SM-194, T-SPX, and SM-181 throughout the fermentation and ripening period. The counts of E. coli, Enterobacteriaceae, and Pseudomonas increased to maximum levels of 3.89, 4.41, and 5.15 log10 colony forming units/g in the control sausages, respectively. At the end of ripening, the levels of histamine were 8.85, 0.32, 7.82, and 3.18 mg/kg for batches C, SM-194, T-SPX, and SM-181, respectively. The results revealed that commercial starter cultures, particularly starter cultures SM-194 and SM-181, made a great contribution to histamine reduction. In addition, batches inoculated with starter cultures showed a stronger acidification and lower level of total volatile base nitrogen than the control sample during production (P < 0.05). In conclusion, it seems that the inoculation of commercial starter cultures, particularly starter cultures SM-194 and SM-181, contributes to improving microbial quality, hygienic quality and food safety of fermented sausages.

  16. Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques.

    PubMed

    Auld, Ryan R; Myre, Maxine; Mykytczuk, Nadia C S; Leduc, Leo G; Merritt, Thomas J S

    2013-05-01

    We characterized the bacterial community from an AMD tailings pond using both classical culturing and modern direct sequencing techniques and compared the two methods. Acid mine drainage (AMD) is produced by the environmental and microbial oxidation of minerals dissolved from mining waste. Surprisingly, we know little about the microbial communities associated with AMD, despite the fundamental ecological roles of these organisms and large-scale economic impact of these waste sites. AMD microbial communities have classically been characterized by laboratory culturing-based techniques and more recently by direct sequencing of marker gene sequences, primarily the 16S rRNA gene. In our comparison of the techniques, we find that their results are complementary, overall indicating very similar community structure with similar dominant species, but with each method identifying some species that were missed by the other. We were able to culture the majority of species that our direct sequencing results indicated were present, primarily species within the Acidithiobacillus and Acidiphilium genera, although estimates of relative species abundance were only obtained from direct sequencing. Interestingly, our culture-based methods recovered four species that had been overlooked from our sequencing results because of the rarity of the marker gene sequences, likely members of the rare biosphere. Further, direct sequencing indicated that a single genus, completely missed in our culture-based study, Legionella, was a dominant member of the microbial community. Our results suggest that while either method does a reasonable job of identifying the dominant members of the AMD microbial community, together the methods combine to give a more complete picture of the true diversity of this environment. PMID:23485423

  17. 7 CFR 504.2 - Fees for deposit and requisition of microbial cultures.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 6 2010-01-01 2010-01-01 false Fees for deposit and requisition of microbial cultures... cultures. (a) Depositors of microbial cultures must pay a one-time $500 user fee for each culture deposited on or after November 1, 1983. (b) For cultures deposited on or after November 1, 1983,...

  18. 7 CFR 504.2 - Fees for deposit and requisition of microbial cultures.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 6 2013-01-01 2013-01-01 false Fees for deposit and requisition of microbial cultures... cultures. (a) Depositors of microbial cultures must pay a one-time $500 user fee for each culture deposited on or after November 1, 1983. (b) For cultures deposited on or after November 1, 1983,...

  19. 7 CFR 504.2 - Fees for deposit and requisition of microbial cultures.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 6 2011-01-01 2011-01-01 false Fees for deposit and requisition of microbial cultures... cultures. (a) Depositors of microbial cultures must pay a one-time $500 user fee for each culture deposited on or after November 1, 1983. (b) For cultures deposited on or after November 1, 1983,...

  20. 7 CFR 504.2 - Fees for deposit and requisition of microbial cultures.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 6 2012-01-01 2012-01-01 false Fees for deposit and requisition of microbial cultures... cultures. (a) Depositors of microbial cultures must pay a one-time $500 user fee for each culture deposited on or after November 1, 1983. (b) For cultures deposited on or after November 1, 1983,...

  1. 7 CFR 504.2 - Fees for deposit and requisition of microbial cultures.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 6 2014-01-01 2014-01-01 false Fees for deposit and requisition of microbial cultures... cultures. (a) Depositors of microbial cultures must pay a one-time $500 user fee for each culture deposited on or after November 1, 1983. (b) For cultures deposited on or after November 1, 1983,...

  2. Microbial population dynamics during fed-batch operation of commercially available garbage composters.

    PubMed

    Narihiro, T; Abe, T; Yamanaka, Y; Hiraishi, A

    2004-09-01

    Microbial populations in terms of quantity, quality, and activity were monitored during 2 months of start-up operation of commercially available composters for fed-batch treatment of household biowaste. All the reactors, operated at a waste-loading rate of 0.7 kg day(-1) (wet wt), showed a mass reduction efficiency of 88-93%. The core temperature in the reactors fluctuated between 31 degrees C and 58 degrees C due to self-heating. The pH declined during the early stage of operation and steadied at pH 7.4-9.3 during the fully acclimated stage. The moisture content was 48-63% early in the process and 30-40% at the steady state. Both direct total counts and plate counts of bacteria increased via two phases (designated phases I, II) and reached an order of magnitude of 10(11) cells g(-1) (dry wt) at the steady state. Microbial community changes during the start-up period were studied by culture-independent quinone profiling and denatured gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA. In all the reactors, ubiquinones predominated during phase I, whereas partially saturated menaquinones became predominant during phase II. This suggested that there was a drastic population shift from ubiquinone-containing Proteobacteria to Actinobacteria during the start-up period. The DGGE analysis of the bacterial community in one of the reactors also demonstrated a drastic population shift during phase I and the predominance of members of the phyla Proteobacteria and Bacteroidetes during the overall period. But this molecular analysis failed to detect actinobacterial clones from the reactor at any stage.

  3. Microbial dynamics of commercial makgeolli depending on the storage temperature.

    PubMed

    Kim, Hye-Ryun; Lee, Ae Ran; Kim, Jae-Ho; Ahn, Byung-Hak

    2012-08-01

    Market fresh makgeolli was stored at different temperatures of 4°C and 25°C to assess the change of the microbial diversity according to the storage temperature and period. Yeast counts increased until day 3 of storage and decreased thereafter. General and lactic acid bacterial counts continuously increased during storage. The data indicated that the control of growth of microorganisms, particularly general bacteria and lactic acid bacteria (LAB), is essential. Total acid levels started to decrease in the makgeolli stored at 4°C, and increased from day 6 of storage in the makgeolli stored at 25°C. The increase of total acid in the non-refrigerated condition greatly affected the quality of makgeolli. In both the fresh makgeolli samples stored at 4°C and 25°C, yeast (Saccharomyces cerevisiae) and molds (Aspergillus tubingensis, Candida glaebosa, and Aspergillus niger) were noted. Denaturing gradient gel electrophoresis (DGGE) band patterns were almost constant regardless of the storage period. As for bacteria, Lactobacillus crustorum, L. brevis, and Microlaena stipoides were found in the makgeolli stored at 4°C, and L. crustorum, Lactobacillus sp., L. plantarum, L. brevis, L. rhamnosus, and L. similis were found in the makgeolli stored at 25°C. In particular, in the makgeolli stored at 25°C, L. crustorum and L. plantarum presented dark bands and were identified as the primary microorganisms that affected spoilage of fresh makgeolli. PMID:22713986

  4. Microbial lipid production by oleaginous Rhodococci cultured in lignocellulosic autohydrolysates.

    PubMed

    Wei, Zhen; Zeng, Guangming; Huang, Fang; Kosa, Matyas; Sun, Qining; Meng, Xianzhi; Huang, Danlian; Ragauskas, Arthur J

    2015-09-01

    Metabolic synthesis of single cell oils (SCOs) for biodiesel application by heterotrophic oleaginous microorganisms is being hampered by the high cost of culture media. This study investigated the possibility of using loblolly pine and sweetgum autohydrolysates as economic feedstocks for microbial lipid production by oleaginous Rhodococcus opacus (R. opacus) PD630 and DSM 1069. Results revealed that when the substrates were detoxified by the removal of inhibitors (such as HMF-hydroxymethyl-furfural), the two strains exhibited viable growth patterns after a short adaptation/lag phase. R. opacus PD630 accumulated as much as 28.6 % of its cell dry weight (CDW) in lipids while growing on detoxified sweetgum autohydrolysate (DSAH) that translates to 0.25 g/l lipid yield. The accumulation of SCOs reached the level of oleagenicity in DSM 1069 cells (28.3 % of CDW) as well, while being cultured on detoxified pine autohydrolysate (DPAH), with the maximum lipid yield of 0.31 g/l. The composition of the obtained microbial oils varied depending on the substrates provided. These results indicate that lignocellulosic autohydrolysates can be used as low-cost fermentation substrates for microbial lipid production by wild-type R. opacus species. Consequently, the variety of applications for aqueous liquors from lignocellulosic pretreatment has been expanded, allowing for the further optimization of the integrated biorefinery.

  5. Bacterial Cellulose as a Substrate for Microbial Cell Culture

    PubMed Central

    Yin, Na; Santos, Thiago M. A.; Auer, George K.; Crooks, John A.; Oliver, Piercen M.

    2014-01-01

    Bacterial cellulose (BC) has a range of structural and physicochemical properties that make it a particularly useful material for the culture of bacteria. We studied the growth of 14 genera of bacteria on BC substrates produced by Acetobacter xylinum and compared the results to growth on the commercially available biopolymers agar, gellan, and xanthan. We demonstrate that BC produces rates of bacterial cell growth that typically exceed those on the commercial biopolymers and yields cultures with higher titers of cells at stationary phase. The morphology of the cells did not change during growth on BC. The rates of nutrient diffusion in BC being higher than those in other biopolymers is likely a primary factor that leads to higher growth rates. Collectively, our results suggest that the use of BC may open new avenues in microbiology by facilitating bacterial cell culture and isolation. PMID:24441155

  6. Petroleum storage tank cleaning using commercial microbial culture products

    SciTech Connect

    Schneider, D.R.; Entzeroth, L.C.; Timmis, A.; Whiteside, A.; Hoskins, B.C.

    1995-12-31

    The removal of paraffinic bottom accumulations from refinery storage tanks represents an increasingly costly area of petroleum storage management. Microorganisms can be used to reduce paraffinic bottoms by increasing the solubility of bottom material and by increasing the wax-carrying capacity of carrier oil used in the cleaning process. The economic savings of such treatments are considerable. The process is also intrinsically safer than alternative methods, as it reduces and even eliminates the need for personnel to enter the tank during the cleaning process. Both laboratory and field sample analyses can be used to document changes in tank material during the treatment process. These changes include increases in volatile content and changes in wax distribution. Several case histories illustrating these physical and chemical changes are presented along with the economics of treatment.

  7. Monitoring microbial populations on wide-body commercial passenger aircraft.

    PubMed

    McKernan, Lauralynn Taylor; Wallingford, Kenneth M; Hein, Misty J; Burge, Harriet; Rogers, Christine A; Herrick, Robert

    2008-03-01

    Although exposure to bacteria has been assessed in cabin air previously, minimal numbers of samples have been collected in-flight. The purpose of this research was to comprehensively characterize bacterial concentrations in the aircraft cabin. Twelve randomly selected flights were sampled on Boeing-767 aircraft, each with a flight duration between 4.5 and 6.5 h. N-6 impactors were used to collect sequential, triplicate air samples in the front and rear of coach class during six sampling intervals throughout each flight: boarding, mid-climb, early cruise, mid-cruise, late cruise and deplaning. Comparison air samples were also collected inside and outside the airport terminals at the origin and destination cities. The MIXED procedure in SAS was used to model the mean and the covariance matrix of the natural log-transformed bacterial concentrations. A total of 513 airborne culturable bacterial samples were collected. During flight (mid-climb and cruise intervals), a model-adjusted geometric mean (GM) of 136 total colony-forming units per cubic meter of air sampled (CFU x m(-3)) and geometric standard deviation of 2.1 were observed. Bacterial concentrations were highest during the boarding (GM 290 CFU x m(-3)) and deplaning (GM 549 CFU x m(-3)) processes. Total bacterial concentrations observed during flight were significantly lower than GMs for boarding and deplaning (P values <0.0001-0.021) in the modeled results. Our findings highlight the fact that aerobiological concentrations can be dynamic and underscore the importance of appropriate sample size and design. The genera analysis indicates that passenger activity and high occupant density contribute to airborne bacterial generation. Overall, our research demonstrates that the bacteria recovered on observed flights were either common skin-surface organisms (primarily gram-positive cocci) or organisms common in dust and outdoor air.

  8. Culturability as an indicator of succession in microbial communities

    NASA Technical Reports Server (NTRS)

    Garland, J. L.; Cook, K. L.; Adams, J. L.; Kerkhof, L.

    2001-01-01

    Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to

  9. [Microbial maps and blood cultures in acute leukemia].

    PubMed

    Rossi, M; Roberti, M G; Paolino, F

    1976-12-29

    Microbial maps were performed taking swabs from nose, pharinx, external auditory meatus, groin, vagina, sputum and urine cultures in 69 cases of acute leukaemia, in order: to assess the germs' incidence in an "open ward" department; to eliminate the most dangerous pathogens with local treatment or with a selective therapy without broad-specturm antibiotics; to check, in the 43 cases followed from onset, the changes occurring during the admission and the disease progression; to collect data for comparison with a "sterile" ward. The local decontamination had only a temporary effect. During the course of the disease new, particularly dangerous, pathogens were cultured. Blood cultures were positive in 15% of the patients with fever at the onset of the disease, and in 36.9% of the patients with fever during the disease progression. These values were virtually the same as those observed in the acute stage of C.M.L. (35.7%). In akute leukaemia E. coli (35%) was the most common, followed by P. aeruginosa (20%), Klebsiella (15%), S. alpha haemolyticus (10%) and others. There was little or no relationship between the germs in the maps and those in the blood cultures, though it must be remembered that no stool cultures were examined. PMID:1035410

  10. Microbial community dynamics in thermophilic undefined milk starter cultures.

    PubMed

    Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

    2016-01-18

    Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

  11. Microbial community dynamics in thermophilic undefined milk starter cultures.

    PubMed

    Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

    2016-01-18

    Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

  12. Microbial Diversity of a Camembert-Type Cheese Using Freeze-Dried Tibetan Kefir Coculture as Starter Culture by Culture-Dependent and Culture-Independent Methods

    PubMed Central

    Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

    2014-01-01

    The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese. PMID:25360757

  13. Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures.

    PubMed

    Beier, Sara; Rivers, Adam R; Moran, Mary Ann; Obernosterer, Ingrid

    2015-05-01

    Phenotypic plasticity (PP) is the development of alternate phenotypes of a given taxon as an adaptation to environmental conditions. Methodological limitations have restricted the quantification of PP to the measurement of a few traits in single organisms. We used metatranscriptomic libraries to overcome these challenges and estimate PP using the expressed genes of multiple heterotrophic organisms as a proxy for traits in a microbial community. The metatranscriptomes captured the expression response of natural marine bacterial communities grown on differing carbon resource regimes in continuous cultures. We found that taxa with different magnitudes of PP coexisted in the same cultures, and that members of the order Rhodobacterales had the highest levels of PP. In agreement with previous studies, our results suggest that continuous culturing may have specifically selected for taxa featuring a rather high range of PP. On average, PP and abundance changes within a taxon contributed equally to the organism's change in functional gene abundance, implying that both PP and abundance mediated observed differences in community function. However, not all functional changes due to PP were directly reflected in the bulk community functional response: gene expression changes in individual taxa due to PP were partly masked by counterbalanced expression of the same gene in other taxa. This observation demonstrates that PP had a stabilizing effect on a community's functional response to environmental change.

  14. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy

    PubMed Central

    Mlynáriková, Katarína; Samek, Ota; Bernatová, Silvie; Růžička, Filip; Ježek, Jan; Hároniková, Andrea; Šiler, Martin; Zemánek, Pavel; Holá, Veronika

    2015-01-01

    Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar. PMID:26610516

  15. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy.

    PubMed

    Mlynáriková, Katarína; Samek, Ota; Bernatová, Silvie; Růžička, Filip; Ježek, Jan; Hároniková, Andrea; Šiler, Martin; Zemánek, Pavel; Holá, Veronika

    2015-11-24

    Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar.

  16. [Microbial contamination of the air in the commercial production of poultry meat].

    PubMed

    Baĭkov, B D; Petkov, G

    1987-01-01

    Microbiologic studies were carried out on industrial premises for the raising of broiler birds on deep litter over a flooring area of 2000 m2 at mechanical ventilation of negative pressure. The microbial count was established through culturing in meat-and-peptone agar regarding the presence of coli bacteria, microscopic fungi, hemolytic cocci and Salmonellae in the air. Studies were also performed to establish the contamination of the atmospheric air at a distance of 10 m surrounding the premises, of the litter as well as of the feed and the soil in immediate proximity to the buildings. It was found that as a result of raising the 'biologic loading' of the ecotope by 60 per cent the microbial contamination of the air in the industrial buildings rose. The basic sources of contamination were the deep litter, the atmospheric air introduced by the ventilation system, the soil, and the feed.

  17. Vers une culture des affaires? Mentalites, comportements, representations dans la classe de francais commercial (Toward a Business Culture? Attitudes, Behaviors, and Representations in the Commercial French Classroom).

    ERIC Educational Resources Information Center

    Bousquet, Gilles

    1993-01-01

    An exploration of the nature and range of international expertise necessary for students and users of commercial French attempts to note the points where knowledge of law, politics, culture, and business practice takes over from mere accumulation of facts or linguistic competence to facilitate genuine, productive, and culturally appropriate…

  18. Turning Russian specialized microbial culture collections into resource centers for biotechnology.

    PubMed

    Ivshina, Irena B; Kuyukina, Maria S

    2013-11-01

    Specialized nonmedical microbial culture collections contain unique bioresources that could be useful for biotechnology companies. Cooperation between collections and companies has suffered from shortcomings in infrastructure and legislation, hindering access to holdings. These challenges may be overcome by the transformation of collections into national bioresource centers and integration into international microbial resource networks.

  19. Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches.

    PubMed

    Mounier, J; Monnet, C; Jacques, N; Antoinette, A; Irlinger, F

    2009-07-31

    The microbial diversity of the surface of a commercial red-smear cheese, Livarot cheese, sold on the retail market was studied using culture-dependent and independent approaches. Forty yeasts and 40 bacteria from the cheese surface were collected, dereplicated using single-strand conformation polymorphism (SSCP) analysis and identified using rRNA gene sequencing for the culture-dependent approach. The culture-independent approach involved cloning and sequencing of the 16S rRNA gene and SSCP analysis from total DNA extracted from the cheese. The most dominant bacteria were Microbacterium gubbeenense, Leucobacter komagatae and Gram-negative bacteria from the Gamma-Proteobacteria class. Fluorescence in situ hybridization (FISH) analysis was also used to study the cheese microbial diversity with class-level and specific rRNA-targeted probes for bacteria and yeasts, respectively. FISH analysis confirmed that Gamma-Proteobacteria were important microorganisms in this cheese. Four specific FISH probes targeting the dominant yeasts present in the cheese, Candida catenulata, Candida intermedia, Geotrichum spp. and Yarrowia lipolytica, were also designed and evaluated. These probes allowed the detection of these yeasts directly in cheese. The use of the rRNA gene-based approach combined with FISH analysis was useful to investigate the diversity of a surface microbial consortium from cheese.

  20. Yeasts and hygienic-sanitary microbial indicators in water buffalo mozzarella produced and commercialized in Minas Gerais, Brazil.

    PubMed

    Facchin, Susanne; Barbosa, Anne C; Carmo, Luiz S; Silva, Maria Crisolita C; Oliveira, Afonso L; Morais, Paula B; Rosa, Carlos A

    2013-01-01

    The aim of this work was to study the yeast populations and the main hygienic-sanitary microbial indicators in water buffalo mozzarella produced and commercialized in Minas Gerais, Brazil. Forty-two water buffalo mozzarella samples were purchased from retail outlets in Belo Horizonte. In addition, five samples of consecutive starter cultures, curd before acidification, acidified curd and mozzarella were collected at an industry in the city of Oliveira. Only three of the five water samples analyzed were suitable for consumption according to Brazilian sanitary standards. Four milk samples were highly contaminated with fecal coliforms, and did not meet the minimal hygienic-sanitary standards according to Brazilian regulations. Only one sample of buffalo muzzarela purchased from retail outlets exceeded the limit for coagulase-positive Staphylococcus. Eleven samples showed counts of thermotolerant coliforms higher than 5 × 10(3) CFU.g(-1), but still lower than the maximum permitted by the Brazilian laws. Salmonella spp. and Listeria monocytogenes were not isolated. Debaryomyces hansenii, Candida lusitaniae and C. parapsilosis were the prevalent yeast species isolated from cheese. Among samples from the production stages, the acidified curd presented the highest numbers of yeasts, with C. catenulata being the most frequent species isolated. Some opportunistic yeast species such as C. guilliermondii, C. tropicalis, C. parapsilosis, C. lusitaniae, C. catenulata, C. rugosa and C. krusei occurred in the mozzarella cheese samples analyzed. The mozzarella cheese presented a low microbial load as compared to other cheese already studied, and the yeast biota included species typical of cheese and also opportunistic pathogens.

  1. Yeasts and hygienic-sanitary microbial indicators in water buffalo mozzarella produced and commercialized in Minas Gerais, Brazil

    PubMed Central

    Facchin, Susanne; Barbosa, Anne C.; Carmo, Luiz S.; Silva, Maria Crisolita C.; Oliveira, Afonso L.; Morais, Paula B.; Rosa, Carlos A.

    2013-01-01

    The aim of this work was to study the yeast populations and the main hygienic-sanitary microbial indicators in water buffalo mozzarella produced and commercialized in Minas Gerais, Brazil. Forty-two water buffalo mozzarella samples were purchased from retail outlets in Belo Horizonte. In addition, five samples of consecutive starter cultures, curd before acidification, acidified curd and mozzarella were collected at an industry in the city of Oliveira. Only three of the five water samples analyzed were suitable for consumption according to Brazilian sanitary standards. Four milk samples were highly contaminated with fecal coliforms, and did not meet the minimal hygienic-sanitary standards according to Brazilian regulations. Only one sample of buffalo muzzarela purchased from retail outlets exceeded the limit for coagulase-positive Staphylococcus. Eleven samples showed counts of thermotolerant coliforms higher than 5 × 103 CFU.g−1, but still lower than the maximum permitted by the Brazilian laws. Salmonella spp. and Listeria monocytogenes were not isolated. Debaryomyces hansenii, Candida lusitaniae and C. parapsilosis were the prevalent yeast species isolated from cheese. Among samples from the production stages, the acidified curd presented the highest numbers of yeasts, with C. catenulata being the most frequent species isolated. Some opportunistic yeast species such as C. guilliermondii, C. tropicalis, C. parapsilosis, C. lusitaniae, C. catenulata, C. rugosa and C. krusei occurred in the mozzarella cheese samples analyzed. The mozzarella cheese presented a low microbial load as compared to other cheese already studied, and the yeast biota included species typical of cheese and also opportunistic pathogens. PMID:24516436

  2. DNA-based, culture-independent strategies for evaluating microbial communities in food-associated ecosystems.

    PubMed

    Giraffa, G; Neviani, E

    2001-07-20

    Culture-independent molecular techniques are now available to study microbial ecosystems. They are opening interesting perspectives to problems related to composition and population dynamics of microbial communities in various environmental niches (e.g., soil, water) and foods. In fermented food products, estimates of true microbial diversity is often difficult chiefly on account of the inability to cultivate most of the viable bacteria. The increasing knowledge of gene sequences and the concomitant development of new culture-independent molecular techniques are providing new and effective tools to compare the diversity of microbial communities and to monitor population dynamics in minimally disturbed samples. In this review, recent advances in these techniques are reported. Possible applications to food-associated microbial ecosystems are emphasised. PMID:11482566

  3. Reconstituted yogurt from yogurt cultured milk powder mix has better overall characteristics than reconstituted yogurt from commercial yogurt powder.

    PubMed

    Song, Lijie; Aryana, Kayanush J

    2014-10-01

    For manufacture of commercial yogurt powder, yogurt has to go through a drying process, which substantially lowers the yogurt culture counts, so the potential health benefits of the yogurt culture bacteria are reduced. Also, upon reconstitution, commercial yogurt powder does not taste like yogurt and has an off-flavor. The objective was to study the microbial, physicochemical, and sensory characteristics of reconstituted yogurt from yogurt cultured milk powder (YCMP) mix and reconstituted yogurt from commercial yogurt powder (CYP). The CYP reconstituted yogurt was the control and YCMP mix reconstituted yogurt was the treatment. Microbial and physicochemical characteristics of the CYP reconstituted yogurt and YCMP mix reconstituted yogurt were analyzed daily for the first week and then weekly for a period of 8 wk. Sensory consumer testing of CYP reconstituted yogurt and YCMP mix reconstituted yogurt was conducted with 100 consumers. At 56 d, YCMP mix reconstituted yogurt had 5 log cfu/mL higher counts of Streptococcus thermophilus than the control (CYP reconstituted yogurt). Also, Lactobacillus bulgaricus counts of YCMP mix reconstituted yogurt were 6.55 log cfu/mL at 28 d and were 5.35 log cfu/mL at 56 d, whereas the CYP reconstituted yogurt from 28 d onwards had a count of <10 cfu/mL. The YCMP mix reconstituted yogurt also had significantly higher apparent viscosity and sensory scores for appearance, color, aroma, taste, thickness, overall liking, consumer acceptability, and purchase intent than CYP reconstituted yogurt. Overall, YCMP mix reconstituted yogurt had more desirable characteristics than CYP reconstituted yogurt.

  4. Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods.

    PubMed

    Yan, Yin-zhuo; Qian, Yu-lin; Ji, Feng-di; Chen, Jing-yu; Han, Bei-zhong

    2013-05-01

    Koji-making is a key process for production of high quality soy sauce. The microbial composition during koji-making was investigated by culture-dependent and culture-independent methods to determine predominant bacterial and fungal populations. The culture-dependent methods used were direct culture and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone libraries. There were differences between the results obtained by different methods. However, sufficient overlap existed between the different methods to identify potentially significant microbial groups. 16 and 20 different bacterial species were identified using culture-dependent and culture-independent methods, respectively. 7 species could be identified by both methods. The most predominant bacterial genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culture-dependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition during soy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product.

  5. Production of microbial medium from defatted brebra (Milletia ferruginea) seed flour to substitute commercial peptone agar

    PubMed Central

    Andualem, Berhanu; Gessesse, Amare

    2013-01-01

    Objective To investigate and optimize microbial media that substitute peptone agar using brebra seed defatted flour. Methods 'Defatted process, inoculums preparation, evaluation of bacterial growth, preparation of cooked and hydrolyzed media and growth turbidity of tested bacteria were determined. Results Two percent defatted flour was found to be suitable concentration for the growth of pathogenic bacteria: Escherichia coli (ATCC 25922) (E. coli), Pseudomonas aeruginosa (ATCC 27853), Salmonella (NCTC 8385) and Shigella flexneri (ATCC 12022) (S. flexneri), while 3% defatted flour was suitable for Staphylococcus aureus (ATCC 25923) (S. aureus). E. coli (93±1) and S. flexneri (524±1) colony count were significantly (P≤0.05) greater in defatted flour without supplement than in supplemented medium. E. coli [(3.72×109±2) CFU/mL], S. aureus [(7.4×109±2) CFU/mL], S. flexneri [(4.03×109±2) CFU/mL] and Salmonella [(2.37×109±1) CFU/mL] in non-hydrolyzed sample were statistically (P≤0.05) greater than hydrolyzed one and commercial peptone agar. Colony count of Salmonella [(4.55×109±3) CFU/mL], S. flexneri [(5.40×109±3) CFU/mL] and Lyesria moncytogenes (ATCC 19116) [(5.4×109±3) CFU/mL] on raw defatted flour agar was significantly (P≤0.05) greater than cooked defatted flour and commercial peptone agar. Biomass of E. coli, S. aureus, Salmonella and Enterococcus faecalis in non-hydrolyzed defatted flour is highly increased over hydrolyzed defatted flour and commercial peptone broth. Conclusions The defatted flour agar was found to be better microbial media or comparable with peptone agar. The substances in it can serve as sources of carbon, nitrogen, vitamins and minerals that are essential to support the growth of microorganisms without any supplements. Currently, all supplements of peptone agar are very expensive in the market. PMID:24075344

  6. Short communication: Microbial quality of raw milk following commercial long-distance hauling.

    PubMed

    Darchuk, Emily M; Meunier-Goddik, Lisbeth; Waite-Cusic, Joy

    2015-12-01

    Hauling is a critical part of the commercial milk supply chain, yet very few studies have aimed to understand its effect on raw milk quality. This study focused on the effect of extended-duration tanker use during hauling on raw milk quality at a commercial facility. Standard tanker use [cleaned-in-place (CIP) once per 24h] served as a control and an incremental between-load water rinse with sanitizer treatment (RS) was evaluated to mitigate any effect from extended duration hauling. During this study, 1 commercial truck with 2 trailers was monitored for 10d. The truck collected milk at a large dairy farm, transported the milk to a manufacturing facility, and then returned to the same farm for a second load. Each round-trip journey took between 10 and 12h, allowing for 2 loads per 24-h use period. Following the second delivery, the truck was cleaned by CIP treatment starting a new treatment day. Producer samples were collected from the raw milk bulk tank on the farm before loading milk into the tanker. The same milk was sampled directly out of the tanker truck before unloading at the manufacturer. Effect on individual bacteria count, thermophilic spore count, and preliminary incubation count was quantified through common industry tests. Surface sponge swabs were also used to monitor tanker sanitation and the efficacy of cleaning treatments. Results did not identify a negative effect on raw milk quality due to extended duration hauling. Whereas the addition of RS did not provide any measurable quality benefits for the microbial milk quality, swab results demonstrated that the RS treatment was able to reduce surface bacteria in the tanker, although not to the same level as the full CIP treatment. Based on this study, current CIP practices for long distance milk hauling appear to be effective in mitigating any measurable effect on raw milk quality. PMID:26506549

  7. Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing.

    PubMed

    Patro, Jennifer N; Ramachandran, Padmini; Barnaba, Tammy; Mammel, Mark K; Lewis, Jada L; Elkins, Christopher A

    2016-01-01

    Millions of people consume dietary supplements either following a doctor's recommendation or at their own discretion to improve their overall health and well-being. This is a rapidly growing trend, with an associated and expanding manufacturing industry to meet the demand for new health-related products. In this study, we examined the contents and microbial viability of several popular probiotic products on the United States market. Culture-independent methods are proving ideal for fast and efficient analysis of foodborne pathogens and their associated microbial communities but may also be relevant for analyzing probiotics containing mixed microbial constituents. These products were subjected to next-generation whole-genome sequencing and analyzed by a custom in-house-developed k-mer counting method to validate manufacturer label information. In addition, the batch variability of respective products was examined to determine if any changes in their formulations and/or the manufacturing process occurred. Overall, the products we tested adhered to the ingredient claims and lot-to-lot differences were minimal. However, there were a few discrepancies in the naming of closely related Lactobacillus and Bifidobacterium species, whereas one product contained an apparent Enterococcus contaminant in two of its three lots. With the microbial contents of the products identified, we used traditional PCR and colony counting methods to comparatively assess our results and verify the viability of the microbes in these products with regard to the labeling claims. Of all the supplements examined, only one was found to be inaccurate in viability. Our use of next-generation sequencing as an analytical tool clearly demonstrated its utility for quickly analyzing commercially available products containing multiple microbes to ensure consumer safety. IMPORTANCE The rapidly growing supplement industry operates without a formal premarket approval process. Consumers rely on product labels to

  8. Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing.

    PubMed

    Patro, Jennifer N; Ramachandran, Padmini; Barnaba, Tammy; Mammel, Mark K; Lewis, Jada L; Elkins, Christopher A

    2016-01-01

    Millions of people consume dietary supplements either following a doctor's recommendation or at their own discretion to improve their overall health and well-being. This is a rapidly growing trend, with an associated and expanding manufacturing industry to meet the demand for new health-related products. In this study, we examined the contents and microbial viability of several popular probiotic products on the United States market. Culture-independent methods are proving ideal for fast and efficient analysis of foodborne pathogens and their associated microbial communities but may also be relevant for analyzing probiotics containing mixed microbial constituents. These products were subjected to next-generation whole-genome sequencing and analyzed by a custom in-house-developed k-mer counting method to validate manufacturer label information. In addition, the batch variability of respective products was examined to determine if any changes in their formulations and/or the manufacturing process occurred. Overall, the products we tested adhered to the ingredient claims and lot-to-lot differences were minimal. However, there were a few discrepancies in the naming of closely related Lactobacillus and Bifidobacterium species, whereas one product contained an apparent Enterococcus contaminant in two of its three lots. With the microbial contents of the products identified, we used traditional PCR and colony counting methods to comparatively assess our results and verify the viability of the microbes in these products with regard to the labeling claims. Of all the supplements examined, only one was found to be inaccurate in viability. Our use of next-generation sequencing as an analytical tool clearly demonstrated its utility for quickly analyzing commercially available products containing multiple microbes to ensure consumer safety. IMPORTANCE The rapidly growing supplement industry operates without a formal premarket approval process. Consumers rely on product labels to

  9. Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing

    PubMed Central

    Patro, Jennifer N.; Ramachandran, Padmini; Barnaba, Tammy; Mammel, Mark K.; Lewis, Jada L.

    2016-01-01

    ABSTRACT Millions of people consume dietary supplements either following a doctor’s recommendation or at their own discretion to improve their overall health and well-being. This is a rapidly growing trend, with an associated and expanding manufacturing industry to meet the demand for new health-related products. In this study, we examined the contents and microbial viability of several popular probiotic products on the United States market. Culture-independent methods are proving ideal for fast and efficient analysis of foodborne pathogens and their associated microbial communities but may also be relevant for analyzing probiotics containing mixed microbial constituents. These products were subjected to next-generation whole-genome sequencing and analyzed by a custom in-house-developed k-mer counting method to validate manufacturer label information. In addition, the batch variability of respective products was examined to determine if any changes in their formulations and/or the manufacturing process occurred. Overall, the products we tested adhered to the ingredient claims and lot-to-lot differences were minimal. However, there were a few discrepancies in the naming of closely related Lactobacillus and Bifidobacterium species, whereas one product contained an apparent Enterococcus contaminant in two of its three lots. With the microbial contents of the products identified, we used traditional PCR and colony counting methods to comparatively assess our results and verify the viability of the microbes in these products with regard to the labeling claims. Of all the supplements examined, only one was found to be inaccurate in viability. Our use of next-generation sequencing as an analytical tool clearly demonstrated its utility for quickly analyzing commercially available products containing multiple microbes to ensure consumer safety. IMPORTANCE The rapidly growing supplement industry operates without a formal premarket approval process. Consumers rely on

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

    PubMed

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

    2012-09-01

    Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840. PMID:22984871

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

    PubMed

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

    2012-09-01

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

  12. Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures.

    PubMed

    Vázquez-Nion, D; Rodríguez-Castro, J; López-Rodríguez, M C; Fernández-Silva, I; Prieto, B

    2016-07-01

    Microbial communities of natural subaerial biofilms developed on granitic historic buildings of a World Heritage Site (Santiago de Compostela, NW Spain) were characterized and cultured in liquid BG11 medium. Environmental barcoding through next-generation sequencing (Pacific Biosciences) revealed that the biofilms were mainly composed of species of Chlorophyta (green algae) and Ascomycota (fungi) commonly associated with rock substrata. Richness and diversity were higher for the fungal than for the algal assemblages and fungi showed higher heterogeneity among samples. Cultures derived from natural biofilms showed the establishment of stable microbial communities mainly composed of Chlorophyta and Cyanobacteria. Although most taxa found in these cultures were not common in the original biofilms, they are likely common pioneer colonizers of building stone surfaces, including granite. Stable phototrophic multi-species cultures of known microbial diversity were thus obtained and their reliability to emulate natural colonization on granite should be confirmed in further experiments. PMID:27192622

  13. Subaerial biofilms on granitic historic buildings: microbial diversity and development of phototrophic multi-species cultures.

    PubMed

    Vázquez-Nion, D; Rodríguez-Castro, J; López-Rodríguez, M C; Fernández-Silva, I; Prieto, B

    2016-07-01

    Microbial communities of natural subaerial biofilms developed on granitic historic buildings of a World Heritage Site (Santiago de Compostela, NW Spain) were characterized and cultured in liquid BG11 medium. Environmental barcoding through next-generation sequencing (Pacific Biosciences) revealed that the biofilms were mainly composed of species of Chlorophyta (green algae) and Ascomycota (fungi) commonly associated with rock substrata. Richness and diversity were higher for the fungal than for the algal assemblages and fungi showed higher heterogeneity among samples. Cultures derived from natural biofilms showed the establishment of stable microbial communities mainly composed of Chlorophyta and Cyanobacteria. Although most taxa found in these cultures were not common in the original biofilms, they are likely common pioneer colonizers of building stone surfaces, including granite. Stable phototrophic multi-species cultures of known microbial diversity were thus obtained and their reliability to emulate natural colonization on granite should be confirmed in further experiments.

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

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

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

  15. Application of multiple antimicrobial interventions for microbial decontamination of commercial beef trim.

    PubMed

    Kang, D H; Koohmaraie, M; Siragusa, G R

    2001-02-01

    Commercially produced, irregularly sized (range, 100 to 400 cm2), uninoculated beef trim was treated by a previously optimized multihurdle antimicrobial process under spray system or hot air gun with set-up speed (1 cm/s): W (water wash at 65 psi for five passes) + HW (82 degrees C water at 30 psi for three passes) + HA (510 degrees C air for five passes) + L (2% [vol/vol] room temperature lactic acid wash at 30 psi for three passes). After treatment, the trim was finely ground, vacuum packaged, and stored at 4 degrees C for up to 20 days. At regular intervals (0, 5, 10, 15, and 20 days of storage at 4 degrees C), the ground beef was analyzed to measure mesophilic aerobic bacteria (APC), coliforms, psychrotrophic bacteria (PCT), and presumptive lactic acid bacteria (PLAB) and compared with the untreated control. The numbers of APC, coliforms, PCT, and PLAB were reduced to nearly nondetectable levels immediately after treatment, with significant differences compared with the control (P < 0.05), then started to increase after 5 to 10 days of storage at 4 degrees C. After 20 days, microbial populations of treated ground beef were significantly lower than those of nontreated ground beef for the numbers of APC, coliforms, PCT, and PLAB (P < 0.05), with differences of 1.2, 2.4, 1.6, and 1.6 log CFU/g, respectively. Based on microbial reduction and quality aspects, the multihurdle antimicrobial process was identified as an effective intervention to reduce coliforms on beef trim. PMID:11271762

  16. Xanthan gum: an economical partial substitute for agar in microbial culture media.

    PubMed

    Babbar, Shashi B; Jain, Ruchi

    2006-04-01

    Xanthan gum, microbial desiccation-resistant polysaccharide prepared commercially by aerobic submerged fermentation from Xanthomonas campestris, has been successfully used alone and in combination with agar for microbial culture media. As illustrative examples, eight bacteria and eight fungi were grown on media solidified with either agar (A, 1.5%), xanthan gum (X, 1%), or combinations of both (0.9% X + 0.1% A, 0.8% X + 0.2% A, 0.7% X + 0.3% A, 0.6% X + 0.4% A). All fungi and bacteria exhibited normal growth and differentiation in all these treatments. Rather, growth of most of the fungi was better on xanthan (alone) and xanthan + agar media than agar medium. As the media gelled with xanthan gum alone flow, it was not possible to incubate Petri plates in inverted position. Moreover, because of the softness, streaking of bacteria was difficult on such media. However, these problems could be overcome by partially replacing xanthan gum with 0.3% agar. Bacterial enumeration studies carried out for Serratia sp. and Pseudomonas sp. by serial dilution and pour-plate method on agar (1.5%), 0.7%/0.6% X + 0.3%/0.4% A yielded similar counts. Selective media, succinate medium for Pseudomonas sp., and MacConkey broth medium for Escherichia coli gelled with 0.7%/0.6% X + 0.3%/0.4% A did not support growth of other bacteria when inoculated along with the above-mentioned bacteria. Likewise, differential medium, CRMA (Congo red mannitol agar) gelled with xanthan-agar combination could differentiate between Agrobacterium tumefaciens and Rhizobium sp.

  17. Commercial ripening starter microorganisms inoculated into cheese milk do not successfully establish themselves in the resident microbial ripening consortia of a South german red smear cheese.

    PubMed

    Goerges, Stefanie; Mounier, Jérôme; Rea, Mary C; Gelsomino, Roberto; Heise, Valeska; Beduhn, Rüdiger; Cogan, Timothy M; Vancanneyt, Marc; Scherer, Siegfried

    2008-04-01

    Production of smear-ripened cheese critically depends on the surface growth of multispecies microbial consortia comprising bacteria and yeasts. These microorganisms often originate from the cheese-making facility and, over many years, have developed into rather stable, dairy-specific associations. While commercial smear starters are frequently used, it is unclear to what degree these are able to establish successfully within the resident microbial consortia. Thus, the fate of the smear starters of a German Limburger cheese subjected to the "old-young" smearing technique was investigated during ripening. The cheese milk was supplemented with a commercial smear starter culture containing Debaryomyces hansenii, Galactomyces geotrichum, Arthrobacter arilaitensis, and Brevibacterium aurantiacum. Additionally, the cheese surface was inoculated with an extremely stable in-house microbial consortium. A total of 1,114 yeast and 1,201 bacterial isolates were identified and differentiated by Fourier transform infrared spectroscopy. Furthermore, mitochondrial DNA restriction fragment length polymorphism, random amplified polymorphic DNA, repetitive PCR, and pulsed field gel electrophoresis analyses were used to type selected isolates below the species level. The D. hansenii starter strain was primarily found early in the ripening process. The G. geotrichum starter strain in particular established itself after relocation to a new ripening room. Otherwise, it occurred at low frequencies. The bacterial smear starters could not be reisolated from the cheese surface at all. It is concluded that none of the smear starter strains were able to compete significantly and in a stable fashion against the resident microbial consortia, a result which might have been linked to the method of application. This finding raises the issue of whether addition of starter microorganisms during production of this type of cheese is actually necessary.

  18. Beyond Commercialization: Science, Higher Education and the Culture of Neoliberalism

    ERIC Educational Resources Information Center

    Kleinman, Daniel Lee; Feinstein, Noah Weeth; Downey, Greg

    2013-01-01

    Since the 1980s, scholars and others have been engaged in a lively debate about the virtues and dangers of mingling commerce with university science. In this paper, we contend that the commercialization of academic science, and higher education more broadly, are best understood as pieces of a larger story. We use two cases of institutional change…

  19. Commercial bacterial starter cultures for fermented foods of the future.

    PubMed

    Hansen, Egon Bech

    2002-09-15

    Starter cultures for fermented foods are today developed mainly by design rather than by screening. The design principles are based on knowledge of bacterial metabolism and physiology as well as on the interaction with the food product. In the genomics era, we will obtain a wealth of data making design on a rational basis even simpler. The design tools available are food grade tools for genetic, metabolic and protein engineering and an increased use of laboratory automation and high throughput screening methods. The large body of new data will influence the future patterns of regulation. It is currently difficult to predict in what direction the future regulatory requirements will influence innovation in the food industry. It can either become a promoting force for the practical use of biotechnology to make better and safer products, or it can be limiting the use of starter cultures to a few strains with official approval. Successful cultures based on modern technology is expected to be launched in the areas of: probiotics, bioprotection, general improvement of yield and performance for the existing culture market and probably the introduction of cultures for fermenting other food products. A scientific basis for dramatic innovations that could transform the culture industry is currently being established.

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

    PubMed

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

    2014-08-01

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

  1. Temporal and spatial assessment of microbial communities in commercial silages from bunker silos.

    PubMed

    Kraut-Cohen, J; Tripathi, V; Chen, Y; Gatica, J; Volchinski, V; Sela, S; Weinberg, Z; Cytryn, E

    2016-08-01

    Ensiling is a feed preservation method of moist forage crops that generally depends on naturally developing lactic acid bacteria to convert water-soluble carbohydrates into organic acids. While bacterial community dynamics have been previously assessed in bench-scale and pilot ensiling facilities, almost no studies have assessed the microbiomes of large-scale silage facilities. This study analyzed bacterial community composition in mature silage from bunker silos in three commercial production centers as related to pH, organic matter, volatile fatty acid composition, and spatial distribution within the ensiling bunker. It revealed significant physicochemical differences between "preserved" regions situated in the center and along the walls of the silage bunkers that were characterized by high concentrations of lactic acid and other volatiles and pH values below 5, and "spoiled" regions in the corners (shoulders) of the bunkers that had low lactic acid concentrations and high pH values. Preserved silage was dominated (>90 %) by lactic acid bacteria and characterized by high similarity and low taxonomic diversity, whereas spoiled silage had highly diverse microbiomes with low abundances of lactic acid bacteria (<5 %) that were sometimes characterized by high levels of Enterobacteriaceae. Spatial position had a much stronger impact on the microbial community composition than feedstock type, sampling date, or production center location supporting previous studies demonstrating that ecology and not geography is a major driver of environmental microbiomes. PMID:27075739

  2. [Progress in microbial co-culture--A review].

    PubMed

    Xu, Deyang; Wang, Lili; Du, Chunmei

    2015-09-01

    We reviewed the history and applications of microorganism co-cultivation in food, agriculture, industry and sewage purification, and summarized ecology relationships between co-culture microorganisms. Joint mixed culture, sequence mixed culture and immobilized cells mixed culture have been used widely and lots of achievements have been made, for example, obtaining metabolites that are difficult to achieve or too low production in pure culture, transforming traditional fermentation industry, producing energy substance, improving substrate utilization ratio, expanding the scope of substrates and degrading toxic substances. Research reports indicate there are many ecology relationships between microorganisms, such as collaborative metabolism, induction effect, quorum sensing and gene transfer. The ecological interplay mechanism of co-culture microorganisms should have a further research, which will lay the foundation for developing applications of microorganism co-culture. PMID:26762021

  3. Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation.

    PubMed

    Jung, Ji Young; Lee, Se Hee; Lee, Hyo Jung; Seo, Hye-Young; Park, Wan-Soo; Jeon, Che Ok

    2012-02-15

    Kimchi fermentation usually relies upon the growth of naturally-occurring various heterofermentative lactic acid bacteria (LAB). This sometimes makes it difficult to produce kimchi with uniform quality. The use of Leuconostoc mesenteroides as a starter has been considered to produce commercial fermented kimchi with uniform and good quality in Korea. In this study, a combination of a barcoded pyrosequencing strategy and a (1)H NMR technique was used to investigate the effects of Leu. mesenteroides strain B1 as a starter culture for kimchi fermentation. Baechu (Chinese cabbage) and Chonggak (radish) kimchi with and without Leu. mesenteroides inoculation were prepared, respectively and their characteristics that included pH, cell number, bacterial community, and metabolites were monitored periodically for 40 days. Barcoded pyrosequencing analysis showed that the numbers of bacterial operational taxonomic units (OTU) in starter kimchi decreased more quickly than that in non-starter kimchi. Members of the genera Leuconostoc, Lactobacillus, and Weissella were dominant LAB regardless of the kimchi type or starter inoculation. Among the three genera, Leuconostoc was the most abundant, followed by Lactobacillus and Weissella. The use of Leu. mesenteroides as a starter increased the Leuconostoc proportions and decreased the Lactobacillus proportions in both type of kimchi during kimchi fermentation. However, interestingly, the use of the kimchi starter more highly maintained the Weissella proportions of starter kimchi compared to that in the non-starter kimchi until fermentation was complete. Metabolite analysis using the (1)H NMR technique showed that both Baechu and Chonggak kimchi with the starter culture began to consume free sugars earlier and produced a little greater amounts of lactic and acetic acids and mannitol. Metabolite analysis demonstrated that kimchi fermentation using Leu. mesenteroides as a starter was completed earlier with more production of kimchi

  4. Inflight Microbial Monitoring- An Alternative Method to Culture Based Detection Currently Used on the International Space Station

    NASA Technical Reports Server (NTRS)

    Khodadad, Christina L.; Birmele, Michele N.; Roman, Monsi; Hummerick, Mary E.; Smith, David J.; Wheeler, Raymond M.

    2015-01-01

    Previous research has shown that potentially destructive microorganisms and human pathogens have been detected on the International Space Station (ISS). The likelihood of introducing new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Microorganisms introduced to the ISS are readily transferred between crew and subsystems (i.e. ECLSS, environmental control and life support systems). Current microbial characterization methods require enrichment of microorganisms and at least a 48-hour incubation time. This increases the microbial load while detecting only a limited number of the total microorganisms. The culture based method detects approximately 1-10% of the total organisms present and provides no identification. To identify and enumerate ISS microbes requires that samples be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganisms at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.

  5. Inflight Microbial Monitoring-An Alternative Method to Culture Based Detection Currently Used on International Space Station

    NASA Technical Reports Server (NTRS)

    Khodadad, Christina L.; Birmele, Michele N.; Roman, Monsi; Hummerick, Mary E.; Smith, David J.; Wheeler, Raymond M.

    2015-01-01

    Previous research has shown that microorganisms and potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Previous research has shown that microorganisms introduced to the ISS are readily transferred between crew and subsystems and back (i.e. ECLSS, environmental control and life support systems). Current microbial characterization methods require enrichment of microorganisms and a 48-hour incubation time. This increases the microbial load while detecting a limited number of microorganisms. The culture based method detects approximately 1-10% of the total organisms present and provides no identification, To identify and enumerate ISS samples requires that samples to be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganism at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.

  6. Functional implications of the microbial community structure of undefined mesophilic starter cultures

    PubMed Central

    2014-01-01

    This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the population dynamics during cheese making and during starter culture propagation. Furthermore, the link between starter composition and starter functionality will be discussed. Finally, recent advances in predictive metabolic modelling of the multi-strain cultures will be discussed in the context of microbe-microbe interactions. PMID:25185941

  7. Studies on rhizosphere microbial diversity of some commercially important medicinal plants.

    PubMed

    Karthikeyan, B; Jaleel, C Abdul; Lakshmanan, G M A; Deiveekasundaram, M

    2008-03-15

    A preliminary study was made on four medicinal plants viz., Ocimum sanctum L., Coleus forskholii Briq, Catharanthus roseus (L.) G. Don. and Aloe vera in order to identify and enumerate the rhizosphere, non-rhizosphere and diazotrophic microorganisms in soil. The diazotrophic bacterial population studied includes Azospirillum, Azotobacter and Pseudomonas. The rhizosphere bacterial populations were 23.33 x 10(6)g(-1) in O. sanctum followed by C. roseus (20.46 x 10(6)g(-1)), A. vera (18.44 x 10(6)g(-1)) and C. forskholii (16.64 x 10(6)g(-1)). The fungi populations were 19.44 x 10(4)g(-1) in C. roseus, 18.66 x 10(4)g(-1) in O. sanctum, 16.44 x 10(4)g(-1) in A. vera and 14.22 x 10(4)g(-1) in C. forskholii. The actinomycetes population was 12.22 x 10(5)g(-1) in O. sanctum, 10.44 x 10(5)g(-1) in C. roseus, 8.44 x 10(5)g(-1) in A. vera and 6.22 x 10(5)g(-1) in C. forskholii. The diazotrophic bacterial population of Azospirillum, Azotobacter and Pseudomonas is 8.2 x 10(4)g(-1), 12 x 10(4)g(-1), 6 x 10(4)g(-1) in the rhizosphere soil. In all the four medicinal plants the microbial population is more in the rhizosphere soil, when compared to non-rhizosphere soil. These results are helpful in developing a biofertilizer consortium for these commercially grown medicinal plants.

  8. A representative microbial sampling method for large commercial containers of raw beef based on purge.

    PubMed

    Dorsa, W J; Siragusa, S R

    1998-02-01

    The purge from beef combos ( a boxed collection of beef trimmings) was tested as a means of representatively sampling the microbial content of this raw product. In the first experiment, purge was sampled from model beef combos that had been inoculated with bovine feces.. Data from this experiment indicated a strong correlation (r = 0.94) between the total aerobic bacteria counts derived from the purge samples of a model beef combo and the total aerobic bacteria present in a rinse sample of the entire model beef combo. In a second experiment, two 500-g meat pieces were inoculated with an antibiotic-resistant Escherichia coli O157:H7 and place at various levels within a 75-cm meat column. The marked bacteria were retrievable from the purge of the meat column after 24 h, showing that bacteria are carried downward into the purge. During the third part of the study, 90 beef combos (approximately 900 kg beef/combo) were randomly selected at the receiving dock of a commercial grinding facility and sampled using both purge and concurrently used 11-g core samples. Purge samples from these combos recovered significantly greater numbers of mesophilic and psychrotrophic aerobic bacteria, coliforms, and E. coli than core samples from the same combos. Additionally, coliforms and E. coli were recoverable from 100% and 80%, respectively, of the purge samples taken, whereas core samples were only able to recover 60% and 40%, respectively, from the same combos. These findings indicate that a purge sample from a beef combo is a more efficacious sampling method for determining the general bacterial profile and identifying the presence of coliforms and E. coli than randomly taken core samples. PMID:9708274

  9. Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.

    PubMed

    Liang, Shaobo; Gliniewicz, Karol; Mendes-Soares, Helena; Settles, Matthew L; Forney, Larry J; Coats, Erik R; McDonald, Armando G

    2015-03-01

    Three undefined mixed cultures (activated sludge) from different municipal wastewater treatment plants were used as seeds in a novel lactic acid fermentation process fed with potato peel waste (PPW). Anaerobic sequencing batch fermenters were run under identical conditions to produce predominantly lactic acid. Illumina sequencing was used to examine the 16S rRNA genes of bacteria in the three seeds and fermenters. Results showed that the structure of microbial communities of three seeds were different. All three fermentation products had unique community structures that were dominated (>96%) by species of the genus Lactobacillus, while members of this genus constituted <0.1% in seeds. The species of Lactobacillus sp. differed among the three fermentations. Results of this study suggest the structure of microbial communities in lactic acid fermentation of PPW with undefined mixed cultures were robust and resilient, which provided engineering prospects for the microbial utilization of carbohydrate wastes to produce lactic acid.

  10. Determining the safety of microbial cultures for consumption by humans and animals.

    PubMed

    Pariza, Michael W; Gillies, Kevin O; Kraak-Ripple, Sarah F; Leyer, Gregory; Smith, Amy B

    2015-10-01

    Fermented foods and feeds have been consumed for millennia, and microorganisms isolated from traditional fermentations have been used as probiotics. There is interest in developing new microbial cultures for these uses, but to date safety evaluation procedures have only been discussed in general terms. We propose a comprehensive approach for determining the safety of microbial cultures that lack an established history of safe use for their intended new applications. Three scenarios are considered: (1) substantially increased exposure to a culture that has an established record of safety in a more limited application; (2) a new strain without a history of safe use that was isolated from a food or feed that has a history of safe use; and (3) a new strain isolated from a non-food or non-feed source. Our safety evaluation process is based on scientific procedures and is in the form of a decision tree composed of 13 questions. Our decision tree for determining the safety of microbial cultures for consumption by humans or animals is modeled on previous decision trees that are used worldwide to evaluate the safety of microbial enzymes for use in human food or animal feed.

  11. Individually Addressable Arrays of Replica Microbial Cultures Enabled by Splitting SlipChips

    PubMed Central

    Ma, Liang; Datta, Sujit S.; Karymov, Mikhail A; Pan, Qichao; Begolo, Stefano; Ismagilov, Rustem F.

    2014-01-01

    Isolating microbes carrying genes of interest from environmental samples is important for applications in biology and medicine. However, this involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolation and culture. This paper describes the design, fabrication, biological validation, and underlying physics of a microfluidic SlipChip device that addresses this challenge. The device is composed of two conjoined plates containing 1,000 microcompartments, each comprising two juxtaposed wells, one on each opposing plate. Single microbial cells are stochastically confined and subsequently cultured within the microcompartments. Then, we split each microcompartment into two replica droplets, both containing microbial culture, and then controllably separate the two plates while retaining each droplet within each well. We experimentally describe the droplet retention as a function of capillary pressure, viscous pressure, and viscosity of the aqueous phase. Within each pair of replicas, one can be used for genetic analysis, and the other preserves live cells for growth. This microfluidic approach provides a facile way to cultivate anaerobes from complex communities. We validate this method by targeting, isolating, and culturing Bacteroides vulgatus, a core gut anaerobe, from a clinical sample. To date, this methodology has enabled isolation of a novel microbial taxon, representing a new genus. This approach could also be extended to the study of other microorganisms and even mammalian systems, and may enable targeted retrieval of solutions in applications including digital PCR, sequencing, single cell analysis, and protein crystallization. PMID:24953827

  12. Milk kefir: composition, microbial cultures, biological activities, and related products.

    PubMed

    Prado, Maria R; Blandón, Lina Marcela; Vandenberghe, Luciana P S; Rodrigues, Cristine; Castro, Guillermo R; Thomaz-Soccol, Vanete; Soccol, Carlos R

    2015-01-01

    In recent years, there has been a strong focus on beneficial foods with probiotic microorganisms and functional organic substances. In this context, there is an increasing interest in the commercial use of kefir, since it can be marketed as a natural beverage that has health promoting bacteria. There are numerous commercially available kefir based-products. Kefir may act as a matrix in the effective delivery of probiotic microorganisms in different types of products. Also, the presence of kefir's exopolysaccharides, known as kefiran, which has biological activity, certainly adds value to products. Kefiran can also be used separately in other food products and as a coating film for various food and pharmaceutical products. This article aims to update the information about kefir and its microbiological composition, biological activity of the kefir's microflora and the importance of kefiran as a beneficial health substance.

  13. Milk kefir: composition, microbial cultures, biological activities, and related products

    PubMed Central

    Prado, Maria R.; Blandón, Lina Marcela; Vandenberghe, Luciana P. S.; Rodrigues, Cristine; Castro, Guillermo R.; Thomaz-Soccol, Vanete; Soccol, Carlos R.

    2015-01-01

    In recent years, there has been a strong focus on beneficial foods with probiotic microorganisms and functional organic substances. In this context, there is an increasing interest in the commercial use of kefir, since it can be marketed as a natural beverage that has health promoting bacteria. There are numerous commercially available kefir based-products. Kefir may act as a matrix in the effective delivery of probiotic microorganisms in different types of products. Also, the presence of kefir’s exopolysaccharides, known as kefiran, which has biological activity, certainly adds value to products. Kefiran can also be used separately in other food products and as a coating film for various food and pharmaceutical products. This article aims to update the information about kefir and its microbiological composition, biological activity of the kefir’s microflora and the importance of kefiran as a beneficial health substance. PMID:26579086

  14. On the way to commercializing plant cell culture platform for biopharmaceuticals: present status and prospect

    PubMed Central

    Xu, Jianfeng; Zhang, Ningning

    2014-01-01

    Plant cell culture is emerging as an alternative bioproduction system for recombinant pharmaceuticals. Growing plant cells in vitro under controlled environmental conditions allows for precise control over cell growth and protein production, batch-to-batch product consistency and a production process aligned with current good manufacturing practices. With the recent US FDA approval and commercialization of the world’s first plant cell-based recombinant pharmaceutical for human use, β-glucocerebrosidase for treatment of Gaucher’s disease, a new era has come in which plant cell culture shows high potential to displace some established platform technologies in niche markets. This review updates the progress in plant cell culture processing technology, highlights recent commercial successes and discusses the challenges that must be overcome to make this platform commercially viable. PMID:25621170

  15. The effect of electromagnetic fields, from two commercially available water treatment devices, on bacterial culturability.

    PubMed

    Piyadasa, Chathuri; Yeager, Thomas R; Gray, Stephen R; Stewart, Matthew B; Ridgway, Harry F; Pelekani, Con; Orbell, John D

    2016-01-01

    Commercially available pulsed-electromagnetic field (PEMF) devices are currently being marketed and employed to ostensibly manage biofouling. The reliable application and industry acceptance of such technologies require thorough scientific validation - and this is currently lacking. We have initiated proof-of-principle research in an effort to investigate whether such commercially available PEMF devices can influence the viability (culturability) of planktonic bacteria in an aqueous environment. Thus two different commercial PEMF devices were investigated via a static (i.e. non-flowing) treatment system. 'Healthy' Escherichia coli cells, as well as cultures that were physiologically compromised by silver nano-particles, were exposed to the PEMFs from both devices under controlled conditions. Although relatively minor, the observed effects were nevertheless statistically significant and consistent with the hypothesis that PEMF exposure under controlled conditions may result in a decrease in cellular viability and culturability. It has also been observed that under certain conditions bacterial growth is actually stimulated.

  16. The DOE subsurface microbial culture collection at Florida State University. Final technical report, January 16, 1996--February 15, 1997

    SciTech Connect

    Balkwill, D.L.

    1998-05-25

    This report describes the research that supports the Subsurface Science Program by maintaining a culture collection of microorganisms isolated from deep terrestrial subsurface environments (the Subsurface Microbial Culture Collection, or SMCC). The general distribution of cultures and data was identified as an important function of the SMCC. The accomplishments related to this function of the culture collection are described.

  17. Toward Microbioreactor Arrays: A Slow-Responding Oxygen Sensor for Monitoring of Microbial Cultures in Standard 96-Well Plates.

    PubMed

    Glauche, Florian; John, Gernot T; Arain, Sarina; Knepper, Andreas; Neubauer, Antje; Goelling, Detlef; Lang, Christine; Violet, Norman; King, Rudibert; Neubauer, Peter

    2015-08-01

    In this study, a slow-responding chemo-optical sensor for dissolved oxygen (DO) integrated into a 96-well plate was developed. The slow response time ensures that the measured oxygen value does not change much during plate transport to the microplate reader. The sensor therefore permits at-line DO measurement of microbial cultures. Moreover, it eliminates the necessity of individual optical measurement systems for each culture plate, as many plates can be measured successively. Combined with the 96-well format, this increases the experimental throughput enormously. The novel sensor plate (Slow OxoPlate) consists of fluorophores suspended in a polymer matrix that were placed into u-bottom 96-well plates. Response time was measured using sodium sulfite, and a t90 value of 9.7 min was recorded. For application, DO values were then measured in Escherichia coli and Saccharomyces cerevisiae cultures grown under fed-batch-like conditions. Depending on the DO sensor's response time, different information on the oxygenation state of the culture plate was obtained: a fast sensor variant detects disturbance through sampling, whereas the slow sensor indicates oxygen limitation during incubation. A combination of the commercially available OxoPlate and the Slow OxoPlate enables operators of screening facilities to validate their cultivation procedures with regard to oxygen availability. PMID:25720599

  18. Toward Microbioreactor Arrays: A Slow-Responding Oxygen Sensor for Monitoring of Microbial Cultures in Standard 96-Well Plates.

    PubMed

    Glauche, Florian; John, Gernot T; Arain, Sarina; Knepper, Andreas; Neubauer, Antje; Goelling, Detlef; Lang, Christine; Violet, Norman; King, Rudibert; Neubauer, Peter

    2015-08-01

    In this study, a slow-responding chemo-optical sensor for dissolved oxygen (DO) integrated into a 96-well plate was developed. The slow response time ensures that the measured oxygen value does not change much during plate transport to the microplate reader. The sensor therefore permits at-line DO measurement of microbial cultures. Moreover, it eliminates the necessity of individual optical measurement systems for each culture plate, as many plates can be measured successively. Combined with the 96-well format, this increases the experimental throughput enormously. The novel sensor plate (Slow OxoPlate) consists of fluorophores suspended in a polymer matrix that were placed into u-bottom 96-well plates. Response time was measured using sodium sulfite, and a t90 value of 9.7 min was recorded. For application, DO values were then measured in Escherichia coli and Saccharomyces cerevisiae cultures grown under fed-batch-like conditions. Depending on the DO sensor's response time, different information on the oxygenation state of the culture plate was obtained: a fast sensor variant detects disturbance through sampling, whereas the slow sensor indicates oxygen limitation during incubation. A combination of the commercially available OxoPlate and the Slow OxoPlate enables operators of screening facilities to validate their cultivation procedures with regard to oxygen availability.

  19. Influence of combined pollution of antimony and arsenic on culturable soil microbial populations and enzyme activities.

    PubMed

    Wang, Qiongshan; He, Mengchang; Wang, Ying

    2011-01-01

    The effects of both combined and single pollution of antimony (Sb) and arsenic (As) in different concentrations on culturable soil microbial populations and enzyme activities were studied under laboratory conditions. Joint effects of both Sb and As were different from that of Sb or As alone. The inhibition rate of culturable soil microbial populations under Sb and As pollution followed the order: bacterial > fungi > actinomycetes. There existed antagonistic inhibiting effect on urease and acid phophatase and synergistic inhibiting effect on protease under the combined pollution of Sb (III) and As (III). Only urease appeared to be the most sensitive indicator under Sb (V) and As (V) pollution, and there existed antagonistic inhibiting effect on acid phophatase and synergistic inhibiting effect on urease and protease under Sb (V) and As (V) combined pollution at most time. In this study, we also confirmed that the trivalent states of Sb and As were more toxic to all the microbes tested and more inhibitory on microbial enzyme activities then their pentavalent counterparts. The results also suggest that not only the application rate of the two metalloids but also the chemical form of metalloids should be considered while assessing the effect of metalloid on culturable microbial populations and enzyme activities. Urease and acid phosphatase can be used as potential biomarkers to evaluate the intensity of Sb (III) and As (III) stress.

  20. Synergetic effects of microbial binary cultures on microbial fuel cell performance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A binary culture of Lactococcus lactis and Shewanella oneidensis was studied for an efficient conversion of glucose into electricity in a continuously-operated chemostatic electrochemical reactor. The homolactic fermentation bacterium L. lactis fermented glucose almost exclusively to lactate – the ...

  1. A three-dimensional culture system recapitulates placental syncytiotrophoblast development and microbial resistance

    PubMed Central

    McConkey, Cameron A.; Delorme-Axford, Elizabeth; Nickerson, Cheryl A.; Kim, Kwang Sik; Sadovsky, Yoel; Boyle, Jon P.; Coyne, Carolyn B.

    2016-01-01

    In eutherians, the placenta acts as a barrier and conduit at the maternal-fetal interface. Syncytiotrophoblasts, the multinucleated cells that cover the placental villous tree surfaces of the human placenta, are directly bathed in maternal blood and are formed by the fusion of progenitor cytotrophoblasts that underlie them. Despite their crucial role in fetal protection, many of the events that govern trophoblast fusion and protection from microbial infection are unknown. We describe a three-dimensional (3D)–based culture model using human JEG-3 trophoblast cells that develop syncytiotrophoblast phenotypes when cocultured with human microvascular endothelial cells. JEG-3 cells cultured in this system exhibit enhanced fusogenic activity and morphological and secretory activities strikingly similar to those of primary human syncytiotrophoblasts. RNASeq analyses extend the observed functional similarities to the transcriptome, where we observed significant overlap between syncytiotrophoblast-specific genes and 3D JEG-3 cultures. Furthermore, JEG-3 cells cultured in 3D are resistant to infection by viruses and Toxoplasma gondii, which mimics the high resistance of syncytiotrophoblasts to microbial infections in vivo. Given that this system is genetically manipulatable, it provides a new platform to dissect the mechanisms involved in syncytiotrophoblast development and microbial resistance. PMID:26973875

  2. Phenolic profiles of cultivated, in vitro cultured and commercial samples of Melissa officinalis L. infusions.

    PubMed

    Barros, Lillian; Dueñas, Montserrat; Dias, Maria Inês; Sousa, Maria João; Santos-Buelga, Celestino; Ferreira, Isabel C F R

    2013-01-01

    Melissa officinalis L. (lemon balm) is normally consumed as an infusion and presents therapeutic properties, such as sedative, carminative and antispasmodic, also being included in some pharmaceutical preparations. The phenolic profiles of different samples of lemon balm, prepared as infusions, were evaluated by HPLC-DAD-ESI/MS. The profiles were compared in order to understand the differences between cultivated, in vitro cultured and commercial (bags and granulated) samples. All the samples showed a similar phenolic profile, presenting differences only in the quantities found of each compound. Rosmarinic acid was the most abundant compound, being higher in commercial samples, especially in tea bag sample (55.68mg/g of infusion) and lower in in vitro cultured sample (15.46mg/g). Moreover, dimers, trimers and tetramers of caffeic acid were identified and quantified for the first time in lemon balm. Only one flavonoid, luteolin-3'-O-glucuronide was found in all the samples, ranging from 8.43mg/g in commercial granulate sample to 1.22mg/g in in vitro cultured sample. Overall, cultivated and in vitro cultured samples presented the lowest amounts of phenolic compounds (59.59 and 30.21mg/g, respectively); otherwise, commercial samples showed the highest contents (109.24mg/g for tea bag and 101.03mg/g for granulate sample). The present study shows that infusion of lemon balm can be a source of phenolic compounds, known for their bioactive effects. PMID:23017385

  3. Phenolic profiles of cultivated, in vitro cultured and commercial samples of Melissa officinalis L. infusions.

    PubMed

    Barros, Lillian; Dueñas, Montserrat; Dias, Maria Inês; Sousa, Maria João; Santos-Buelga, Celestino; Ferreira, Isabel C F R

    2013-01-01

    Melissa officinalis L. (lemon balm) is normally consumed as an infusion and presents therapeutic properties, such as sedative, carminative and antispasmodic, also being included in some pharmaceutical preparations. The phenolic profiles of different samples of lemon balm, prepared as infusions, were evaluated by HPLC-DAD-ESI/MS. The profiles were compared in order to understand the differences between cultivated, in vitro cultured and commercial (bags and granulated) samples. All the samples showed a similar phenolic profile, presenting differences only in the quantities found of each compound. Rosmarinic acid was the most abundant compound, being higher in commercial samples, especially in tea bag sample (55.68mg/g of infusion) and lower in in vitro cultured sample (15.46mg/g). Moreover, dimers, trimers and tetramers of caffeic acid were identified and quantified for the first time in lemon balm. Only one flavonoid, luteolin-3'-O-glucuronide was found in all the samples, ranging from 8.43mg/g in commercial granulate sample to 1.22mg/g in in vitro cultured sample. Overall, cultivated and in vitro cultured samples presented the lowest amounts of phenolic compounds (59.59 and 30.21mg/g, respectively); otherwise, commercial samples showed the highest contents (109.24mg/g for tea bag and 101.03mg/g for granulate sample). The present study shows that infusion of lemon balm can be a source of phenolic compounds, known for their bioactive effects.

  4. Enhanced power production from microbial fuel cells with high cell density culture.

    PubMed

    Zhai, Dan-Dan; Li, Bing; Sun, Jian-Zhong; Sun, De-Zhen; Si, Rong-Wei; Yong, Yang-Chun

    2016-01-01

    Improvement of power production in a microbial fuel cell (MFC) with a high cell density culture strategy was developed. By using high cell density culture, the voltage output and power density output of the MFC were enhanced about 0.6 and 1.6 times compared to the control, respectively. Further analysis showed that riboflavin concentration in the MFC was dramatically increased from 0.1 mg/L to 1.2 mg/L by high cell density culture. Moreover, the biofilm formation on the anode surface was significantly enhanced by this new strategy. The increased accumulation of electron shuttle (riboflavin) as well as enhanced biofilm formation contributed to the improvement in anodic electrochemical activity and these factors were the underlying mechanism for MFC performance improvement by high cell density culture. This work demonstrated that high cell density culture would be a simple and practical strategy for MFC manipulation.

  5. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils

    PubMed Central

    Stefani, Franck O. P.; Bell, Terrence H.; Marchand, Charlotte; de la Providencia, Ivan E.; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

    2015-01-01

    Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods. PMID:26053848

  6. Managing culture change in the commercial nuclear industry and the DOE weapons complex

    SciTech Connect

    Buhl, A.R. )

    1992-01-01

    Culture is the basic pattern of shared beliefs, behaviors, and assumptions acquired over time by the people in the organization. Culture is learned and can be modified over time. Many failures in managing change in recent years in the commercial nuclear industry and in the DOE weapons complex can be attributed to not accepting the central axiom of safety, health, and environmental matters. This paper presents specific lessons learned from experiences in commercial nuclear power and US Department of Energy weapons facilities restarts: (1) the attributes of problem plants and symptoms that predict impending regulatory doom; (2) the root causes of plant shutdown by regulators; (3) management infrastructure problems; and (4) actions required by management to effect the culture shift necessary to resume operations.

  7. Dipeptidase activity and growth of heat-treated commercial dairy starter culture.

    PubMed

    Garbowska, Monika; Pluta, Antoni; Berthold-Pluta, Anna

    2015-03-01

    Growing expectations of consumers of fermented dairy products urge the search for novel solutions that would improve their organoleptic properties and in the case of rennet cheeses-that would also accelerate their ripening process. The aim of this study was to determine the peptidolytic activities and growth of heat-treated commercial culture of lactic acid bacteria. The analyzed culture was characterized by a relatively high peptidolytic activity. The growth of bacterial culture subjected to heat treatment at 50-80 °C for 15 s, 10 and 3 min was delayed by a few or 10-20 h compared to the control culture. Based on the results achieved, it may be concluded that in the production of rennet cheeses, the application of additional, fermentation-impaired starter cultures (via heating for ten or so minutes) may serve to accelerate their ripening and to improve their sensory attributes.

  8. Comparison of Yacon (Smallanthus sonchifolius) Tuber with Commercialized Fructo-oligosaccharides (FOS) in Terms of Physiology, Fermentation Products and Intestinal Microbial Communities in Rats

    PubMed Central

    UTAMI, Ni Wayan Arya; SONE, Teruo; TANAKA, Michiko; NAKATSU, Cindy H; SAITO, Akihiko; ASANO, Kozo

    2013-01-01

    The yacon (Smallanthus sonchifolius) tuber was examined with regard to its prebiotic effects compared with commercialized fructo-oligosaccharides (FOS). A feed containing 10% yacon tuber, which is equivalent to 5% commercialized FOS in terms of the amount of fructo-oligosaccharides (GF2, GF3 and GF4), was administrated to rats for 28 days. The yacon diet changed the intestinal microbial communities beginning in the first week, resulting in a twofold greater concentration of cecal short-chain fatty acids (SCFAs). The SCFA composition differed, but the cecal pH in rats fed yacon tuber was equal to that in rats fed FOS. Serum triglycerides were lower in rats fed yacon compared with rats fed FOS and the control diet. Cecal size was greater with the yacon tuber diet compared with the control diet. The abundant fermentation in the intestines created a selective environment for the intestinal microbiota, which included Lactobacillus acidophilus, Bifidobacterium pseudolongum, Bifidobacterium animalis and Barnesiella spp. according to identification with culture-independent analysis, 16S rRNA gene PCR-DGGE combined with cloning and sequencing. Barnesiella spp. and B. pseudolongum were only found in the rats fed the yacon diet, while L. acidophilus and B. animalis were found in abundance in rats fed both the yacon and FOS diets. The genus Barnesiella has not previously been reported to be associated with yacon or FOS fermentation. We concluded that the physiological and microbiological effects of the yacon tuber were different from those of FOS. Differences in cecal size, blood triglycerides and microbial community profiles including their metabolites (SCFAs) between the yacon tuber and FOS were shown to be more greatly affected by the yacon tuber rather than FOS. PMID:24936376

  9. Immune modulation by Bacillus subtilus-based direct-fed microbials in commercial broiler chickens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Direct-fed microbials (DFMs), also known as probiotics, have been successfully used to improve the balance of gut microbiota. Spores of Bacillus subtilis, have been used as DFMs for food animals and humans and our previous studies showed that dietary supplementation of broiler chickens with a B. su...

  10. Commercially Available Gas-Permeable Cell Culture Bags May Not Prevent Anoxia in Cultured or Shipped Islets

    PubMed Central

    Avgoustiniatos, E.S.; Hering, B.J.; Rozak, P.R.; Wilson, J.R.; Tempelman, L.A.; Balamurugan, A.N.; Welch, D.P.; Weegman, B.P.; Suszynski, T.M.; Papas, K.K.

    2009-01-01

    Prolonged anoxia has deleterious effects on islets. Gas-permeable cell culture devices can be used to minimize anoxia during islet culture and especially during shipment when elimination of gas-liquid interfaces is required to prevent the formation of damaging gas bubbles. Gas-permeable bags may have several drawbacks, such as propensity for puncture and contamination, difficult islet retrieval, and significantly lower oxygen permeability than silicone rubber membranes (SRM). We hypothesized that oxygen permeability of bags may be insufficient for islet oxygenation. We measured oxygen transmission rates through the membrane walls of three different types of commercially available bags and through SRM currently used for islet shipment. We found that the bag membranes have oxygen transmission rates per unit area about 100-fold lower than SRM. We solved the oxygen diffusion-reaction equation for 150-μm diameter islets seeded at 3000 islet equivalents per cm2, a density adequate to culture and ship an entire human or porcine islet preparation in a single gas-permeable device, predicting that about 40% of the islet volume would be anoxic at 22°C and about 70% would be anoxic at 37°C. Islets of larger size or islets accumulated during shipment would be even more anoxic. The model predicted no anoxia in islets similarly seeded in devices with SRM bottoms. We concluded that commercially available bags may not prevent anoxia during islet culture or shipment; devices with SRM bottoms are more suitable alternatives. PMID:18374080

  11. Accuracy of species identity of commercial bacterial cultures intended for probiotic or nutritional use.

    PubMed

    Huys, Geert; Vancanneyt, Marc; D'Haene, Klaas; Vankerckhoven, Vanessa; Goossens, Herman; Swings, Jean

    2006-11-01

    Independent studies have indicated that the microbiological composition of several commercial probiotic products does not correspond to the product label information. The present study set out to investigate to what extent these problems may be due to the use of misidentified cultures at the onset of production. For this purpose, 213 cultures of lactic acid bacteria (LAB) and propionibacteria intended for probiotic or nutritional use were collected from 26 manufacturers of probiotic products, three international culture collections and one research institute. The accuracy of the taxonomic identity provided by the strain depositor was assessed through a polyphasic approach based on validated and standardized identification methods including fluorescent amplified fragment length polymorphism (FAFLP) and repetitive DNA element (rep)-PCR fingerprinting, protein profiling and partial 16S rDNA sequencing. The majority of the cultures were received as members of the genera Lactobacillus (57%) and Bifidobacterium (22%); however, propionibacteria, enterococci, Lactococcus lactis (subsp. lactis), Streptococcus thermophilus and pediococci were also obtained. Upon reidentification, 46 cases of misidentification at the genus level (n=19) or species level (n=27) were recorded, including 34 commercial probiotic cultures deposited by 10 different companies. The finding that more than 28% of the commercial cultures intended for human and/or animal probiotic use were misidentified at the genus or species level suggests that many cases of probiotic product mislabeling originate from the incorporation of incorrectly identified strains. A large number of these discrepancies could be related to the use of methods with limited taxonomic resolution (e.g., API strips) or that are unsuitable for reliable identification up to species level (e.g., pulsed-field gel electrophoresis and randomly amplified polymorphic DNA analysis). The current study has again highlighted that reliable

  12. Optimizing culture medium for meristem tissue culture of several Saccharum species and commercial hybrids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The optimal range of medium nutrients and plant growth regulators (PGR) was investigated for in vitro culture of diverse sugarcane species and cultivars. Macro-nutrients, nitrogen (N), phosphorous (P) and potassium (K), were essential for growth of leaf primordia. Although the best concentration of ...

  13. On-chip microbial culture for the specific detection of very low levels of bacteria.

    PubMed

    Bouguelia, Sihem; Roupioz, Yoann; Slimani, Sami; Mondani, Laure; Casabona, Maria G; Durmort, Claire; Vernet, Thierry; Calemczuk, Roberto; Livache, Thierry

    2013-10-21

    Microbial culture continues to be the most common protocol for bacterial detection and identification in medicine and agronomics. Using this process may take days to identify a specific pathogen for most bacterial strains. Surface Plasmon Resonance (SPR) detection is an emerging alternative technology that can be used for the detection of bacteria using protein microarrays although typical limits of detection are in the range of 10(3)-10(6) cfu mL(-1), which is not compatible with most Food Safety regulation requirements. In this work, we combine concomitant "on-chip" microbial culture with sensitive SPR detection of bacteria thus allowing rapid specific detection of bacteria pathogens - including Salmonella enterica serovar Enteritidis, Streptococcus pneumoniae and Escherichia coli O157:H7 - cultured on a protein microarray. This Culture-Capture-Measure (CCM) approach significantly decreases both the number of processing steps and the overall assay time for bacterial detection. Signal analysis of SPR responses allowed the fast and quantitative assessment of bacterial concentrations initially present in the sample as low as 2.8 ± 19.6 cfu per milliliter. Altogether, our results show how simple, easy-to-operate, fluidic-less and lo-tec microarrays can be used with unprocessed samples and yield - in a single assay - both qualitative and quantitative information regarding bacterial contamination.

  14. From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

    PubMed

    Garza, Daniel R; Dutilh, Bas E

    2015-11-01

    Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment. PMID:26254872

  15. From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

    PubMed

    Garza, Daniel R; Dutilh, Bas E

    2015-11-01

    Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

  16. Biodegradation kinetics of peptone and 2,6-dihydroxybenzoic acid by acclimated dual microbial culture.

    PubMed

    Cokgor, Emine Ubay; Insel, Guclu; Katipoglu, Tugce; Orhon, Derin

    2011-01-01

    This study evaluated the kinetics of simultaneous biodegradation of peptone mixture and 2,6-dihydroxybenzoic acid (2,6-DHBA) by an acclimated dual microbial culture under aerobic conditions. A laboratory-scale sequencing batch reactor was sustained at steady-state with peptone mixture feeding. During the study period, peptone mixture feeding was continuously supplemented with 2,6-DHBA. Related experimental data were derived from three sets of parallel batch reactors, the first fed with the peptone mixture, the second with 2,6-DHBA and the third one with the two substrates, after acclimation of microbial culture and simultaneous biodegradation of both organics. A mechanistic model was developed for this purpose including the necessary model components and process kinetics for the model calibration of relevant experimental data. Model evaluation provided all biodegradation characteristics and kinetics for both peptone mixture and 2,6-DHBA. It also supported the development of a dual microbial community through acclimation, with the selective growth of a second group of microorganisms specifically capable of metabolizing 2,6-DHBA as an organic carbon source.

  17. Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

    PubMed

    Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

    2016-02-01

    The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future. PMID:26563549

  18. Evaluation of microbial diversity in sulfite-added and sulfite-free wine by culture-dependent and -independent methods.

    PubMed

    Takahashi, Masayuki; Ohta, Tami; Masaki, Kazuo; Mizuno, Akihiro; Goto-Yamamoto, Nami

    2014-05-01

    The difference in microbiota including non-lactic acid bacteria, non-acetic acid bacteria, and wild yeast during winemaking and in the end-products between sulfite-added and sulfite-free wine, was investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and a culture-dependent method. There were differences between the microorganisms detected by PCR-DGGE and those detected by the culture-dependent method, probably because of the selectivity of culture medium and the characteristics of PCR-based method. In both the red wine and white wine, the microbial diversity of the sulfite-added wine was lower than that of the sulfite-free wine during fermentation. Tatumella terrea was detected from the fermenting must by PCR-DGGE and by the culture-dependent method, even though sulfite inhibited its growth to some extent. We confirmed that the addition of sulfite plays an important role in winemaking by inhibiting the growth of unexpected microorganisms, but on the other hand, it was revealed that some microorganisms can survive and grow in sulfite-added fermenting must. We also analyzed 15 samples of commercial wines by the PCR-DGGE method and detected various microorganisms. Among them, Sphingomonas sp., Pseudozyma sp., Ochromonas sp. and Methylophilus sp. were found for the first time in wine as far as we know. We did not identify a specific microorganism that was detected only from wines without sulfite addition. Thus, the microbiota of end-products seemed to be influenced by other factors, such as filtration before bottling, the production equipment and the storage environment.

  19. Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation

    PubMed Central

    Wu, Qun; Ling, Jie

    2014-01-01

    Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified: Saccharomyces cerevisiae, Pichia membranaefaciens, Issatchenkia orientalis, Bacillus licheniformis, and Bacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found that S. cerevisiae was positively correlated to nonanal, and B. licheniformis was positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, while I. orientalis was positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. Although P. membranaefaciens and B. amyloliquefaciens were not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor. PMID:24814798

  20. From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals.

    PubMed

    Van Dien, Stephen

    2013-12-01

    Fermentation of carbohydrate substrates by microorganisms represents an attractive route for the manufacture of industrial chemicals from renewable resources. The technology to manipulate metabolism of bacteria and yeast, including the introduction of heterologous chemical pathways, has accelerated research in this field. However, the public literature contains very few examples of strains achieving the production metrics required for commercialization. This article presents the challenges in reaching commercial titer, yield, and productivity targets, along with other necessary strain and process characteristics. It then reviews various methods in systems biology, synthetic biology, enzyme engineering, and fermentation engineering which can be applied to strain improvement, and presents a strategy for using these tools to overcome the major hurdles on the path to commercialization.

  1. Functional studies of rat, porcine, and human pancreatic islets cultured in ten commercially available media.

    PubMed

    Holmes, M A; Clayton, H A; Chadwick, D R; Bell, P R; London, N J; James, R F

    1995-10-27

    There have been no extensive studies investigating the effect of tissue culture media on the in vitro functional characteristics of rat, porcine and human Islets of Langerhans. We therefore aimed to compare ten commercially available tissue culture media on the basis of their ability to maintain islet viability. Following isolation, islets were cultured free-floating in the ten media (RPMI 1640-11mM glucose (control), RPMI 1640-2.2mM glucose, Dulbecco's MEM, TCM 199, CMRL 1066, Iscove's MEM, Waymouth's MEM, Serum-Free medium, Ex-cell 300, Ham's F-12) and viability was assessed after 24 hr, 3 days, and 7 days on the basis of macroscopic appearance, cell membrane integrity, and insulin secretion in response to glucose stimulation both by dynamic incubation and by perifusion. Each islet species demonstrated physiological insulin release characteristics in all media--however, it was possible to distinguish between the media by comparing the stimulation indices calculated from the insulin release studies. Significantly higher stimulation indices were produced in Iscove's MEM for rat islets, in Ham's F-12 for porcine islets and in CMRL 1066 for human islets. Over the entire culture period a significant deterioration in function was observed in all species cultured in the control media, although this was reversed when islets were cultured in the optimal media. Furthermore, in the case of porcine and human islets a significant improvement in function over the seven-day period was noted in the optimal media. In conclusion, of the commercially available media, the optimal tissue culture medium for rat islets is Iscove's MEM, for porcine islets is Ham's F-12, and for human islets is CMRL 1066. PMID:7482747

  2. Culture-Dependent and -Independent Investigations of Microbial Diversity on Urinary Catheters

    PubMed Central

    Xu, Yijuan; Moser, Claus; Al-Soud, Waleed Abu; Sørensen, Søren; Høiby, Niels; Nielsen, Per Halkjær

    2012-01-01

    Catheter-associated urinary tract infection is caused by bacteria, which ascend the catheter along its external or internal surface to the bladder and subsequently develop into biofilms on the catheter and uroepithelium. Antibiotic-treated bacteria and bacteria residing in biofilm can be difficult to culture. In this study we used culture-based and 16S rRNA gene-based culture-independent methods (fingerprinting, cloning, and pyrosequencing) to determine the microbial diversity of biofilms on 24 urinary catheters. Most of the patients were catheterized for <30 days and had undergone recent antibiotic treatment. In addition, the corresponding urine samples for 16 patients were cultured. We found that gene analyses of the catheters were consistent with cultures of the corresponding urine samples for the presence of bacteria but sometimes discordant for the identity of the species. Cultures of catheter tips detected bacteria more frequently than urine cultures and gene analyses; coagulase-negative staphylococci were, in particular, cultured much more often from catheter tips, indicating potential contamination of the catheter tips during sampling. The external and internal surfaces of 19 catheters were separately analyzed by molecular methods, and discordant results were found in six catheters, suggesting that bacterial colonization intra- and extraluminally may be different. Molecular analyses showed that most of the species identified in this study were known uropathogens, and infected catheters were generally colonized by one to two species, probably due to antibiotic usage and short-term catheterization. In conclusion, our data showed that culture-independent molecular methods did not detect bacteria from urinary catheters more frequently than culture-based methods. PMID:23015674

  3. Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method.

    PubMed

    Costa, Ohana Yonara Assis; Souto, Betulia Morais; Tupinambá, Daiva Domenech; Bergmann, Jessica Carvalho; Kyaw, Cynthia Maria; Kruger, Ricardo Henrique; Barreto, Cristine Chaves; Quirino, Betania Ferraz

    2015-01-01

    Sugarcane ethanol production occurs in non-sterile conditions, and microbial contamination can decrease productivity. In this study, we assessed the microbial diversity of contaminants of ethanol production in an industrial facility in Brazil. Samples obtained at different stages were analyzed by pyrosequencing-based profiling of bacterial and archaeal 16S rRNA genes and the fungal internal transcribed spacer region. A total of 355 bacterial groups, 22 archaeal groups, and 203 fungal groups were identified, and community changes were related to temperature changes at certain stages. After fermentation, Lactobacillus and unclassified Lactobacillaceae accounted for nearly 100 % of the bacterial sequences. Predominant Fungi groups were "unclassified Fungi," Meyerozyma, and Candida. The predominant Archaea group was unclassified Thaumarchaeota. This is the first work to assess the diversity of Bacteria, and Archaea and Fungi associated with the industrial process of sugarcane-ethanol production using culture-independent techniques. PMID:25404204

  4. Microbial diversity in sugarcane ethanol production in a Brazilian distillery using a culture-independent method.

    PubMed

    Costa, Ohana Yonara Assis; Souto, Betulia Morais; Tupinambá, Daiva Domenech; Bergmann, Jessica Carvalho; Kyaw, Cynthia Maria; Kruger, Ricardo Henrique; Barreto, Cristine Chaves; Quirino, Betania Ferraz

    2015-01-01

    Sugarcane ethanol production occurs in non-sterile conditions, and microbial contamination can decrease productivity. In this study, we assessed the microbial diversity of contaminants of ethanol production in an industrial facility in Brazil. Samples obtained at different stages were analyzed by pyrosequencing-based profiling of bacterial and archaeal 16S rRNA genes and the fungal internal transcribed spacer region. A total of 355 bacterial groups, 22 archaeal groups, and 203 fungal groups were identified, and community changes were related to temperature changes at certain stages. After fermentation, Lactobacillus and unclassified Lactobacillaceae accounted for nearly 100 % of the bacterial sequences. Predominant Fungi groups were "unclassified Fungi," Meyerozyma, and Candida. The predominant Archaea group was unclassified Thaumarchaeota. This is the first work to assess the diversity of Bacteria, and Archaea and Fungi associated with the industrial process of sugarcane-ethanol production using culture-independent techniques.

  5. A Moderately Thermophilic Mixed Microbial Culture for Bioleaching of Chalcopyrite Concentrate at High Pulp Density

    PubMed Central

    Wang, Yuguang; Zeng, Weimin; Qiu, Guanzhou; Chen, Xinhua

    2014-01-01

    Three kinds of samples (acid mine drainage, coal mine wastewater, and thermal spring) derived from different sites were collected in China. Thereafter, these samples were combined and then inoculated into a basal salts solution in which different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite) served as energy sources. After that, the mixed cultures growing on different substrates were pooled equally, resulting in a final mixed culture. After being adapted to gradually increasing pulp densities of chalcopyrite concentrate by serial subculturing for more than 2 years, the final culture was able to efficiently leach the chalcopyrite at a pulp density of 20% (wt/vol). At that pulp density, the culture extracted 60.4% of copper from the chalcopyrite in 25 days. The bacterial and archaeal diversities during adaptation were analyzed by denaturing gradient gel electrophoresis and constructing clone libraries of the 16S rRNA gene. The results show that the culture consisted mainly of four species, including Leptospirillum ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum, before adapting to a pulp density of 4%. However, L. ferriphilum could not be detected when the pulp density was greater than 4%. Real-time quantitative PCR was employed to monitor the microbial dynamics during bioleaching at a pulp density of 20%. The results show that A. caldus was the predominant species in the initial stage, while S. acidophilus rather than A. caldus became the predominant species in the middle stage. F. thermophilum accounted for the greatest proportion in the final stage. PMID:24242252

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

    PubMed

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

    2012-12-01

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

  7. Commercial product exploitation from marine microbial biodiversity: some legal and IP issues

    PubMed Central

    Tichet, Camille; Nguyen, Hong Khanh; Yaakoubi, Sefia El; Bloch, Jean‐François

    2010-01-01

    Summary The biodiversity found in the marine environment is remarkable and yet largely unknown compared with the terrestrial one. The associated genetic resource, also wide and unrevealed, has raised a strong interest from the scientific and industrial community. However, despite this growing interest, the discovery of new compounds extracted from marine organisms, more precisely from microorganisms, is ruled by a complex legislation. The access and transfer of genetic resource are ruled by the Convention on Biological Diversity. One of the three core objectives of this convention is to ensure the fair and equitable sharing of benefits generated by the use of genetic resources and to split these benefits between the different stakeholders. From the discovery of a microorganism to the commercialization of a product, three main stakeholders are involved: providers of microorganisms, e.g. academic institutes, the scientists who will perform R&D on biodiversity, and the industrial companies which will commercialize the final product arising from the R&D results. This article describes how difficult and complex it might be to ensure a fair distribution of benefits of this research between the parties. PMID:21255350

  8. Microbial assessment of an upward and downward dehiding technique in a commercial beef processing plant.

    PubMed

    Kennedy, Thomas G; Giotis, Efstathios S; McKevitt, Aideen I

    2014-08-01

    Preventing microbial contamination during dehiding is challenging, and skinning methods are of critical importance for the hygienic status of beef carcasses. Two skinning methods are usually employed: upward hide pulling (UHP) and downward hide pulling (DHP). This study has compared the microbiological contamination of carcasses using both systems in a beef processing plant in the process of changing its dehiding method from UHP to DHP. 100 cm(2) areas from eight carcass sites (ham, chuck, rump, bung, flank, brisket, shin and neck) were sampled on 36 skinned carcasses dehided by each technique. Total viable counts (TVCs) and Enterobacteriaceae counts for each site were determined. No significant differences were observed in total (pooled-samples) carcass contamination regardless of the method used. However, significant differences (p<0.05) in TVCs were observed at the flank, shin, brisket and neck. These differences can be attributed to possible deficiencies in the implementation of the HACCP pre-requisite programmes, and are not necessarily associated with the skinning method per se.

  9. Culturable microbial groups and thallium-tolerant fungi in soils with high thallium contamination.

    PubMed

    Sun, Jialong; Zou, Xiao; Ning, Zengping; Sun, Min; Peng, Jingquan; Xiao, Tangfu

    2012-12-15

    Thallium (Tl) contamination in soil exerts a significant threat to the ecosystem health due to its high toxicity. However, little is known about the effect of Tl on the microbial community in soil. The present study aimed at characterizing the culturable microbial groups in soils which experience for a long time high Tl contamination and elevated Hg and As. The contamination originates from As, Hg and Tl sulfide mineralization and the associated mining activities in the Guizhou Province, Southwest China. Our investigation showed the existence of culturable bacteria, filamentous fungi and actinomyces in long-term Tl-contaminated soils. Some fungal groups grow in the presence of high Tl level up to 1000 mg kg⁻¹. We have isolated and identified nine Tl-tolerant fungal strains based on the morphological traits and ITS analysis. The dominant genera identified were Trichoderma, Penicillium and Paecilomyces. Preliminary data obtained in this study suggested that certain microbes were able to face high Tl pollution in soil and maintain their metabolic activities and resistances. The highly Tl-tolerant fungi that we have isolated are potentially useful in the remediation of Tl-contaminated sites.

  10. Chemical, microbial and physical evaluation of commercial bottled waters in greater Houston area of Texas.

    PubMed

    Saleh, Mahmoud A; Abdel-Rahman, Fawzia H; Woodard, Brooke B; Clark, Shavon; Wallace, Cecil; Aboaba, Adetoun; Zhang, Wenluo; Nance, James H

    2008-03-01

    Due to the increased demand and consumption of bottled water in the United States, there has been a growing concern about the quality of this product. Retail outlets sell local as well as imported bottled water to consumers. Three bottles for each of 35 different brands of bottled water were randomly collected from local grocery stores in the greater Houston area. Out of the 35 different brands, 16 were designated as spring water, 11 were purified and/or fortified tap water, 5 were carbonated water and 3 were distilled water. Chemical, microbial and physical properties of all samples were evaluated including pH, conductivity, bacteria counts, anion concentration, trace metal concentration, heavy metal and volatile organics concentration were determined in all samples. Inductively coupled plasma/mass spectrometry (ICPMS) was used for elemental analysis, gas chromatography with electron capture detector (GCECD) as well as gas chromatography mass spectrometry (GCMS) were used for analysis of volatile organics, ion chromatography (IC) and selective ion electrodes were used for the analysis of anions. Bacterial identification was performed using the Biolog software (Biolog, Inc., Hayward, Ca, USA). The results obtained were compared with guidelines of drinking water recommended by the International Bottled Water Association (IBWA), United States Food and Drug Administration (FDA), United States Environmental Protection Agency (EPA) and the World Health Organization (WHO) drinking water standard. The majority of the analyzed chemicals were below their respective drinking water standards for maximum admissible concentrations (MAC). Volatile organic chemicals were found to be below detection limits. Four of the 35 brands of the bottled water samples analyzed were found to be contaminated with bacteria. PMID:18273738

  11. Microbial ecology studies of spontaneous fermentation: starter culture selection for prickly pear wine production.

    PubMed

    Rodríguez-Lerma, G K; Gutiérrez-Moreno, K; Cárdenas-Manríquez, M; Botello-Álvarez, E; Jiménez-Islas, H; Rico-Martínez, R; Navarrete-Bolaños, J L

    2011-08-01

    A procedure for designing starter cultures for fermentation is illustrated for prickly pear wine production. The illustration includes kinetic studies on inoculated and spontaneous fermentation, microorganism identification studies based on molecular biology tools, and microbial ecology studies, which led to the selection of strains that are capable of synthesizing alcohol and desirable volatile compounds. Results show that a mixed starter inoculum containing Pichia fermentans and Saccharomyces cerevisiae leads to a fermented product that contains 8.37% alcohol (v/v). The gas chromatography and mass spectrometry (GC-MS) analysis shows the presence of 9 major volatile compounds (Isobutanol, Isopentanol, Ethyl acetate, Isoamyl acetate, Ethyl octanoate, Ethyl decanoate, Ethyl 9-decanoate, β-Phenylethyl acetate, and Phenylethyl alcohol) that have ethereal, fruity, aromatic notes that are considered to be essential for a fine wine flavor. These compounds harmonically synergize with the alcohol to produce a fermented product with a unique flavor and taste. Several assays using the mixed culture show that the process is stable, predictable, controllable, and reproducible. Moreover, the results show that a mixed culture leads to a broader range of aromatic products than that produced by a single, pure culture. Therefore, we conclude that combinations of Saccharomyces strains and non-Saccharomyces strains can be used to obtain high-quality fermented beverages from prickly pear juice. PMID:22417507

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

    A novel competition model for describing bacterial growth in mixed culture was developed in this study. Several model candidates were made with our logistic growth model that precisely describes the growth of a monoculture of bacteria. These candidates were then evaluated for the usefulness in describing growth of two competing species in mixed culture using Staphylococcus aureus, Escherichia coli, and Salmonella. Bacterial cells of two species grew at initial doses of 10(3), 10(4), and 10(5) CFU/g at 28ºC. Among the candidates, a model where the Lotka-Volterra model, a general competition model in ecology, was incorporated as a new term in our growth model was the best for describing all types of growth of two competitors in mixed culture. Moreover, the values for the competition coefficient in the model were stable at various combinations of the initial populations of the species. The Baranyi model could also successfully describe the above types of growth in mixed culture when it was coupled with the Gimenez and Dalgaard model. However, the values for the competition coefficients in the competition model varied with the conditions. The present study suggested that our model could be a basic model for describing microbial competition. PMID:24975409

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2015-09-01

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

  16. Biodegradation Of Thiocyanate Using Microbial Consortia Cultured From Gold Mine Tailings

    NASA Astrophysics Data System (ADS)

    Moreau, J. W.; Watts, M. P.; Spurr, L. P.; Vu, H. P.

    2015-12-01

    Some bacteria possess the capability to degrade SCN-; therefore, harnessing this metabolic trait offers a biotechnological remediation strategy for SCN- produced in gold ore processing. A tailings storage facility (TSF) at a gold mine in Victoria, Australia holds large quantities of thiocyanate (SCN-) contaminated mine waste. The surface water in the TSF typically contains SCN- concentrations of >800 mg L-1, and seepage from the facility has contaminated the groundwater at the site. This study aimed to culture SCN-degrading microbes from the TSF, characterize the microbial consortia and test its operational parameters for use in a thiocyanate-degrading bioreactor. Surface samples were obtained from several locations around the TSF facility and used to inoculate medium reflective of the moderately saline and alkaline tailings water at the TSF, in the absence of organic carbon but subject to additions of phosphate and trace metals. Four microbial consortia capable of rapid SCN- degradation were successfully cultured. Sequencing of 16S rRNA genes found that the consortia were dominated by Thiobacillus species, a genus of known SCN- degraders. Lower abundances of other SCN- degraders; Sphingopyxis and Rhodobacter, were also identified. The impact of a number of geochemical conditions, including pH, temperature and SCN- concentration, upon the growth and SCN- degrading capacity of these consortia was determined. These results informed the optimization of a lab-scale thiocyanate degrading bioreactor. In summary, the cultured bacterial consortia proved effective towards SCN- degradation at the prevailing geochemical conditions of the TSF, requiring minimal nutrient additions. These consortia were dominated by genera of known autotrophic SCN- degraders. The comprehensive characterisation of these SCN- degrading consortia will provide the fundamental operational parameters required for deployment of this technique at the field scale.

  17. Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

    USGS Publications Warehouse

    Dowdle, P.R.; Oremland, R.S.

    1998-01-01

    The microbial oxidation of elemental selenium [Se(O)] was studied by employing 75Se(O) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation ranged from 0.0009 to 0.0117 day-1 which were 3-4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.The microbial oxidation of elemental selenium [Se(0)] was studied by employing 75Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(O) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(O) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(O) oxidation

  18. A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell.

    PubMed

    Bourdakos, Nicholas; Marsili, Enrico; Mahadevan, Radhakrishnan

    2014-04-01

    Wastewater-fed microbial fuel cells (MFCs) are a promising technology to treat low-organic carbon wastewater and recover part of the chemical energy in wastewater as electrical power. However, the interactions between electrochemically active and fermentative microorganisms cannot be easily studied in wastewater-fed MFCs because of their complex microbial communities. Defined co-culture MFCs provide a detailed understanding of such interactions. In this study, we characterize the extracellular metabolites in laboratory-scale membrane-less MFCs inoculated with Geobacter sulfurreducens and Escherichia coli co-culture and compare them with pure culture MFCs. G. sulfurreducens MFCs are sparged to maintain anaerobic conditions, while co-culture MFCs rely on E. coli for oxygen removal. G. sulfurreducens MFCs have a power output of 128 mW m(-2) , compared to 63 mW m(-2) from the co-culture MFCs. Analysis of metabolites shows that succinate production in co-culture MFCs decreases current production by G. sulfurreducens and that the removal of succinate is responsible for the increased current density in the late co-culture MFCs. Interestingly, pH adjustment is not required for co-culture MFCs but a base addition is necessary for E. coli MFCs and cultures in vials. Our results show that defined co-culture MFCs provide clear insights into metabolic interactions among bacteria while maintaining a low operational complexity.

  19. A Continuous Culture System for Assessing Microbial Activities in the Piezosphere

    PubMed Central

    Pérez-Rodríguez, Ileana

    2015-01-01

    Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere. PMID:26209666

  20. Crude glycerol as feedstock for polyhydroxyalkanoates production by mixed microbial cultures.

    PubMed

    Moita, R; Freches, A; Lemos, P C

    2014-07-01

    The increase in global biodiesel production makes imperative the development of sustainable processes for the use of its main by-product, crude glycerol. In this study the feasibility of polyhydroxyalkanoates (PHA) production by a mixed microbial community using crude glycerol as feedstock was investigated. The selected culture had the ability to consume both glycerol and methanol fraction present in the crude. However, glycerol seemed to be the only carbon source contributing for the two biopolymers stored: poly-3-hydroxybutyrate (PHB) and glucose biopolymer (GB). In this work the culture reached a maximum PHB content of 47% (cdw) and a productivity of 0.27 g X/L.d, with an aerobic mixed cultures and a real waste substrate with non-volatile fatty acids (VFA) organic matter. The overall PHA yield on total substrate obtained was in the middle range of those reported in literature. The fact that crude glycerol can be used to produce PHA without any pre-treatment step, makes the overall production process economically more competitive, reducing polymer final cost.

  1. A Continuous Culture System for Assessing Microbial Activities in the Piezosphere.

    PubMed

    Foustoukos, Dionysis I; Pérez-Rodríguez, Ileana

    2015-10-01

    Continuous culture under elevated pressures is an important technique for expanding the exploration of microbial growth and survival in extreme environments associated with the deep biosphere. Here we present a benchtop stirred continuous culture bioreactor capable of withstanding temperatures ranging from 25 to 120°C and pressures as high as 69 MPa. The system is configured to allow the employment of media enriched in dissolved gases, under oxic or anoxic conditions, while permitting periodic sampling of the incubated organisms with minimal physical/chemical disturbance inside the reactor. In a pilot experiment, the fermentative growth of the thermopiezophilic bacterium Marinitoga piezophila was investigated continuously for 382 h at 65°C and at pressures ranging from 0.1 to 40 MPa while the medium flow rate was varied from 2 to 0.025 ml/min. The enhanced growth observed at 30 and 40 MPa and 0.025 ml/min supports the pressure preferences of M. piezophila when grown fermentatively. This assay successfully demonstrates the capabilities of the bioreactor for continuous culturing at a variety of dilution rates, pressures, and temperatures. We anticipate that this technology will accelerate our understanding of the physiological and metabolic status of microorganisms under temperature, pressure, and energy regimes resembling those of the Earth's piezosphere.

  2. Biotechnologically produced microbial alginate dressings show enhanced gel forming capacity compared to commercial alginate dressings of marine origin.

    PubMed

    Hoefer, Dirk; Schnepf, Julia K; Hammer, Timo R; Fischer, Melissa; Marquardt, Christoph

    2015-04-01

    Marine alginate fibre dressings are well established in wound management. Alginate fibres can absorb plenty of wound exudate due to their gel forming abilities and ion exchange. Alginates from bacteria have never been studied for medical applications so far, although the microbial polymer raises expectations for improved gelling capacity due to its unique O-acetylation. To prove the gelling capacity of bacterial alginate, we extracted the co-polymer from fermentation of the soil bacterium Azotobacter vinelandii ATCC 9046, cultivated on crude glycerol as an alternative carbon source. Bacterial alginate was isolated in high purity and extruded by a wet spinning method. Fibre structure and properties were characterised by infrared spectroscopy, NMR, GPC, scanning electron microscopy and tensile testing. The fibres could be processed into biocompatible needle web dressings, which showed more than twice the gel formation in saline compared to commercial dressings made of marine alginates. Gelled dressings of bacterial alginate formed stable hydrogels of sufficient shape and strength for wound healing applications. This work suggests that the increased gel formation of bacterial alginate from A. vinelandii may be optimal for the preparation of novel wound dressings.

  3. Towards generation of bioactive peptides from meat industry waste proteins: Generation of peptides using commercial microbial proteases.

    PubMed

    Ryder, Kate; Bekhit, Alaa El-Din; McConnell, Michelle; Carne, Alan

    2016-10-01

    Five commercially available food-grade microbial protease preparations were evaluated for their ability to hydrolyse meat myofibrillar and connective tissue protein extracts to produce bioactive peptides. A bacterial-derived protease (HT) extensively hydrolysed both meat protein extracts, producing peptide hydrolysates with significant in vitro antioxidant and ACE inhibitor activities. The hydrolysates retained bioactivity after simulated gastrointestinal hydrolysis challenge. Gel permeation chromatography sub-fractionation of the crude protein hydrolysates showed that the smaller peptide fractions exhibited the highest antioxidant and ACE inhibitor activities. OFFGEL electrophoresis of the small peptides of both hydrolysates showed that low isoelectric point peptides had antioxidant activity; however, no consistent relationship was observed between isoelectric point and ACE inhibition. Cell-based assays indicated that the hydrolysates present no significant cytotoxicity towards Vero cells. The results indicate that HT protease hydrolysis of meat myofibrillar and connective tissue protein extracts produces bioactive peptides that are non-cytotoxic, should be stable in the gastrointestinal tract and may contain novel bioactive peptide sequences.

  4. Towards generation of bioactive peptides from meat industry waste proteins: Generation of peptides using commercial microbial proteases.

    PubMed

    Ryder, Kate; Bekhit, Alaa El-Din; McConnell, Michelle; Carne, Alan

    2016-10-01

    Five commercially available food-grade microbial protease preparations were evaluated for their ability to hydrolyse meat myofibrillar and connective tissue protein extracts to produce bioactive peptides. A bacterial-derived protease (HT) extensively hydrolysed both meat protein extracts, producing peptide hydrolysates with significant in vitro antioxidant and ACE inhibitor activities. The hydrolysates retained bioactivity after simulated gastrointestinal hydrolysis challenge. Gel permeation chromatography sub-fractionation of the crude protein hydrolysates showed that the smaller peptide fractions exhibited the highest antioxidant and ACE inhibitor activities. OFFGEL electrophoresis of the small peptides of both hydrolysates showed that low isoelectric point peptides had antioxidant activity; however, no consistent relationship was observed between isoelectric point and ACE inhibition. Cell-based assays indicated that the hydrolysates present no significant cytotoxicity towards Vero cells. The results indicate that HT protease hydrolysis of meat myofibrillar and connective tissue protein extracts produces bioactive peptides that are non-cytotoxic, should be stable in the gastrointestinal tract and may contain novel bioactive peptide sequences. PMID:27132822

  5. Improvement of Ayran quality by the selection of autochthonous microbial cultures.

    PubMed

    Baruzzi, Federico; Quintieri, Laura; Caputo, Leonardo; Cocconcelli, PierSandro; Borcakli, Mehlika; Owczarek, Lubomiła; Jasińska, Urszula T; Skąpska, Sylwia; Morea, Maria

    2016-12-01

    Ayran is a traditional Turkish milk drink which is fermented and salted. Inadequate production and storage conditions contribute to its variable organoleptic quality and stability during shelf-life. A thorough physico-chemical, nutritional and microbial characterization of artisanal Ayran was carried out in order to standardize its overall quality without altering its original traits. Ayran microbial ecosystem was largely dominated by Streptococcus thermophilus (ST) and Lactobacillus delbrueckii subsp. bulgaricus (LDB). High counts of other lactic acid bacteria species, including Lactobacillus helveticus (LH), Lactobacillus fermentum (LF), and Lactobacillus paracasei (LP), were also found. Selected LDB, LP and LH strains grew well in milk displaying fast acidification and high proteolysis, differently from ST and LF strains that did not cause noticeable changes. A selected autochthonous three-strain culture (TSC), composed of one strain of LDB, LP and ST, was applied for the pilot-scale production of traditional Ayran. The Ayran produced with this TSC resulted in the most extensive shelf-life (one month) and in the best terms of its nutritional and sensory quality nevertheless altering its typical pleasant yogurt and cottage cheese notes. This TSC is at disposal of SMEs who need to standardize the overall quality of this traditional fermented milk, preserving its typical traits. PMID:27554150

  6. Microbial oxidation of elemental selenium in soil slurries and bacterial cultures

    SciTech Connect

    Dowdle, P.R.; Oremland, R.S.

    1998-12-01

    The microbial oxidation of elemental selenium [Se(0)] was studied by employing {sup 75}Se(0) as a tracer. Live, oxic soil slurries demonstrated a linear production of mostly Se(IV), with the formation of smaller quantities of Se(VI). Production of both Se(IV) and Se(VI) was inhibited by autoclaving, formalin, antibiotics, azide, and 2,4-dinitrophenol, thereby indicating the involvement of microbes. Oxidation of Se(0) in slurries was enhanced by addition of acetate, glucose, or sulfide, which implied involvement of chemoheterotrophs as well as chemoautotrophic thiobacilli. Cultures of Thiobacillus ASN-1, Leptothrix MnB1, and a heterotrophic soil enrichment all oxidized Se(0) with Se(VI) observed as the major product rather than Se(IV). This indicated that microbial oxidation in soils is partly constrained by the adsorption of Se(IV) onto soil surfaces. Rate constants for unamended soil slurry Se(0) oxidation ranged from 0.0009 to 0.0117 day{sup {minus}1} which were 3--4 orders of magnitude lower than those reported for dissimilatory Se(VI) reduction in organic-rich, anoxic sediments.

  7. Biochar as a novel niche for culturing microbial communities in composting.

    PubMed

    Sun, Daquan; Lan, Yu; Xu, Elvis Genbo; Meng, Jun; Chen, Wenfu

    2016-08-01

    Biochar has been applied as a bulk agent or an additive to compost. The mixture of biochar and compost has been considered to exert synergistic effect as a soil amendment. In a composting system, the macro-porous sites of biochar may act as a novel niche that selects and cultures the microorganisms from the bulk compost. A variety of volatile organic carbons (VOCs) such as aromatic hydrocarbons and aliphatics were detected in biochar pellets (BC) pyrolyzed at 100°C. In the mesosphilic phase, the water-soluble carbon (WSC) and water-soluble phenols (WSP) in biochar increased from 2.1 to 26mgkg(-1) and 5.9 to 101μgkg(-1), respectively. These labile carbons however, were subjected to a rapid metabolism over the composting course. We further compared the responses of microbial community in BC to those in the bulk organic matter. Both Shannon-Wiener and Richness indexes of bacterial communities were higher in BC than in the adjacent compost (ADJ) and the bulk organic matter (control). As for fungal communities, the two indexes were higher in BC than ADJ and control only in the mature phase. During the composting course, the bacterial activity was higher than the fungal counterpart in terms of the changes of corresponding biomarkers, glucosamine and muramic acids. The results suggested that the diversified labile carbons sources including VOCs and WSC in BC could influence the structure of microbial community and resulted in an enhanced carbon catabolic capacity. PMID:27184446

  8. Extraction of polyhydroxyalkanoates from mixed microbial cultures: Impact on polymer quality and recovery.

    PubMed

    Samorì, Chiara; Abbondanzi, Federica; Galletti, Paola; Giorgini, Loris; Mazzocchetti, Laura; Torri, Cristian; Tagliavini, Emilio

    2015-01-01

    Polyhydroxyalkanoates (PHAs) can be extracted from mixed microbial cultures (MMCs) by means of dimethyl carbonate (DMC) or combination of DMC and sodium hypochlorite (NaClO). The protocol based on DMC, a green solvent never used before for the extraction of PHAs from MMC, allows an overall polymer recovery of 63%; also the purity and the molecular weight of the recovered polymers are good (98% and 1.2 MDa, respectively). The use of NaClO pretreatment before DMC extraction increases the overall PHA recovery (82%) but lowers the mean molecular weight to 0.6-0.2 MDa. A double extraction with DMC results to be the method of choice for the recovery of high quality PHAs from attractive but challenging MMCs. PMID:25889806

  9. Extraction of polyhydroxyalkanoates from mixed microbial cultures: Impact on polymer quality and recovery.

    PubMed

    Samorì, Chiara; Abbondanzi, Federica; Galletti, Paola; Giorgini, Loris; Mazzocchetti, Laura; Torri, Cristian; Tagliavini, Emilio

    2015-01-01

    Polyhydroxyalkanoates (PHAs) can be extracted from mixed microbial cultures (MMCs) by means of dimethyl carbonate (DMC) or combination of DMC and sodium hypochlorite (NaClO). The protocol based on DMC, a green solvent never used before for the extraction of PHAs from MMC, allows an overall polymer recovery of 63%; also the purity and the molecular weight of the recovered polymers are good (98% and 1.2 MDa, respectively). The use of NaClO pretreatment before DMC extraction increases the overall PHA recovery (82%) but lowers the mean molecular weight to 0.6-0.2 MDa. A double extraction with DMC results to be the method of choice for the recovery of high quality PHAs from attractive but challenging MMCs.

  10. Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.

    PubMed

    Hanson, Andrea J; Paszczynski, Andrzej J; Coats, Erik R

    2016-03-01

    The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices. PMID:26790989

  11. Kinetic analysis of high-concentration isopropanol biodegradation by a solvent-tolerant mixed microbial culture.

    PubMed

    Bustard, Mark T; Meeyoo, Vissanu; Wright, Phillip C

    2002-06-20

    The ability of a previously enriched microbial population to utilize isopropanol (IPA) as the sole carbon source within a minimal salts medium is studied. The advantage of prior enrichment procedures for the improvement of IPA biodegradation performance is demonstrated for an IPA concentration of up to 24 g L(-1). Results showing the interrelationship between temperature and substrate utilization and inhibition levels at temperatures of between 2 degrees C and 45 degrees C are examined. Models of inhibition based on enzyme kinetics are assessed via nonlinear analysis, in order to accurately represent the growth kinetics of this solvent-tolerant mixed culture. The model that best describes the data is the Levenspiel substrate inhibition model, which can predict the maximum substrate level above which growth is completely limited. This is the first report of IPA treatment of up to 24 g L(-1) by an aerobic solvent-tolerant population. PMID:11992536

  12. Kinetic analysis of high-concentration isopropanol biodegradation by a solvent-tolerant mixed microbial culture.

    PubMed

    Bustard, Mark T; Meeyoo, Vissanu; Wright, Phillip C

    2002-06-20

    The ability of a previously enriched microbial population to utilize isopropanol (IPA) as the sole carbon source within a minimal salts medium is studied. The advantage of prior enrichment procedures for the improvement of IPA biodegradation performance is demonstrated for an IPA concentration of up to 24 g L(-1). Results showing the interrelationship between temperature and substrate utilization and inhibition levels at temperatures of between 2 degrees C and 45 degrees C are examined. Models of inhibition based on enzyme kinetics are assessed via nonlinear analysis, in order to accurately represent the growth kinetics of this solvent-tolerant mixed culture. The model that best describes the data is the Levenspiel substrate inhibition model, which can predict the maximum substrate level above which growth is completely limited. This is the first report of IPA treatment of up to 24 g L(-1) by an aerobic solvent-tolerant population.

  13. Homogeneous Matrix Deposition on Dried Agar for MALDI Imaging Mass Spectrometry of Microbial Cultures

    NASA Astrophysics Data System (ADS)

    Hoffmann, Thomas; Dorrestein, Pieter C.

    2015-11-01

    Matrix deposition on agar-based microbial colonies for MALDI imaging mass spectrometry is often complicated by the complex media on which microbes are grown. This Application Note demonstrates how consecutive short spray pulses of a matrix solution can form an evenly closed matrix layer on dried agar. Compared with sieving dry matrix onto wet agar, this method supports analyte cocrystallization, which results in significantly more signals, higher signal-to-noise ratios, and improved ionization efficiency. The even matrix layer improves spot-to-spot precision of measured m/z values when using TOF mass spectrometers. With this technique, we established reproducible imaging mass spectrometry of myxobacterial cultures on nutrient-rich cultivation media, which was not possible with the sieving technique.

  14. Microbial β-glucosidases from cow rumen metagenome enhance the saccharification of lignocellulose in combination with commercial cellulase cocktail

    PubMed Central

    2012-01-01

    Background A complete saccharification of plant polymers is the critical step in the efficient production of bio-alcohols. Beta-glucosidases acting in the degradation of intermediate gluco-oligosaccharides produced by cellulases limit the yield of the final product. Results In the present work, we have identified and then successfully cloned, expressed, purified and characterised 4 highly active beta-glucosidases from fibre-adherent microbial community from the cow rumen. The enzymes were most active at temperatures 45–55°C and pH 4.0-7.0 and exhibited high affinity and activity towards synthetic substrates such as p-nitrophenyl-beta-D-glucopyranoside (pNPbetaG) and pNP-beta-cellobiose, as well as to natural cello-oligosaccharides ranging from cellobiose to cellopentaose. The apparent capability of the most active beta-glucosidase, herein named LAB25g2, was tested for its ability to improve, at low dosage (31.25 units g-1 dry biomass, using pNPbetaG as substrate), the hydrolysis of pre-treated corn stover (dry matter content of 20%; 350 g glucan kg-1 dry biomass) in combination with a beta-glucosidase-deficient commercial Trichoderma reseei cellulase cocktail (5 units g-1 dry biomass in the basis of pNPbetaG). LAB25g2 increased the final hydrolysis yield by a factor of 20% (44.5 ± 1.7% vs. 34.5 ± 1.5% in control conditions) after 96–120 h as compared to control reactions in its absence or in the presence of other commercial beta-glucosidase preparations. The high stability (half-life higher than 5 days at 50°C and pH 5.2) and 2–38000 fold higher (as compared with reported beta-glucosidases) activity towards cello-oligosaccharides may account for its performance in supplementation assays. Conclusions The results suggest that beta-glucosidases from yet uncultured bacteria from animal digestomes may be of a potential interest for biotechnological processes related to the effective bio-ethanol production in combination with low dosage of commercial cellulases

  15. Resistance to alternative management in fisheries: economic and cultural considerations of North Carolina's commercial fishers.

    PubMed

    Crosson, Scott

    2011-01-01

    Research in recent decades has shown that although conventional fisheries management strategies such as fishing seasons, size limits, or gear restrictions can provide sufficient biological protection to fisheries stocks, they do not necessarily lead to satisfactory social or economic outcomes. In their stead, the merits and shortcomings of a variety of alternate management systems, including individual transferable quotas, have been proposed, implemented, and analyzed. Few investigations, however, have examined actual fishers' preferences for different management systems. Integrating results from a mail survey of North Carolina commercial fishers with their individual harvest histories and sociodemographic profiles shows that economic and cultural variables both play a significant role in management system preference. The analysis introduces the use of the Herfindahl-Hirschman Index (HHI), a measure of investment diversity, as a measure of diversity in fisheries harvests and demonstrates an association with management preferences. Social and family factors are also notable indicators.

  16. Impact of microbial cultures on proteolysis and release of bioactive peptides in fermented milk.

    PubMed

    Chaves-López, Clemencia; Serio, Annalisa; Paparella, Antonello; Martuscelli, Maria; Corsetti, Aldo; Tofalo, Rosanna; Suzzi, Giovanna

    2014-09-01

    This study aimed at evaluating co-cultures of selected microorganisms for their proteolytic activity and capability to produce fermented milk enriched with ACE-inhibitory (ACEI) peptides. Selected yeasts (Torulaspora delbruekii KL66A, Galactomyces geotrichum KL20B, Pichia kudriavzevii KL84A and Kluyveromyces marxianus KL26A) and lactic acid bacteria strains (Lactobacillus plantarum LAT03, Lb. plantarum KLAT01 and the not virulent Enterococcus faecalis KE06) were screened as single cultures for their capacity of releasing ACEI peptides without producing bitter taste. Three strains cultures (yeast, Lb. plantarum and E. faecalis) were performed to evaluate the combined impact on microbial growth, lactic acid production, citric acid consumption, proteolysis, ACEI activity, and bitter taste after 36 h of fermentation at 28 °C. While G. geotrichum KL20B showed a strong stimulating effect on Lb. plantarum strains and the production of peptides with ACEI activity, the presence of T. delbruekii KL26A in the cultures was deleterious both to ACEI activity and product taste. The most effective combination was P. kudriavzevii KL84A, Lb. plantarum LAT3, E. faecalis KL06, which showed the highest ACEI activity (IC50 = 30.63 ± 1.11 μg ml(-1)) and gave no bitter taste for 7 days at 6 °C. Our results highlight the importance of choosing the strains combination carefully, to obtain a high yield of ACEI activity without bitter taste.

  17. Impact of microbial cultures on proteolysis and release of bioactive peptides in fermented milk.

    PubMed

    Chaves-López, Clemencia; Serio, Annalisa; Paparella, Antonello; Martuscelli, Maria; Corsetti, Aldo; Tofalo, Rosanna; Suzzi, Giovanna

    2014-09-01

    This study aimed at evaluating co-cultures of selected microorganisms for their proteolytic activity and capability to produce fermented milk enriched with ACE-inhibitory (ACEI) peptides. Selected yeasts (Torulaspora delbruekii KL66A, Galactomyces geotrichum KL20B, Pichia kudriavzevii KL84A and Kluyveromyces marxianus KL26A) and lactic acid bacteria strains (Lactobacillus plantarum LAT03, Lb. plantarum KLAT01 and the not virulent Enterococcus faecalis KE06) were screened as single cultures for their capacity of releasing ACEI peptides without producing bitter taste. Three strains cultures (yeast, Lb. plantarum and E. faecalis) were performed to evaluate the combined impact on microbial growth, lactic acid production, citric acid consumption, proteolysis, ACEI activity, and bitter taste after 36 h of fermentation at 28 °C. While G. geotrichum KL20B showed a strong stimulating effect on Lb. plantarum strains and the production of peptides with ACEI activity, the presence of T. delbruekii KL26A in the cultures was deleterious both to ACEI activity and product taste. The most effective combination was P. kudriavzevii KL84A, Lb. plantarum LAT3, E. faecalis KL06, which showed the highest ACEI activity (IC50 = 30.63 ± 1.11 μg ml(-1)) and gave no bitter taste for 7 days at 6 °C. Our results highlight the importance of choosing the strains combination carefully, to obtain a high yield of ACEI activity without bitter taste. PMID:24929726

  18. Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

    PubMed

    Panosyan, Hovik; Birkeland, Nils-Kåre

    2014-11-01

    The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. PMID:24740751

  19. Harnessing the landscape of microbial culture media to predict new organism-media pairings.

    PubMed

    Oberhardt, Matthew A; Zarecki, Raphy; Gronow, Sabine; Lang, Elke; Klenk, Hans-Peter; Gophna, Uri; Ruppin, Eytan

    2015-10-13

    Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain-media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism-media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism's 16S rDNA sequence, facilitating future cultivation efforts.

  20. Transient concentrations of NaCl affect the PHA accumulation in mixed microbial culture.

    PubMed

    Palmeiro-Sánchez, T; Fra-Vázquez, A; Rey-Martínez, N; Campos, J L; Mosquera-Corral, A

    2016-04-01

    The present study explores the feasibility of the accumulation of polyhydroxyalkanoates (PHAs) under the presence of transient concentrations of added sodium chloride, by means of a mixed microbial culture (MMC). This culture was enriched on a mixture of volatile fatty acids (VFAs) containing 0.8g Na(+)/L as NaOH. This MMC presented a maximum PHA accumulation capacity of 53wt% with 27Cmol% HV. Accumulation experiments performed with added NaCl at concentrations of 7, 13 and 20g/L shown that this salt provoked a decrease of the biomass PHA production rate, with an IC50 value close to 7gNaCl/L. The accumulated PHA was lower than the corresponding value of the assay without the addition of salt. Furthermore, the composition of the biopolymer, in terms of HB:HV ratio, changed from 2.71 to 6.37Cmol/Cmol, which means a HV decrease between 27 and 14Cmol%. Summarizing, the PHA accumulation by a MMC non-adapted to saline conditions affected the polymer composition and lead to lower production yields and rates than in absence of added NaCl. PMID:26780589

  1. Fermentation by the human large intestine microbial community in an in vitro semicontinuous culture system.

    PubMed Central

    Miller, T L; Wolin, M J

    1981-01-01

    A semicontinuous culture of the microbial community of the human large intestine that was maintained over 81 days is described. The initial inoculum was feces, and about 200 ml of nutrient suspension was fed to 500 ml of fermentor contents once or twice daily. The nutrient suspension contained comminuted fibrous food, sodium deoxycholate, urea, acid-hydrolyzed casein, vitamins, and salts. The fermentation was monitored, and the major products were acetate, propionate, butyrate, methane, hydrogen, and carbon dioxide. The concentration of anaerobic bacteria was 2 X 10(9) per ml of culture contents and was 100 times that of fecal coliforms. When the nutrient suspension contained lettuce, celery, carrots, and unsweetened applesauce, the predominant nonsporeforming anaerobes isolated were Bacteroides species. When carrots and applesauce were omitted, the predominant nonsporeforming isolates were Fusobacterium species. On both diets, clostridia were isolated that resembled Clostridium clostridiiforme. The fermentation and bacteriological analyses indicated that the in vitro ecosystem appears to be a reasonable facsimile of the large intestine ecosystem. Images PMID:7027952

  2. Harnessing the landscape of microbial culture media to predict new organism-media pairings.

    PubMed

    Oberhardt, Matthew A; Zarecki, Raphy; Gronow, Sabine; Lang, Elke; Klenk, Hans-Peter; Gophna, Uri; Ruppin, Eytan

    2015-01-01

    Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain-media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism-media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism's 16S rDNA sequence, facilitating future cultivation efforts. PMID:26460590

  3. Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

    PubMed

    Panosyan, Hovik; Birkeland, Nils-Kåre

    2014-11-01

    The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively.

  4. How commercial and ``violent'' video games can promote culturally sensitive science learning: some questions and challenges

    NASA Astrophysics Data System (ADS)

    Kwah, Helen

    2012-12-01

    In their paper, Muñoz and El-Hani propose to bring video games into science classrooms to promote culturally sensitive ethics and citizenship education. Instead of bringing "educational" games, Muñoz and El-Hani take a more creative route and include games such as Fallout 3® precisely because they are popular and they reproduce ideological and violent representations of gender, race, class, nationality, science and technology. However, there are many questions that arise in bringing these commercial video games into science classrooms, including the questions of how students' capacities for critical reflection can be facilitated, whether traditional science teachers can take on the role of using such games in their classrooms, and which video games would be most appropriate to use. In this response, I raise these questions and consider some of the challenges in order to further the possibility of implementing Muñoz and El-Hani's creative proposal for generating culturally sensitive science classrooms.

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

    PubMed

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

    2016-07-01

    Utilization of commercially available rapid platforms for microbial identification from positive blood cultures is useful during periods of, or in laboratories with, limited expert staffing. We compared the results of the FilmArray® BCID Panel performed by non-expert technologists to those of conventional methods for organism identification performed by skilled microbiologists. Within 8 h of signalling positive by a continuous monitoring blood culture system, positive bottles were analysed by the FilmArray BCID Panel. Data from these analyses were compared to standard-of-care testing, which included conventional and automated methods. To gauge the ease of use of the BCID Panel by non-expert staff, technologists unfamiliar with diagnostic bacteriology performed the testing without prior knowledge of the Gram stain results, or even whether organisms were detected. Identifications of 172/200 (86 %) positive blood cultures using the BCID Panel were consistent with identifications provided by standard-of-care methods. Standard-of-care testing identified organisms in 20 positive blood cultures, which were not represented on the BCID Panel. Seven (3.5 %) blood cultures demonstrated a discrepancy between the methods, which could not be attributed to either a lack of representation on the panel or unclear separate detection of organisms in a mixed blood culture of a shared genus or grouping of organisms, e.g. Staphylococcus or Enterobacteriaceae . One (0.5 %) blood culture yielded invalid results on two separate panels, so it was eliminated from the study. The easy-to-use FilmArray® technology shows good correlation with blood culture identification and antibiotic resistance detection performed by conventional methods. This technology may be particularly useful in laboratories with limited staffing or limited technical expertise. PMID:27170288

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

    PubMed

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

    2016-07-01

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

  7. Skew-laplace and cell-size distribution in microbial axenic cultures: statistical assessment and biological interpretation.

    PubMed

    Julià, Olga; Vidal-Mas, Jaume; Panikov, Nicolai S; Vives-Rego, Josep

    2010-01-01

    We report a skew-Laplace statistical analysis of both flow cytometry scatters and cell size from microbial strains primarily grown in batch cultures, others in chemostat cultures and bacterial aquatic populations. Cytometry scatters best fit the skew-Laplace distribution while cell size as assessed by an electronic particle analyzer exhibited a moderate fitting. Unlike the cultures, the aquatic bacterial communities clearly do not fit to a skew-Laplace distribution. Due to its versatile nature, the skew-Laplace distribution approach offers an easy, efficient, and powerful tool for distribution of frequency analysis in tandem with the flow cytometric cell sorting.

  8. Skew-Laplace and Cell-Size Distribution in Microbial Axenic Cultures: Statistical Assessment and Biological Interpretation

    PubMed Central

    Julià, Olga; Vidal-Mas, Jaume; Panikov, Nicolai S.; Vives-Rego, Josep

    2010-01-01

    We report a skew-Laplace statistical analysis of both flow cytometry scatters and cell size from microbial strains primarily grown in batch cultures, others in chemostat cultures and bacterial aquatic populations. Cytometry scatters best fit the skew-Laplace distribution while cell size as assessed by an electronic particle analyzer exhibited a moderate fitting. Unlike the cultures, the aquatic bacterial communities clearly do not fit to a skew-Laplace distribution. Due to its versatile nature, the skew-Laplace distribution approach offers an easy, efficient, and powerful tool for distribution of frequency analysis in tandem with the flow cytometric cell sorting. PMID:20592754

  9. Chronic impact of tetracycline on nitrification kinetics and the activity of enriched nitrifying microbial culture.

    PubMed

    Katipoglu-Yazan, Tugce; Merlin, Christophe; Pons, Marie-Noëlle; Ubay-Cokgor, Emine; Orhon, Derin

    2015-04-01

    This study evaluated the chronic impact of tetracycline on biomass with enriched nitrifying community sustained in a lab-scale activated sludge system. For this purpose, a fill and draw reactor fed with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia was sustained at a sludge age of 15 days. At steady-state, the reactor operation was continued with a daily tetracycline dosing of 50 mg/L for more than 40 days, with periodic monitoring of the microbial composition, the nitrifying bacteria abundance, as well as the amoA and 16S rRNA gene activity, using molecular techniques. Changes in the kinetics of nitrification were quantified by modelling concentration profiles of major nitrogen fractions and oxygen uptake rate profiles derived from parallel batch experiments. Activated sludge modeling results indicated inhibitory impact of tetracycline on the growth of nitrifiers with a significant increase of the half saturation coefficients in corresponding rate equations. Tetracycline also inactivated biomass components of the enriched culture at a gradually increasing rate with time of exposure, leading to total collapse of nitrification. Molecular analyses revealed significant changes in the composition of the microbial community throughout the observation period. They also showed that continuous exposure to tetracycline inflicted significant reduction in amoA mRNA and 16S rRNA levels directly affecting nitrification. The chronic impact was much more pronounced on the ammonia oxidizing bacteria (AOB) community. These observations explained the basis of numerical changes identified in the growth kinetics of nitrifiers under stress conditions.

  10. Chronic impact of tetracycline on nitrification kinetics and the activity of enriched nitrifying microbial culture.

    PubMed

    Katipoglu-Yazan, Tugce; Merlin, Christophe; Pons, Marie-Noëlle; Ubay-Cokgor, Emine; Orhon, Derin

    2015-04-01

    This study evaluated the chronic impact of tetracycline on biomass with enriched nitrifying community sustained in a lab-scale activated sludge system. For this purpose, a fill and draw reactor fed with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia was sustained at a sludge age of 15 days. At steady-state, the reactor operation was continued with a daily tetracycline dosing of 50 mg/L for more than 40 days, with periodic monitoring of the microbial composition, the nitrifying bacteria abundance, as well as the amoA and 16S rRNA gene activity, using molecular techniques. Changes in the kinetics of nitrification were quantified by modelling concentration profiles of major nitrogen fractions and oxygen uptake rate profiles derived from parallel batch experiments. Activated sludge modeling results indicated inhibitory impact of tetracycline on the growth of nitrifiers with a significant increase of the half saturation coefficients in corresponding rate equations. Tetracycline also inactivated biomass components of the enriched culture at a gradually increasing rate with time of exposure, leading to total collapse of nitrification. Molecular analyses revealed significant changes in the composition of the microbial community throughout the observation period. They also showed that continuous exposure to tetracycline inflicted significant reduction in amoA mRNA and 16S rRNA levels directly affecting nitrification. The chronic impact was much more pronounced on the ammonia oxidizing bacteria (AOB) community. These observations explained the basis of numerical changes identified in the growth kinetics of nitrifiers under stress conditions. PMID:25616640

  11. Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures

    PubMed Central

    Glass, Jennifer B.; Axler, Richard P.; Chandra, Sudeep; Goldman, Charles R.

    2012-01-01

    Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2–4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state. PMID:22993512

  12. Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia.

    PubMed

    Samarajeewa, A D; Hammad, A; Masson, L; Khan, I U H; Scroggins, R; Beaudette, L A

    2015-01-01

    Characterization of commercial microbial consortia products for human and environmental health risk assessment is a major challenge for regulatory agencies. As a means to develop an approach to assess the potential environmental risk of these products, research was conducted to compare four genomics methods for characterizing bacterial communities; (i) Denaturing Gradient Gel Electrophoresis (DGGE), (ii) Clonal-Restriction Fragment Length Polymorphism (C/RFLP), (iii) partial 16S rDNA amplification, cloning followed by Sanger sequencing (PRACS) and (iv) Next-Generation Sequencing (NGS) based on Ion Torrent technology. A commercially available microbial consortium, marketed as a remediation agent for degrading petroleum hydrocarbon contamination in soil and water, was assessed. The bacterial composition of the commercial microbial product was characterized using the above four methods. PCR amplification of 16S rDNA was performed targeting the variable region V6 for DGGE, C/RFLP and PRACS and V5 for Ion Torrent sequencing. Ion Torrent technology was shown to be a promising tool for initial screening by detecting the majority of bacteria in the consortium that were also detected by DGGE, C/RFLP and PRACS. Additionally, Ion Torrent sequencing detected some of the bacteria that were claimed to be in the product, while three other methods failed to detect these specific bacteria. However, the relative proportions of the microbial composition detected by Ion Torrent were found to be different from DGGE, C/RFLP and PRACS, which gave comparable results across these three methods. The discrepancy of the Ion Torrent results may be due to the short read length generated by this technique and the targeting of different variable regions on the 16S rRNA gene used in this study. Arcobacter spp. a potential pathogenic bacteria was detected in the product by all methods, which was further confirmed using genus and species-specific PCR, RFLP and DNA-based sequence analyses. However

  13. Effects of 2-hydroxy-4-(methylthio) butanoic acid (HMB) on microbial growth in continuous culture.

    PubMed

    Noftsger, S M; St-Pierre, N R; Karnati, S K R; Firkins, J L

    2003-08-01

    2-Hydroxy-4-(methylthio) butanoic acid (HMB) positively affects milk composition and yield, potentially through ruminal actions. Four continuous culture fermenters were used to determine the optimal concentration of HMB for digestibility of organic matter (OM), neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose and synthesis of microbial N. A highly degradable mix of hay and grain was used as a basal diet to simulate a typical lactation diet. Three concentrations of HMB (0, 0.055, and 0.110%) and one concentration of dl-Met (0.097%) were infused into the fermenters according to a 4 x 4 Latin square design. Digesta samples were collected during the last 3 d of each of the four 10-d experimental periods. Digestibility of OM, hemicellulose, and NDF was largely insensitive to treatment. Digestibility of ADF showed a quadratic effect to supplementation of HMB, with 0.055% having lower digestibility than 0 or 0.110%. Total production of VFA was not influenced by HMB supplementation, but differences in concentration and production of individual VFA were seen. Isobutyrate increased linearly with increasing HMB supplementation. Propionate concentration decreased linearly with increased HMB supplementation, but propionate production showed a quadratic trend (P = 0.13). A higher concentration of acetate was detected for dl-Met compared with the highest HMB concentration. There were trends (P < 0.15) for dl-Met to decrease the production of isobutyrate and to lower the concentration of butyrate when compared with HMB. Microbial efficiency was not different among treatments. The proportion of bacterial N produced from NH3-N decreased linearly with increasing HMB, and bacteria receiving dl-Met synthesized more N from NH3-N than those receiving HMB. These data suggest that supplementation of HMB may have a sparing effect on branched chain volatile fatty acids because the fatty acids are not needed to provide carbon for synthesis of valine, isoleucine and

  14. Effects of commercial marinade seasoning and a natural blend of cultured sugar and vinegar on Campylobacter jejuni and Salmonella Typhimurium and the texture of chicken breasts.

    PubMed

    Park, Na Yoon; Hong, Soo Hyeon; Yoon, Ki Sun

    2014-03-01

    Marination using various ingredients has been widely used to improve microbial safety and quality of chicken products at retail markets. The objective of this study was to investigate the effects of commercial marinade seasoning and cultured sugar/vinegar blend on Campylobacter jejuni and Salmonella Typhimurium populations during refrigerated storage. In addition, their effects on the texture of precooked chicken breasts during frozen and refrigerated storage was investigated. Chicken breasts inoculated with 4.5 to 5.0 log cfu/g of C. jejuni and Salmonella Typhimurium were treated with 3% cultured sugar/vinegar blend with and without 0.6% polish rub seasoning containing 32% herb content. Breasts were then vacuum-packaged and stored at 4 and 10°C. Survival and growth curves were fitted to the Baranyi equation to determine survival and growth kinetics of C. jejuni and Salmonella Typhimurium. In addition, the vacuum-packaged precooked chicken breasts with different marination treatments were subjected to 3 freeze-thaw cycles and shear force was measured. At 4°C, the populations of C. jejuni and Salmonella Typhimurium decreased, regardless of treatment group during storage. The greatest survival for C. jejuni was observed in untreated chicken breasts. At 10°C, the growth of Salmonella Typhimurium was completely prevented in precooked chicken breasts treated with 3% cultured sugar/vinegar blend, regardless of the presence of 0.6% seasoning. The 3% cultured sugar/vinegar blend also improved the tenderness of frozen chicken breasts and refrigerated, ready-to-eat chicken breast. Therefore, a natural blend of cultured sugar and vinegar can be used as antimicrobial and texture-modifying agents for poultry meat and poultry products.

  15. Benchmarking of commercially available CHO cell culture media for antibody production.

    PubMed

    Reinhart, David; Damjanovic, Lukas; Kaisermayer, Christian; Kunert, Renate

    2015-06-01

    In this study, eight commercially available, chemically defined Chinese hamster ovary (CHO) cell culture media from different vendors were evaluated in batch culture using an IgG-producing CHO DG44 cell line as a model. Medium adaptation revealed that the occurrence of even small aggregates might be a good indicator of cell growth performance in subsequent high cell density cultures. Batch experiments confirmed that the culture medium has a significant impact on bioprocess performance, but high amino acid concentrations alone were not sufficient to ensure superior cell growth and high antibody production. However, some key amino acids that were limiting in most media could be identified. Unbalanced glucose and amino acids led to high cell-specific lactate and ammonium production rates. In some media, persistently high glucose concentrations probably induced the suppression of respiration and oxidative phosphorylation, known as Crabtree effect, which resulted in high cell-specific glycolysis rates along with a continuous and high lactate production. In additional experiments, two of the eight basal media were supplemented with feeds from two different manufacturers in six combinations, in order to understand the combined impact of media and feeds on cell metabolism in a CHO fed-batch process. Cell growth, nutrient consumption and metabolite production rates, antibody production, and IgG quality were evaluated in detail. Concentrated feed supplements boosted cell concentrations almost threefold and antibody titers up to sevenfold. Depending on the fed-batch strategy, fourfold higher peak cell concentrations and eightfold increased IgG titers (up to 5.8 g/L) were achieved. The glycolytic flux was remarkably similar among the fed-batches; however, substantially different specific lactate production rates were observed in the different media and feed combinations. Further analysis revealed that in addition to the feed additives, the basal medium can make a considerable

  16. Polyhydroxyalkanoates production with mixed microbial cultures: from culture selection to polymer recovery in a high-rate continuous process.

    PubMed

    Villano, Marianna; Valentino, Francesco; Barbetta, Andrea; Martino, Lucrezia; Scandola, Mariastella; Majone, Mauro

    2014-06-25

    Polyhydroxyalkanoates (PHA) production with mixed microbial cultures (MMC) has been investigated by means of a sequential process involving three different stages, consisting of a lab-scale sequencing batch reactor for MMC selection, a PHA accumulation reactor and a polymer extraction reactor. All stages were performed under continuous operation for at least 4 months to check the overall process robustness as well as the related variability of polymer composition and properties. By operating both biological stages at high organic loads (8.5 and 29.1 gCOD/Ld, respectively) with a synthetic mixture of acetic and propionic acid, it was possible to continuously produce PHA at 1.43 g/Ld with stable performance (overall, the storage yield was 0.18 COD/COD). To identify the optimal operating conditions of the extraction reactor, two digestion solutions have been tested, NaOH (1m) and NaClO (5% active Cl2). The latter resulted in the best performance both in terms of yield of polymer recovery (around 100%, w/w) and purity (more than 90% of PHA content in the residual solids, on a weight basis). In spite of the stable operating conditions and performance, a large variation was observed for the HV content, ranging between 4 and 20 (%, w/w) for daily samples after accumulation and between 9 and 13 (%, w/w) for weekly average samples after extraction and lyophilization. The molecular weight of the produced polymer ranged between 3.4 × 10(5) and 5.4 × 10(5)g/mol with a large polydispersity index. By contrast, TGA and DSC analysis showed that the thermal polymer behavior did not substantially change over time, although it was strongly affected by the extraction agent used (NaClO or NaOH).

  17. Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

    NASA Astrophysics Data System (ADS)

    Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

    2014-12-01

    Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

  18. Temperature effects on microbial respiration assessed with CO2-exchange and continuous culture techniques

    NASA Astrophysics Data System (ADS)

    Lehmeier, C.; Min, K.; Song, C.; Ballantyne, F.; Billings, S. A.

    2012-12-01

    Recent work attempts to incorporate requirements of soil microorganisms for carbon and other resources, and how these requirements may respond to temperature, into theoretical concepts of soil organic matter decomposition and climate change. Because of the difficulties of measuring resource fluxes in natural soils, empirical data to guide these concepts remain scarce. Here, we present an experimental system that combines continuous culture techniques with CO2 measurements to study carbon fluxes through microbes in a reductionist, controlled environment amenable to experimental manipulation. In this pilot study, we quantified mass specific respiration rates (MSR) and δ13C of respired CO2 of Pseudomonas fluorescens, a Gram-negative bacterium common to soils, grown at 15°C and 25°C with otherwise identical environmental conditions. The microbes were grown in a 1.9 L bioreactor, in 0.9 L of nutrient medium with C:N:P atomic ratios of 100:10:3, and with 10 mM cellobiose as the carbon source. A peristaltic pump continuously supplied the bioreactor with sterile medium, and removed medium from the bioreactor, at a rate of 63 mL h-1. Both vessels were contained within a temperature incubator, and stir bars provided continuously well mixed volumes. CO2-free air was continuously bubbled through the reactor medium so to provide the microbes with O2; a cavity ring down spectrometer withdrew reactor headspace air and measured concentration and δ13C of the CO2. Air supply was regulated with a pressure/mass flow controller to approx. 27 mL min-1. In both temperature regimes, the pH of the bioreactor as well as concentration and δ13C of the CO2 in the head space air were constant over the course of 1 d, such that any imbalances in the CO2-H2CO3 equilibrium were considered negligible in the assessment of microbial respiration rates and the δ13C of respired CO2. After this time period, reactor medium was passed through a 0.22 μm filter and the filtrate dried for 24 h to obtain

  19. Systematic comparison of nutraceuticals and antioxidant potential of cultivated, in vitro cultured and commercial Melissa officinalis samples.

    PubMed

    Dias, Maria Inês; Barros, Lillian; Sousa, Maria João; Ferreira, Isabel C F R

    2012-06-01

    Melissa officinalis (lemon balm) infusions are used worldwide for digestive, analgesic and other pharmaceutical applications. Herein, the nutraceuticals production and antioxidant potential in garden cultivated, in vitro cultured and two commercial samples (bags and granulated) of lemon balm was compared. The profile of in vitro cultured lemon balm is closer of garden cultivated sample than of both commercial samples (bag or granulate). It presented the highest levels of proteins and ash, and the lowest energetic value. The most favorable n6/n3 ration, as also the highest PUFA (mostly α-linolenic acid), tocopherols (including α-, γ- and δ-isoforms) and ascorbic acid contents were also observed in this sample. Nevertheless, it was the commercial bag lemon balm that gave the highest antioxidant activity and the highest levels of phenolics and flavonoids. As far as we kwon, this is the first comparison of nutraceuticals and antioxidant potential of cultivated, in vitro cultured and commercial lemon balm samples. Moreover, it proved that in vitro culture might be used to stimulate vitamins production. PMID:22445737

  20. Systematic comparison of nutraceuticals and antioxidant potential of cultivated, in vitro cultured and commercial Melissa officinalis samples.

    PubMed

    Dias, Maria Inês; Barros, Lillian; Sousa, Maria João; Ferreira, Isabel C F R

    2012-06-01

    Melissa officinalis (lemon balm) infusions are used worldwide for digestive, analgesic and other pharmaceutical applications. Herein, the nutraceuticals production and antioxidant potential in garden cultivated, in vitro cultured and two commercial samples (bags and granulated) of lemon balm was compared. The profile of in vitro cultured lemon balm is closer of garden cultivated sample than of both commercial samples (bag or granulate). It presented the highest levels of proteins and ash, and the lowest energetic value. The most favorable n6/n3 ration, as also the highest PUFA (mostly α-linolenic acid), tocopherols (including α-, γ- and δ-isoforms) and ascorbic acid contents were also observed in this sample. Nevertheless, it was the commercial bag lemon balm that gave the highest antioxidant activity and the highest levels of phenolics and flavonoids. As far as we kwon, this is the first comparison of nutraceuticals and antioxidant potential of cultivated, in vitro cultured and commercial lemon balm samples. Moreover, it proved that in vitro culture might be used to stimulate vitamins production.

  1. Dynamic metabolic modelling of volatile fatty acids conversion to polyhydroxyalkanoates by a mixed microbial culture.

    PubMed

    Pardelha, Filipa; Albuquerque, Maria G E; Reis, Maria A M; Oliveira, Rui; Dias, João M L

    2014-06-25

    In this work, we present a dynamic metabolic model that describes the uptake of complex mixtures of volatile fatty acids (VFA) and respective conversion into PHA by mixed microbial cultures (MMC). This model builds upon a previously published flux balance analysis model [1] that identified the minimization of TCA cycle activity as the key metabolic objective to predict PHA storage fluxes and respective composition. The model was calibrated either with experimental data of PHA production from fermented sugar cane molasses or from synthetic mixtures of VFA. All PHA production experiments were performed using a MMC selected with fermented sugar cane molasses under feast and famine regimen. The model was able to capture the process dynamics denoted by an excellent fit between experimental and computed time profiles of concentrations with the regression coefficients always above 0.92. The introduced VFA uptake regulatory factor reflects the decrease of acetyl-CoA and propionyl-CoA available to TCA cycle in conformity with the hypothesis that the minimization of TCA cycle is a key metabolic objective for MMC subjected to feast and famine regimen for the maximization of PHA production.

  2. Characterization of polyhydroxyalkanoates synthesized from microbial mixed cultures and of their nanobiocomposites with bacterial cellulose nanowhiskers.

    PubMed

    Martínez-Sanz, Marta; Villano, Marianna; Oliveira, Catarina; Albuquerque, Maria G E; Majone, Mauro; Reis, Maria; Lopez-Rubio, Amparo; Lagaron, Jose M

    2014-06-25

    The present work reports on the production and characterization of polyhydroxyalkanoates (PHAs) with different valerate contents, which were synthesized from microbial mixed cultures, and the subsequent development of nanocomposites incorporating bacterial cellulose nanowhiskers (BCNW) via solution casting processing. The characterization of the pure biopolyesters showed that the properties of PHAs may be strongly modified by varying the valerate ratio in the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) copolymer, as expected. Increasing the valerate content was seen to greatly decrease the melting temperature and enthalpy of the material, as well as its rigidity and stiffness, resulting in a more ductile behaviour. Additionally, the higher valerate PHA displayed higher permeability to water and oxygen and higher moisture sensitivity. Subsequently, BCNW were incorporated into both PHA grades, achieving a high level of dispersion for a 1 wt.-% loading, whereas some agglomeration took place for 3 wt.-% BCNW. As evidenced by DSC analyses, BCNW presented a nucleating effect on the PHA matrices. BCNW also increased the thermal stability of the polymeric matrices when properly dispersed due to strong matrix-filler interactions. Barrier properties were seen to depend on relative humidity and improved at low nanofiller loadings and low relative humidity.

  3. Polyhydroxyalkanoates (PHAs) production from fermented cheese whey by using a mixed microbial culture.

    PubMed

    Colombo, Bianca; Pepè Sciarria, Tommy; Reis, Maria; Scaglia, Barbara; Adani, Fabrizio

    2016-10-01

    Two fermented cheese wheys (FCW), FCW1 composed of lactic, acetic and butyric acids in the proportion of 58/16/26 (% CODOrganic Acid (OA)) and FCW2 composed of acetic, propionic, butyric, lactic and valeric acids in the proportion of 58/19/13/6/4 (% CODOA) were used to produce polyhydroxyalkanoates (PHAs) by using a pre-selected mixed microbial culture (MMC). PHA accumulation gave for fermented FCW1 a PHA yield (Ytot) of 0.24±0.02mgCODPHAmgCODSolubleSubstrate(SS)(-1) and a total PHA production, referred to the substrate used, of 60gPHAkgcheesewheyTotalSolids(TS)(-1). For fermented FCW2 results were: PHA yield (Ytot) of 0.42±0.03mgCODPHAmgCODSS(-1) and PHA from a substrate of 70gPHAkgcheesewheyTS(-1). Qualitatively, PHAs from FCW1 was made up exclusively of 3-hydroxybutyrate (HB), while those obtained from FCW2 were composed of 40% of 3-hydroxyvalerate (HV) and 60% of HB.

  4. Polyhydroxyalkanoates (PHAs) production from fermented cheese whey by using a mixed microbial culture.

    PubMed

    Colombo, Bianca; Pepè Sciarria, Tommy; Reis, Maria; Scaglia, Barbara; Adani, Fabrizio

    2016-10-01

    Two fermented cheese wheys (FCW), FCW1 composed of lactic, acetic and butyric acids in the proportion of 58/16/26 (% CODOrganic Acid (OA)) and FCW2 composed of acetic, propionic, butyric, lactic and valeric acids in the proportion of 58/19/13/6/4 (% CODOA) were used to produce polyhydroxyalkanoates (PHAs) by using a pre-selected mixed microbial culture (MMC). PHA accumulation gave for fermented FCW1 a PHA yield (Ytot) of 0.24±0.02mgCODPHAmgCODSolubleSubstrate(SS)(-1) and a total PHA production, referred to the substrate used, of 60gPHAkgcheesewheyTotalSolids(TS)(-1). For fermented FCW2 results were: PHA yield (Ytot) of 0.42±0.03mgCODPHAmgCODSS(-1) and PHA from a substrate of 70gPHAkgcheesewheyTS(-1). Qualitatively, PHAs from FCW1 was made up exclusively of 3-hydroxybutyrate (HB), while those obtained from FCW2 were composed of 40% of 3-hydroxyvalerate (HV) and 60% of HB. PMID:27420156

  5. Cross-cultural perception of six commercial olive oils: A study with Spanish and US consumers.

    PubMed

    Vázquez-Araújo, L; Adhikari, K; Chambers, E; Chambers, D H; Carbonell-Barrachina, A A

    2015-09-01

    A cross-cultural study was conducted with Spanish and US consumers to gain an insight into the preferred characteristics of olive oils in both countries. Six commercial olive oils (four samples from Spain and two samples from the US) were analyzed by a highly trained panel (descriptive analysis) and also by two consumers' groups (100 consumers from Spain and 100 from the US). Demographic, acceptability, and Just-About-Right data were collected to study the preferences of both groups, and the relationships with descriptive data were explored to determine the drivers of like/dislike. The Spanish extra virgin olive oils and the imported US extra virgin olive oil were characterized by having bitter, pungent, and more green notes, and were preferred by the Spanish consumers. The US consumers liked the bland Spanish refined olive oil, and the Californian olive oil that was characterized by fruity, floral, and sweet notes. The results showed that the Spanish consumers were more aware about olive oil quality in general than their US counterparts, maybe because of a higher usage of the product in Spain. The present study provides essential data which might help producers in designing and promoting olive oils matching US consumers' requirements, an emerging market for this Mediterranean product. PMID:25028154

  6. Cross-cultural perception of six commercial olive oils: A study with Spanish and US consumers.

    PubMed

    Vázquez-Araújo, L; Adhikari, K; Chambers, E; Chambers, D H; Carbonell-Barrachina, A A

    2015-09-01

    A cross-cultural study was conducted with Spanish and US consumers to gain an insight into the preferred characteristics of olive oils in both countries. Six commercial olive oils (four samples from Spain and two samples from the US) were analyzed by a highly trained panel (descriptive analysis) and also by two consumers' groups (100 consumers from Spain and 100 from the US). Demographic, acceptability, and Just-About-Right data were collected to study the preferences of both groups, and the relationships with descriptive data were explored to determine the drivers of like/dislike. The Spanish extra virgin olive oils and the imported US extra virgin olive oil were characterized by having bitter, pungent, and more green notes, and were preferred by the Spanish consumers. The US consumers liked the bland Spanish refined olive oil, and the Californian olive oil that was characterized by fruity, floral, and sweet notes. The results showed that the Spanish consumers were more aware about olive oil quality in general than their US counterparts, maybe because of a higher usage of the product in Spain. The present study provides essential data which might help producers in designing and promoting olive oils matching US consumers' requirements, an emerging market for this Mediterranean product.

  7. Furry pet allergens, fungal DNA and microbial volatile organic compounds (MVOCs) in the commercial aircraft cabin environment.

    PubMed

    Fu, Xi; Lindgren, Torsten; Guo, Moran; Cai, Gui-Hong; Lundgren, Håkan; Norbäck, Dan

    2013-06-01

    There has been concern about the cabin environment in commercial aircraft. We measured cat, dog and horse allergens and fungal DNA in cabin dust and microbial volatile organic compounds (MVOCs) in cabin air. Samples were collected from two European airline companies, one with cabins having textile seats (TSC) and the other with cabins having leather seats (LSC), 9 airplanes from each company. Dust was vacuumed from seats and floors in the flight deck and different parts of the cabin. Cat (Fel d1), dog (Can f1) and horse allergens (Equ cx) were analyzed by ELISA. Five sequences of fungal DNA were analyzed by quantitative PCR. MVOCs were sampled on charcoal tubes in 42 TSC flights, and 17 compounds were analyzed by gas chromatography mass spectrometry (GC-MS) with selective ion monitoring (SIM). MVOC levels were compared with levels in homes from Nordic countries. The weight of dust was 1.8 times larger in TSC cabins as compared to LSC cabins (p < 0.001). In cabins with textile seats, the geometric mean (GM) concentrations of Fel d1, Can f1 and Equ cx were 5359 ng g(-1), 6067 ng g(-1), and 13 703 ng g(-1) (GM) respectively. Levels of Fel d1, Can f1 and Equ cx were 50 times, 27 times and 75 times higher respectively, in TSC cabins as compared to LSC cabins (p < 0.001). GM levels of Aspergillus/Penicillium DNA, Aspergillus versicolor DNA, Stachybotrys chartarum DNA and Streptomyces DNA were all higher in TSC as compared to LSC (p < 0.05). The sum of MVOCs in cabin air (excluding butanols) was 3192 ng m(-3) (GM), 3.7 times higher than in homes (p < 0.001) and 2-methyl-1-butanol and 3-methyl-1-butanol concentrations were 15-17 times higher as compared to homes (p < 0.001). Concentrations of isobutanol, 1-butanol, dimethyldisulfide, 2-hexanone, 2-heptanone, 3-octanone, isobutyl acetate and ethyl-2-methylbutyrate were lower in cabin air as compared to homes (p < 0.05). In conclusion, textile seats are much more contaminated by pet allergens and fungal DNA than leather

  8. Furry pet allergens, fungal DNA and microbial volatile organic compounds (MVOCs) in the commercial aircraft cabin environment.

    PubMed

    Fu, Xi; Lindgren, Torsten; Guo, Moran; Cai, Gui-Hong; Lundgren, Håkan; Norbäck, Dan

    2013-06-01

    There has been concern about the cabin environment in commercial aircraft. We measured cat, dog and horse allergens and fungal DNA in cabin dust and microbial volatile organic compounds (MVOCs) in cabin air. Samples were collected from two European airline companies, one with cabins having textile seats (TSC) and the other with cabins having leather seats (LSC), 9 airplanes from each company. Dust was vacuumed from seats and floors in the flight deck and different parts of the cabin. Cat (Fel d1), dog (Can f1) and horse allergens (Equ cx) were analyzed by ELISA. Five sequences of fungal DNA were analyzed by quantitative PCR. MVOCs were sampled on charcoal tubes in 42 TSC flights, and 17 compounds were analyzed by gas chromatography mass spectrometry (GC-MS) with selective ion monitoring (SIM). MVOC levels were compared with levels in homes from Nordic countries. The weight of dust was 1.8 times larger in TSC cabins as compared to LSC cabins (p < 0.001). In cabins with textile seats, the geometric mean (GM) concentrations of Fel d1, Can f1 and Equ cx were 5359 ng g(-1), 6067 ng g(-1), and 13 703 ng g(-1) (GM) respectively. Levels of Fel d1, Can f1 and Equ cx were 50 times, 27 times and 75 times higher respectively, in TSC cabins as compared to LSC cabins (p < 0.001). GM levels of Aspergillus/Penicillium DNA, Aspergillus versicolor DNA, Stachybotrys chartarum DNA and Streptomyces DNA were all higher in TSC as compared to LSC (p < 0.05). The sum of MVOCs in cabin air (excluding butanols) was 3192 ng m(-3) (GM), 3.7 times higher than in homes (p < 0.001) and 2-methyl-1-butanol and 3-methyl-1-butanol concentrations were 15-17 times higher as compared to homes (p < 0.001). Concentrations of isobutanol, 1-butanol, dimethyldisulfide, 2-hexanone, 2-heptanone, 3-octanone, isobutyl acetate and ethyl-2-methylbutyrate were lower in cabin air as compared to homes (p < 0.05). In conclusion, textile seats are much more contaminated by pet allergens and fungal DNA than leather

  9. Design of serum-free medium for suspension culture of CHO cells on the basis of general commercial media.

    PubMed

    Miki, Hideo; Takagi, Mutsumi

    2015-08-01

    The design of serum-free media for suspension culture of genetically engineered Chinese hamster ovary (CHO) cells using general commercial media as a basis was investigated. Subcultivation using a commercial serum-free medium containing insulin-like growth factor (IGF)-1 with or without FCS necessitated additives other than IGF-1 to compensate for the lack of FCS and improve cell growth. Suspension culture with media containing several combinations of growth factors suggested the effectiveness of addition of both IGF-1 and the lipid signaling molecule lysophosphatidic acid (LPA) for promoting cell growth. Subcultivation of CHO cells in suspension culture using the commercial serum-free medium EX-CELL™302, which contained an IGF-1 analog, supplemented with LPA resulted in gradually increasing specific growth rate comparable to the serum-containing medium and in almost the same high antibody production regardless of the number of generations. The culture with EX-CELL™302 supplemented with LPA in a jar fermentor with pH control at 6.9 showed an apparently higher cell growth rate than the cultures without pH control and with pH control at 6.8. The cell growth in the medium supplemented with aurintricarboxylic acid (ATA), which was much cheaper than IGF-1, in combination with LPA was synergistically promoted similarly to that in the medium supplemented with IGF-1 and LPA. In conclusion, the serum-free medium designed on the basis of general commercial media could support the growth of CHO cells and antibody production comparable to serum-containing medium in suspension culture. Moreover, the possibility of cost reduction by the substitution of IGF-1 with ATA was also shown.

  10. Aeration remediation of a polluted waterway increases near-surface coarse and culturable microbial aerosols.

    PubMed

    Dueker, M Elias; O'Mullan, Gregory D

    2014-04-15

    Aeration remediation is currently used in polluted urban waterways to increase oxygen levels in the water column. Recent studies have provided increasing evidence that the bursting of bubbles at water surfaces introduced by aeration, or other surface disturbances, can transfer viable bacteria to the air. In heavily sewage-polluted waterways these water-originated bacterial aerosols may pose as a health risk to recreators in small boats or residents inhabiting the shoreline. Nonetheless, few studies have explored aerosols above active aeration remediation projects in waterways or investigated how bacterial aerosols change with vertical distance from aeration activities. This study, conducted at the Newtown Creek superfund site in Brooklyn, NY, USA, measured coarse aerosol particles and culturable bacteria in near-surface air above waters undergoing aeration remediation. Regardless of aeration operation culturable bacterial fallout was greater near-surface (0.6m above water) than previously-reported measurements made at 2.5m. Molecular analysis of the 16S rRNA gene sequences from isolated bacteria demonstrates that water and air shared a large number of bacterial genera and that the genera present in the near-surface aerosols (0.6m) contained water-associated Vibrio and Caulobacter, which were not present at 2.5m, despite the smaller sequence library size from the near-surface. Also, the near-surface microbial assemblage had significantly greater association with sequences detected previously in aquatic environments compared to the 2.5m library. We found compelling evidence that aeration activity contributed to this vertical gradient in bacterial aerosol concentrations and identity. Similar to results from 2.5m, concentrations of near-surface respirable coarse aerosols (<10 um) increased significantly when aeration was occurring. Culturable bacterial aerosol fallout was also greater near-surface when the aerator was on compared to simultaneous measurements made at 2

  11. Culture dependent and independent genomic identification of Alicyclobacillus species in contaminated commercial fruit juices.

    PubMed

    Osopale, Babasola Adewunmi; Witthuhn, Cornelia Regina; Albertyn, Jacobus; Oguntoyinbo, Folarin Anthony

    2016-06-01

    Alicyclobacillus is a genus of thermo-acidophilic, endospore-forming, bacteria species which occasionally cause spoilage of heat-processed fruit juices by producing guaiacol taint. In this study, Alicyclobacillus contamination of commercial fruit juices in West Africa was investigated using culture-dependent and -independent approaches. Firstly, a total of 225 fruit juice products from Ghana (n = 39) and Nigeria (n = 186) were enriched with yeast-starch-glucose (YSG) broth (pH 3.7) following heat shock at 80 °C for 10 min. Alicyclobacillus was detected in 11.6% (26) of samples. Isolates were identified to the genus taxonomic level by genus-specific PCR which targeted the squalene-hopene-cyclase (shc) gene followed by analysis of the almost-complete 16S ribosomal RNA (rRNA) gene sequences that identified 16 Alicyclobacillus acidoterrestris, 7 Alicyclobacillus acidocaldarius and 3 Alicyclobacillus genomic species 1 (Alicyclobacillus sp. 1). Whole-genome fingerprinting using PCR-RAPD primers Ba-10, F-61 and F-64 grouped the 16 A. acidoterrestris isolates into two genetic clusters. Furthermore, high performance liquid chromatographic (HPLC) analyses revealed the activity of vanillic-acid decarboxylase (vdc) in all A. acidoterrestris isolates due to guaiacol production from vanillic-acid. Lastly, species-specific PCR-DGGE targeting the 16S rRNA gene clearly discriminated between the guaiacol-producing A. acidoterrestris and the non-spoilage A. acidocaldarius group. Information provided by this study is fundamental to the development of effective strategies for the improvement of quality and shelf-life of processed tropical fruit juices in W. Africa. PMID:26919814

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  13. Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches

    PubMed Central

    García-Moyano, Antonio; Austnes, Andreas Erling; Lanzén, Anders; González-Toril, Elena; Aguilera, Ángeles; Øvreås, Lise

    2015-01-01

    Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential

  14. Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches

    PubMed Central

    García-Moyano, Antonio; Austnes, Andreas Erling; Lanzén, Anders; González-Toril, Elena; Aguilera, Ángeles; Øvreås, Lise

    2015-01-01

    Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential

  15. Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches.

    PubMed

    García-Moyano, Antonio; Austnes, Andreas Erling; Lanzén, Anders; González-Toril, Elena; Aguilera, Ángeles; Øvreås, Lise

    2015-10-13

    Svalbard, situated in the high Arctic, is an important past and present coal mining area. Dozens of abandoned waste rock piles can be found in the proximity of Longyearbyen. This environment offers a unique opportunity for studying the biological control over the weathering of sulphide rocks at low temperatures. Although the extension and impact of acid mine drainage (AMD) in this area is known, the native microbial communities involved in this process are still scarcely studied and uncharacterized. Several abandoned mining areas were explored in the search for active AMD and a culture-independent approach was applied with samples from two different runoffs for the identification and quantification of the native microbial communities. The results obtained revealed two distinct microbial communities. One of the runoffs was more extreme with regards to pH and higher concentration of soluble iron and heavy metals. These conditions favored the development of algal-dominated microbial mats. Typical AMD microorganisms related to known iron-oxidizing bacteria (Acidithiobacillus ferrivorans, Acidobacteria and Actinobacteria) dominated the bacterial community although some unexpected populations related to Chloroflexi were also significant. No microbial mats were found in the second area. The geochemistry here showed less extreme drainage, most likely in direct contact with the ore under the waste pile. Large deposits of secondary minerals were found and the presence of iron stalks was revealed by microscopy analysis. Although typical AMD microorganisms were also detected here, the microbial community was dominated by other populations, some of them new to this type of system (Saccharibacteria, Gallionellaceae). These were absent or lowered in numbers the farther from the spring source and they could represent native populations involved in the oxidation of sulphide rocks within the waste rock pile. This environment appears thus as a highly interesting field of potential

  16. Rapid Culture-Independent Microbial Analysis Aboard the International Space Station (ISS)

    NASA Astrophysics Data System (ADS)

    Maule, Jake; Wainwright, Norm; Steele, Andrew; Monaco, Lisa; Morris, Heather; Gunter, Daniel; Damon, Michael; Wells, Mark

    2009-10-01

    A new culture-independent system for microbial monitoring, called the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was operated aboard the International Space Station (ISS). LOCAD-PTS was launched to the ISS aboard Space Shuttle STS-116 on December 9, 2006, and has since been used by ISS crews to monitor endotoxin on cabin surfaces. Quantitative analysis was performed within 15 minutes, and sample return to Earth was not required. Endotoxin (a marker of Gram-negative bacteria and fungi) was distributed throughout the ISS, despite previous indications that most bacteria on ISS surfaces were Gram-positive. Endotoxin was detected at 24 out of 42 surface areas tested and at every surface site where colony-forming units (cfu) were observed, even at levels of 4-120 bacterial cfu per 100 cm2, which is below NASA in-flight requirements (<10,000 bacterial cfu per 100 cm2). Absent to low levels of endotoxin (<0.24 to 1.0 EU per 100 cm2; defined in endotoxin units, or EU) were found on 31 surface areas, including on most panels in Node 1 and the US Lab. High to moderate levels (1.01 to 14.7 EU per 100 cm2) were found on 11 surface areas, including at exercise, hygiene, sleeping, and dining facilities. Endotoxin was absent from airlock surfaces, except the Extravehicular Hatch Handle (>3.78 EU per 100 cm2). Based upon data collected from the ISS so far, new culture-independent requirements (defined in EU) are suggested, which are verifiable in flight with LOCAD-PTS yet high enough to avoid false alarms. The suggested requirements are intended to supplement current ISS requirements (defined in cfu) and would serve a dual purpose of safeguarding crew health (internal spacecraft surfaces <20 EU per 100 cm2) and monitoring forward contamination during Constellation missions (surfaces periodically exposed to the external environment, including the airlock and space suits, <0.24 EU per 100 cm2).

  17. Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Eder, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; Cady, Sherry L.; DesMarais, David J.; Hope, Janet M.; Summons, Roger E.

    2001-01-01

    Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarker and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber, Thermocrinis sp. HI, Hydrogenobacter thermophilus, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyl moieties. The fatty acids of all cultured organisms were dominated by very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as C-18:0 monoethers with the exception of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known "pink-streamer community" (PSC), siliceous filaments of a microbial consortia growing in the outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono- and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic. Additional information is contained in the original extended abstract.

  18. Culture-independent characterization of a novel microbial community at a hydrothermal vent at Brothers volcano, Kermadec arc, New Zealand

    NASA Astrophysics Data System (ADS)

    Stott, M. B.; Saito, J. A.; Crowe, M. A.; Dunfield, P. F.; Hou, S.; Nakasone, E.; Daughney, C. J.; Smirnova, A. V.; Mountain, B. W.; Takai, K.; Alam, M.

    2008-08-01

    The bacterial and archaeal diversity of a hydrothermal vent microbial community at Brothers volcano situated in the Kermadec arc, ˜400 km off the north coast of New Zealand, was examined using culture-independent molecular analysis. An unusual microbial community was detected with only 1% and 40% of the bacterial phylotypes exhibiting >92% small subunit (SSU) rRNA gene sequence similarity with cultivated and noncultivated microbes, respectively. Of the 29 bacterial representative phylotypes, over one third of the SSU rRNA gene sequences retrieved belonged to uncultivated candidate divisions including OP1, OP3, OP5, OP8, OD1, and OP11. All archaeal phylotypes belonged to the phylum Euryarchaeota in the uncultivated groups deep hydrothermal vent euryarchaeotal (DHVE) I and II or to the phylum Korarchaeota. Like the bacterial clone library, only a small proportion of archaeal SSU rRNA gene sequences (˜2% and 20%) displayed >92% sequence identity with any archaeal isolates or noncultivated microbes, respectively. Although the bacterial phylotypes detected were phylogenetically most similar to microbial communities detected in methane, hydrocarbon, and carbon dioxide-based hydrothermal and seep environments, no phylotypes directly associated with anaerobic methane oxidation and mcrA activity could be detected. The geochemical composition of the vent fluids at the Brothers-lower cone sample site is unusual and we suggest that it may play a prominent role in the species selection of this microbial community.

  19. Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

    PubMed Central

    Koskey, Amber M.; Fisher, Jenny C.; Traudt, Mary F.; Newton, Ryan J.

    2014-01-01

    Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB. Enterococcaceae and Enterobacteriaceae were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed Catellicoccus marimammalium as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcus indoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as Enterococcus spp., 1.2% were identified as Streptococcus spp., and none were identified as C. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of C. marimammalium 16S rRNA gene sequences (>50-fold) relative to typical mEI culturable Enterococcus spp. C. marimammalium therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment. PMID:24242244

  20. Microbial succession in response to pollutants in batch-enrichment culture.

    PubMed

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  1. Microbial succession in response to pollutants in batch-enrichment culture

    PubMed Central

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  2. Microbial Mediation of Dolomite Precipitation in Natural Environments, Culture Experiments and Molecular Studies

    NASA Astrophysics Data System (ADS)

    Meister, P.; Nealson, K.; McKenzie, J. A.; Warthmann, R.; Vasconcelos, C.

    2005-12-01

    Although dolomite [CaMg(CO3)2] is a common carbonate mineral in sedimentary rocks, it is rarely observed forming in modern environments, and, until recently, experimental precipitation under Earth surface conditions proved impossible. With the discovery of microbial mediated dolomite formation in culture experiments with sulfate-reducing bacteria, it has become apparent that microbes play an important role in overcoming the kinetic barrier of mineral precipitation and, thus, may represent a key factor controlling early diagenetic processes throughout Earth history. The detailed mechanisms of these processes, however, remain poorly understood. Recent studies of dolomite layers in organic carbon-rich hemipelagic sediments recovered on the Peru margin during Ocean Drilling Program Leg 201 (Meister et al., in prep.) indicate precipitation at the interface between the sulphate reduction and methanogenic zones. At this chemical front, alkalinity is strongly increased, sulphate ions, a possible inhibitor of dolomite precipitation, are efficiently removed, and highest total cell densities were counted (up to 10 to the 9 cells / cm3; Shipboard Scientific Party, 2003). These results strengthen the model that microbes are involved in dolomite formation, providing the appropriate chemical conditions, whereas the high cell density may kinetically control the strictly focused precipitation process. We are currently conducting a systematic study of the precipitation of dolomite and other carbonate minerals in the Ca-Mg-bicarbonate-system. In preliminary experiments under aerobic conditions we used agar plates with a marine medium to grow a bacterium isolated from sediments of the San Pedro basin (California), an upwelling area similar to the Peru margin. We observed that the crystals formed only inside of the colonies and showed a dumbbell-shaped morphology similar to dolomite produced in anaerobic experiments. X-ray diffraction patterns revealed, however, that the product was

  3. Detection of periodontopathogenic bacteria in pregnant women by traditional anaerobic culture method and by a commercial molecular genetic method.

    PubMed

    Urbán, Edit; Terhes, Gabriella; Radnai, Márta; Gorzó, István; Nagy, Elisabeth

    2010-06-01

    To culture facultative and strict anaerobic bacteria is a well-established method for analyzing subgingival plaque samples. Micro-IDent and micro-IDent Plus (HAIN Lifescience GmbH, Nehren, Germany) tests are two commercially available rapid PCR-based methods for the identification and quantification of putative periodontopathogen bacteria. In this study, we compared these commercial PCR-based hybridization methods with conventional anaerobic culture technique. A total of 36 subgingival plaque samples were collected from periodontal pockets of pregnant women with chronic localized periodontitis. Aliquots of these samples were evaluated with species-specific probes provided by micro-IDent and micro-IDent Plus tests simultaneously, and from the same samples anaerobic and capnophylic bacteria were cultured on selective media. The overall agreement between both methods was excellent for Eubacterium nodatum, Tannerella forsythia and Porphyromonas gingivalis (97-92%), fair for Capnocytophaga sp, Eikenella corrodens, Actinobacillus actinomycetemcomitans, and Prevotella intermedia (91-89%) and poor for Fusobacterium nucleatum, Parvimonas micra (Micromonas micros), and Campylobacter rectus (86-78%). Discrepancies in the results may be explained by inability of culture method to distinguish between closely related taxa (e.i P. intermedia/Prevotella. nigrescens), and problems of keeping periodontopathogen bacteria viable, which is required for successful detection by standard culture method. Nucleic acid-based methods may replace cultivation method as frequently used methods in microbiological diagnosis of progressive periodontitis, thus micro-IDent and micro-IDent Plus tests can be recommended where culture of periodontopathogenic bacteria is not performed in routine microbiology laboratories to analyze subgingival plaque samples.

  4. A novel approach to recycle bacterial culture waste for fermentation reuse via a microbial fuel cell-membrane bioreactor system.

    PubMed

    Li, Jian; Zhu, Yuan; Zhuang, Liangpeng; Otsuka, Yuichiro; Nakamura, Masaya; Goodell, Barry; Sonoki, Tomonori; He, Zhen

    2015-09-01

    Biochemical production processes require water and nutrient resources for culture media preparation, but aqueous waste is generated after the target products are extracted. In this study, culture waste (including cells) produced from a lab-scale fermenter was fed into a microbial fuel cell-membrane bioreactor (MFC-MBR) system. Electrical energy was generated via the interaction between the microbial consortia and the solid electrode in the MFC. The treated wastewater was reclaimed in this process which was reused as a solvent and a nutrient source in subsequent fermentation. Polarization testing showed that the MFC produced a maximum current density of 37.53 A m(-3) with a maximum power density of 5.49 W m(-3). The MFC was able to generate 0.04 kWh of energy per cubic meter of culture waste treated. The lab-scale fermenters containing pure cultures of an engineered Pseudomonas spp. were used to generate 2-pyrone-4,6-dicarboxylic acid (PDC), a high value platform chemical. When the MFC-MBR-treated wastewater was used for the fermenter culture medium, a specific bacterial growth rate of 1.00 ± 0.05 h(-1) was obtained with a PDC production rate of 708.11 ± 64.70 mg PDC L(-1) h(-1). Comparable values for controls using pure water were 0.95 ± 0.06 h(-1) and 621.01 ± 22.09 mg PDC L(-1) h(-1) (P > 0.05), respectively. The results provide insight on a new approach for more sustainable bio-material production while at the same time generating energy, and suggest that the treated wastewater can be used as a solvent and a nutrient source for the fermentation production of high value platform chemicals.

  5. The DOE subsurface microbial culture collection at Florida State University. Interim technical report, 15 August 1993--15 March 1994

    SciTech Connect

    Balkwill, D.L.

    1994-03-15

    This research is a renewal of a project to support research in the Deep Microbiology Subprogram of the Subsurface Science Program, by maintaining a culture collection of microorganisms isolated from subsurface environments (SMCC). Approximately 2,400 new subsurface microbial isolates were incorporated into the SMCC during the period August 15, 1993 to March 15, 1994. Colony morphological characteristics were determined for each of the 2,400 newly incorporated strains. Cell morphological characteristics were determined for 1,100 of the new isolates, and 21 selected physiological traits were determined for 2,200 of the new isolates.

  6. Impact of lactate on growth of cultures of cecal bacteria from commercial broilers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultures of beneficial bacteria used in probiotics produce and utilize organic acids that may play a role in the ability of the cultures to inhibit colonization of poultry by enteropathogens. Cecal contents of adult poultry contain many of these beneficial bacteria, and earlier experiments showed th...

  7. Microbial communities in the garbage composting with rice hull as an amendment revealed by culture-dependent and -independent approaches.

    PubMed

    Takaku, Hiroaki; Kodaira, Shoko; Kimoto, Ayumi; Nashimoto, Masayuki; Takagi, Masamichi

    2006-01-01

    The diversity and succession of microbial communities during the garbage composting with rice hull as an amendment were studied by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal primers. Based on temperature changes, the composting process could be divided into thermophilic, cooling-down, and maturing stages. The DGGE profiles and clone library analysis revealed that the microbial community drastically changed during the composting process from the thermophilic to the maturing stages. The dominant bacterial group changed from the phylum Firmicutes in the thermophilic stage to the phylum Bacteroidetes in the maturing stage. This change in microbial communities may be significant for the composting process. The diversity of cultivated bacteria isolated from samples taken at various stages of the composting process was low. A total of 87 isolates were classified as belonging to only four different groups. These groups were also detected in the DGGE profiles and by the clone library analysis. Our study indicated that a combination of culture-dependent and -independent approaches could be very useful for monitoring both bacterial diversity and the succession of communities during the composting process. This study would be beneficial for assessing the ecological consequences of disposal of organic waste.

  8. Compound-specific Isotope Analysis of Cyanobacterial Pure cultures and Microbial Mats: Effects of Photorespiration?

    NASA Technical Reports Server (NTRS)

    Jahnke, L. L.; Summons, R. E.

    2006-01-01

    Microbial mats are considered modern homologs of Precambrian stromatolites. The carbon isotopic compositions of organic matter and biomarker lipids provide clues to the depositional environments of ancient mat ecosystems. As the source of primary carbon fixation for over two billion years, an understanding of cyanobacterial lipid biosynthesis, associated isotopic discriminations, and the influence of physiological factors on growth and isotope expression is essential to help us compare modern microbial ecosystems to their ancient counterparts. Here, we report on the effects of photorespiration (PR) on the isotopic composition of cyanobacteria and biomarker lipids, and on potential PR effects associated with the composition of various microbial mats. The high light, high O2 and limiting CO2 conditions often present at the surface of microbial mats are known to support PR in cyanobacteria. The oxygenase function of ribulose bisphosphate carboxylase/oxygenase can result in photoexcretion of glycolate and subsequent degration by heterotrophic bacteria. We have found evidence which supports an isotopic depletion (increased apparent E) scaled to O2 level associated with growth of Phormidium luridum at low CO2 concentrations (less than 0.04%). Similar to previous studies, isotopic differences between biomass and lipid biomarkers, and between lipid classes were positively correlated with overall fractionation, and should provide a means of estimating the influence of PR on overall isotopic composition of microbial mats. Several examples of microbial mats growing in the hydrothermal waters of Yellowstone National Park and the hypersaline marine evaporation ponds at Guerrero Negro, Baja Sur Mexico will be compared with a view to PR as a possible explanation of the relatively heavy C-isotope composition of hypersaline mats.

  9. Assessment of the effects of cinnamon leaf oil on rumen microbial fermentation using two continuous culture systems.

    PubMed

    Fraser, G R; Chaves, A V; Wang, Y; McAllister, T A; Beauchemin, K A; Benchaar, C

    2007-05-01

    Two continuous culture (CC) systems, the rumen simulation technique (Rusitec) and a dual-flow (DF) fermenter, were used to evaluate effects of the essential oil from cinnamon leaf (CIN) on rumen microbial fermentation. Incubations (d 1 through 8 for adaptation and d 9 through 16 for sampling) were conducted concurrently in the 2 systems, with CIN added at 0 (control) and 500 mg/L of rumen fluid culture. Eight Rusitec (920 mL; dilution rate = 2.9%/h) and 6 DF (1,300 mL; dilution rate = 6.3%/h) fermenters were randomly assigned to treatment. Inoculum was prepared from 4 ruminally cannulated lactating Holstein cows fed a total mixed ration consisting of 51% forage and 49% concentrate (dry matter basis). Ruminal pH, total volatile fatty acid (VFA) concentration, and diet digestibility were reduced by CIN addition in the Rusitec but were not affected by CIN administration in the DF. The addition of CIN in the Rusitec decreased apparent N disappearance, NH3-N concentration, and molar proportions of branched-chain VFA. In contrast, in the DF no effect of CIN was observed on apparent N degradation, NH3-N concentration, and molar proportion of branched-chain VFA. In the Rusitec, the molar proportion of acetate was similar between treatments on d 9 and 13, but was lower from d 10 to 12 and higher on d 14 to 16 with CIN than with control (interaction of treatment x sampling day). The molar proportion of acetate remained unaffected by CIN addition in the DF. In both CC systems, the molar proportion of propionate was decreased whereas that of butyrate was increased by CIN addition. In the DF, CIN decreased microbial N flow and efficiency of microbial protein synthesis. Protozoa numbers were lower with CIN than with control in both CC fermenters. In the Rusitec, CIN increased 15N enrichment in total bacterial fractions, but no effect was observed on the production of microbial N. This study showed that CIN exhibited antimicrobial activity in both CC systems, but the effects were

  10. The potential of a polyphasic PCR-dGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo Mozzarella cheese production: bias of culture-dependent and culture-independent analyses.

    PubMed

    Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S

    2001-12-01

    A polyphasic PCR-DGGE approach was used to describe the microbial population occurring in natural whey cultures (NWCs) for water-buffalo Mozzarella cheese production. Total microbial community was assessed without cultivation by analyzing DNA directly extracted from the original samples of NWC. In addition, DNA extracted from bulks of cells formed by harvesting colonies from the serial dilution agar plates of a variety of culture media was used to profile the "cultivable" community. The 16S rDNA V3 region was amplified using DNA from NWC as well as DNA from bulks as templates and the amplicons were separated by DGGE. The microbial entities occurring in NWCs were identified by partial 16S rDNA sequencing of DGGE bands: four lactic acid bacteria (LAB) closest relative of Streptococcus thermophilus, Lactococcus lactis, Lactobacillus delbrueckii and Lactobacillus crispatus were revealed by the analysis of DNA directly extracted from NWC while two other LAB, Lactobacillus fermentum and Enterococcus faecalis, were identified by analyzing DNA from the cultivable community. The developed PCR-DGGE analysis of the "cultivable" community showed good potential in evaluating microbial diversity of a dairy environment: it usefully highlighted the bias introduced by selective amplification when compared to the analysis of the total community from NWC and allowed suitability of media and growth conditions to be evaluated. Moreover, it could be used to complete the culture independent study of microbial diversity to give information on concentration ratios among species occurring in a particular environment and can be proposed for rapid identification of dominant microorganisms in alternative to traditional tools.

  11. Microbial characterization of anode-respiring bacteria within biofilms developed from cultures previously enriched in dissimilatory metal-reducing bacteria.

    PubMed

    Pierra, Mélanie; Carmona-Martínez, Alessandro A; Trably, Eric; Godon, Jean-Jacques; Bernet, Nicolas

    2015-11-01

    This work evaluated the use of a culture enriched in DMRB as a strategy to enrich ARB on anodes. DMRB were enriched with Fe(III) as final electron acceptor and then transferred to a potentiostatically-controlled system with an anode as sole final electron acceptor. Three successive iron-enrichment cultures were carried out. The first step of enrichment revealed a successful selection of the high current-producing ARB Geoalkalibacter subterraneus. After few successive enrichment steps, the microbial community analysis in electroactive biofilms showed a significant divergence with an impact on the biofilm electroactivity. Enrichment of ARB in electroactive biofilms through the pre-selection of DMRB should therefore be carefully considered.

  12. Novel technique for scaling up of micropropagated Ruta graveolens shoots using liquid culture systems: a step towards commercialization.

    PubMed

    Diwan, Renuka; Malpathak, Nutan

    2008-06-01

    Wide applications of Ruta graveolens L. in pharmaceutical industry has led to increased interest in large-scale plant production, with emphasis on use of in vitro cultures. Earlier reports describe use of in vitro germinated seedlings for raising shoot cultures and not regeneration. There is only a single regeneration protocol of R. graveolens; however, it employs conventional labour intensive techniques deterring automation. The aim of present investigation was to establish a cost effective protocol for large-scale plant production. We report for the first time a one-step protocol with improved regeneration efficiency for multiple shoots induction employing liquid culture systems. Effect of polyamines (putrescine and spermine) on growth and furanocoumarin was studied. Addition of spermine enhanced the number of multiple shoots formed (2.5-fold) and reduced the time taken by half. Spermine addition resulted in 1.47-fold in furanocoumarin production. The selected shoot line, RS2 was successfully scaled up to 5L in culture vessels, with 1.53-fold increase in biomass without affecting the productivity of these cultures. This proves to be a commercially feasible alternative to bioreactors for large-scale biomass and furanocoumarin production.

  13. Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Edger, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; DesMarais, David J.; Cady, Sherry; Hope, Janet M.; Summons, Roger E.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarkers and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber. "Thermocrinis sp. HI", Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyls. The fatty acids of all cultured organisms were dominated by a very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as CIS() monoethers with the expection of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known 'pink-streamers community' (PSC), siliceous filaments of a microbial consortia growing in the upper outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic Aquificales n-C-20:1 and cy-C-21, and in addition, a series of iso-branched fatty acids from i-C-15:0 to i-C-21:0, With i-C-17:0 dominant in the PSC and i-C-19:0 in the biofilm, suggesting the presence of two major bacterial groups. Bacteriohopanepolyols were absent and the minute quantities of archaeol detected showed that Archaea were only minor constituents. Carbon isotopic compositions of the PSC yielded information about community structure and likely physiology. Biomass was C-13-depleted (10.9%) relative to available

  14. Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure.

    PubMed

    Hanson, Andrea J; Guho, Nicholas M; Paszczynski, Andrzej J; Coats, Erik R

    2016-09-01

    Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures (MMCs). To maximize PHA production, MMCs are enriched for bacteria with a high polymer storage capacity through the application of aerobic dynamic feeding (ADF) in a sequencing batch reactor (SBR), which consequently induces a feast-famine metabolic response. Though the feast-famine response is generally understood empirically at a macro-level, the molecular level is less refined. The objective of this study was to investigate the microbial community composition and proteome profile of an enriched MMC cultivated on fermented dairy manure. The enriched MMC exhibited a feast-famine response and was capable of producing up to 40 % (wt. basis) PHA in a fed-batch reactor. High-throughput 16S rRNA gene sequencing revealed a microbial community dominated by Meganema, a known PHA-producing genus not often observed in high abundance in enrichment SBRs. The application of the proteomic methods two-dimensional electrophoresis and LC-MS/MS revealed PHA synthesis, energy generation, and protein synthesis prominently occurring during the feast phase, corroborating bulk solution variable observations and theoretical expectations. During the famine phase, nutrient transport, acyl-CoA metabolism, additional energy generation, and housekeeping functions were more pronounced, informing previously under-determined MMC functionality under famine conditions. During fed-batch PHA production, acetyl-CoA acetyltransferase and PHA granule-bound phasin proteins were in increased abundance relative to the SBR, supporting the higher PHA content observed. Collectively, the results provide unique microbial community structural and functional insight into feast-famine PHA production from waste feedstocks using MMCs. PMID:27147532

  15. Microbial Ecophysiology of Whey Biomethanation: Comparison of Carbon Transformation Parameters, Species Composition, and Starter Culture Performance in Continuous Culture

    PubMed Central

    Chartrain, M.; Bhatnagar, L.; Zeikus, J. G.

    1987-01-01

    Changes in lactose concentration and feed rate altered bacterial growth and population levels in a whey-processing chemostat. The bacterial population and methane production levels increased in relation to increased lactose concentrations comparable to those in raw whey (6%) and converted over 96% of the substrate to methane, carbon dioxide, and cells. Sequential increases in the chemostat dilution rate demonstrated excellent biomethanation performance at retention times as low as 25 h. Retention times shorter than 25 h caused prevalent bacterial populations and methane production to decrease, and intermediary carbon metabolites accumulated in the following order: acetate, butyrate, propionate, lactate, ethanol, and lactose. Bacterial species dominated in the chemostat as a function of their enhanced substrate uptake and growth kinetic properties. The substrate uptake kinetic properties displayed by the mixed chemostat population were equivalent to those of individual species measured in pure culture, whereas the growth kinetic properties of species in mixed culture were better than those measured in pure culture. A designed starter culture consisting of Leuconostoc mesenteroides, Desulfovibrio vulgaris, Methanosarcina barkeri, and Methanobacterium formicicum displayed biomethanation performance, which was similar to that of a diverse adapted mixed-culture inoculum, in a continuous contact digestor system to which 10 g of dry whey per liter was added. Preserved starter cultures were developed and used as inocula for the start-up of a continuous anaerobic digestion process that was effective for biomethanation of raw whey at a retention time of 100 h. Images PMID:16347341

  16. mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species.

    PubMed

    Brzostowicz, Patricia C; Walters, Dana M; Thomas, Stuart M; Nagarajan, Vasantha; Rouvière, Pierre E

    2003-01-01

    mRNA differential display has been used to identify cyclohexanone oxidation genes in a mixed microbial community derived from a wastewater bioreactor. Thirteen DNA fragments randomly amplified from the total RNA of an enrichment subculture exposed to cyclohexanone corresponded to genes predicted to be involved in the degradation of cyclohexanone. Nine of these DNA fragments are part of genes encoding three distinct Baeyer-Villiger cyclohexanone monooxygenases from three different bacterial species present in the enrichment culture. In Arthrobacter sp. strain BP2 and Rhodococcus sp. strain Phi2, the monooxygenase is part of a gene cluster that includes all the genes required for the degradation of cyclohexanone, while in Rhodococcus sp. strain Phi1 the genes surrounding the monooxygenase are not predicted to be involved in this degradation pathway but rather seem to belong to a biosynthetic pathway. Furthermore, in the case of Arthrobacter strain BP2, three other genes flanking the monooxygenase were identified by differential display, demonstrating that the repeated sampling of bacterial operons shown earlier for a pure culture (D. M. Walters, R. Russ, H. Knackmuss, and P. E. Rouvière, Gene 273:305-315, 2001) is also possible for microbial communities. The activity of the three cyclohexanone monooxygenases was confirmed and characterized following their expression in Escherichia coli.

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

    PubMed

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

    2016-03-01

    The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it has many limitations that include uneven matrix coverage and limitation in the types of matrices that could be employed in studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over where matrix is applied, and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces. PMID:26729451

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  19. Automated analysis of food-borne pathogens using a novel microbial cell culture, sensing and classification system.

    PubMed

    Xiang, Kun; Li, Yinglei; Ford, William; Land, Walker; Schaffer, J David; Congdon, Robert; Zhang, Jing; Sadik, Omowunmi

    2016-02-21

    We hereby report the design and implementation of an Autonomous Microbial Cell Culture and Classification (AMC(3)) system for rapid detection of food pathogens. Traditional food testing methods require multistep procedures and long incubation period, and are thus prone to human error. AMC(3) introduces a "one click approach" to the detection and classification of pathogenic bacteria. Once the cultured materials are prepared, all operations are automatic. AMC(3) is an integrated sensor array platform in a microbial fuel cell system composed of a multi-potentiostat, an automated data collection system (Python program, Yocto Maxi-coupler electromechanical relay module) and a powerful classification program. The classification scheme consists of Probabilistic Neural Network (PNN), Support Vector Machines (SVM) and General Regression Neural Network (GRNN) oracle-based system. Differential Pulse Voltammetry (DPV) is performed on standard samples or unknown samples. Then, using preset feature extractions and quality control, accepted data are analyzed by the intelligent classification system. In a typical use, thirty-two extracted features were analyzed to correctly classify the following pathogens: Escherichia coli ATCC#25922, Escherichia coli ATCC#11775, and Staphylococcus epidermidis ATCC#12228. 85.4% accuracy range was recorded for unknown samples, and within a shorter time period than the industry standard of 24 hours. PMID:26818563

  20. Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weaning and transport stress can have a negative impact on the piglet's immune system and intestinal microbiota. The objective of this study was to determine the influence of a yeast product on innate immunity and microbial ecology of the gastrointestinal tract following stress of weaning and trans...

  1. Prescreening bacterial colonies for bioactive molecules with Janus plates, a SBS standard double-faced microbial culturing system.

    PubMed

    Sánchez-Hidalgo, Marina; Pascual, Javier; de la Cruz, Mercedes; Martín, Jesús; Kath, Gary S; Sigmund, Janet M; Masurekar, Prakash; Vicente, Francisca; Genilloud, Olga; Bills, Gerald F

    2012-08-01

    Despite the availability of many culture-based antibiotic screening methods, the lack of sensitive automated methods to identify functional molecules directly from microbial cells still limits the search for new biologically active compounds. The effectiveness of antibiotic detection is influenced by the solubility of the assayed compounds, indicator strain sensitivity, culture media and assay configuration. We describe a qualitative high throughput screening system for detecting cell-perturbing molecules from bacterial colonies employing two opposed agar layers sequentially formed in prototype Society for Biomolecular Screening (SBS) plates, named Janus plates. Direct assay of microbial colonies against target organisms in opposed agar layers overcomes some of the limitations of agar overlay methods. The system enables the rapid detection of extracellular cell-perturbing molecules, e.g., antibiotics, excreted directly from environmental isolates. The source bacterial colonies remain separate from the target organism. The growth layer is prepared and grown independently, so environmental strains can be grown for longer intervals, at temperatures and in media that favor their growth and metabolite expression, while the assay layer with pathogens, usually requiring nutrient-rich medium and elevated temperatures, are added later. Colonies to be tested can be precisely arrayed on the first agar surface, thus avoiding dispersion and disturbance of potential antibiotic-producing colonies by overlaying agar with the target strain. The rectangular SBS configuration facilitates factorial replication of dense microbial colony arrays for testing with multiple assays and assay conditions employing robotic colony pickers and pin tools. Opposed agar layers only slightly reduced the effectiveness for detecting growth inhibition from pure antibiotics compared to single-layer agar diffusion assays. The Janus plate enabled an automation-assisted workflow where a lone operator can

  2. Characteristics of miniature Cheddar-type cheese made by microbial rennet from Bacillus amyloliquefaciens: a comparison with commercial calf rennet.

    PubMed

    An, Zhigang; He, Xiaoling; Gao, Weidong; Zhao, Wei; Zhang, Weibing

    2014-02-01

    Miniature Cheddar-type cheeses were produced using microbial rennet from Bacillus amyloliquefaciens (milk-clotting enzyme [MCE]) or calf rennet (CAR). With the exception of pH, there were no significant differences in gross composition between MCE-cheese (MCE-C) and CAR-cheese (CAR-C). The pH value of CAR-C was significantly higher than that of MCE-C at 40 and 60 d of ripening. The total nitrogen content of the pH 4.6-soluble fraction obtained from MCE-C was higher than that obtained from CAR-C. However, nitrogen content of the 12% TCA-soluble fraction was similar between CAR-C and MCE-C. The extent of α(s1)-casein and β-casein hydrolysis, measured by urea-PAGE, was similar in both cheese samples. The hydrolysis of β-casein was lower than that of α(s1)-casein. Different reverse phase-high-performance liquid chromatography peptide profiles of ethanol-soluble and ethanol-insoluble fractions were obtained from CAR-C and MCE-C. The peptide content in the 2 cheese samples increased throughout ripening; the ratio of hydrophobic to hydrophilic peptides was lower in MCE-C than in CAR-C. Compared with CAR-C, MCE-C was softer as a result of higher protein hydrolysis. Microbial rennet from B. amyloliquefaciens contributed to higher proteolytic rates, which reduced ripening time. PMID:24446932

  3. A Cross-Cultural Study of Implicatures in Brazilian TV Commercials.

    ERIC Educational Resources Information Center

    Silva, Rosangela Souto

    A study investigated the extent to which native speakers (NSs) and non-native speakers (NNSs) of Portuguese understand implicatures in Brazilian television commercials in Portuguese. Subjects were nine Brazilian graduate students and 11 American students of Portuguese at the University of Illinois at Urbana/Champaign. Correct inference of the…

  4. Changes in microbial contamination levels of porcine carcasses and fresh pork in slaughterhouses, processing lines, retail outlets, and local markets by commercial distribution.

    PubMed

    Choi, Y M; Park, H J; Jang, H I; Kim, S A; Imm, J Y; Hwang, I G; Rhee, M S

    2013-06-01

    The objective of this study was to evaluate the changes in microbial contamination levels of each porcine carcass and fresh pork in a general distribution process. A total of 100 commercial pigs were sampled (six sampling sites per individual, total 600 samples) at four sequential stages: slaughterhouse (after carcass grading and boning), processing line, retail outlet, and local market. No significant differences were observed in the contaminant percentages among sampling sites and sample collection years (P>0.05) with the exception of Bacillus cereus. The contaminant percentage of B. cereus at 1st collection year was higher than these of 2nd collection year (28.31% vs. 12.26%, P<0.05). B. cereus and Listeria monocytogenes were the most frequently detected pathogenic bacteria in the slaughterhouse and markets, respectively. On the other hand, Escherichia coli O157:H7 and Yersinia enterocolitica were not detected in carcasses or pork collected from any carcass sites and pork samples. However, the frequency of pathogenic bacteria in end-products at local markets was not highly related to the initial contamination of porcine carcasses in the slaughterhouse. Thus, the improvement of microbial safety for pork end-products requires hygienic control of porcine carcasses and meat cutting during all operations in the slaughterhouse, processing line, retail outlet, and local market.

  5. A simple and cost effective liquid culture system for the micropropagation of two commercially important apple rootstocks.

    PubMed

    Mehta, Mohina; Ram, Raja; Bhattacharya, Amita

    2014-07-01

    The two commercially important apple rootstocks i.e., MM106 and B9 were micropropagated using a liquid culture system. Three different strengths of 0.8% agar solidified PGR free basal MS medium were first tested to optimize the culture media for both the rootstocks. Full strength medium (MS0) supported maximum in vitro growth, multiplication, rooting and survival under field conditions as opposed to quarter and half strength media. When three different volumes of liquid MS0 were tested, highest in vitro growth, multiplication, rooting and also survival under field conditions were achieved in 20 mL liquid MS0. The cost of one litre of liquid medium was also reduced by 8 times to Rs. 6.29 as compared to solid medium. The cost of 20 mL medium was further reduced to Rs. 0.125.

  6. Comparison of two commercially available rapid detection methods and a conventional culture method to detect naturally occurring salmonellae on broiler carcasses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many different screening devices and sampling methods have been used to detect the presence of naturally occurring Salmonella on commercially processed broiler carcasses. The objective of this study was to compare two commercial screening systems (BAX® and Roka®) to a standard cultural procedure use...

  7. Aeroponics for the culture of organisms, tissues and cells.

    PubMed

    Weathers, P J; Zobel, R W

    1992-01-01

    Characteristics of aeroponics are discussed. Contrast is made, where appropriate, with hydroponics and aero-hydroponics as applies to research and commercial applications of nutrient mist technology. Topics include whole plants, plant tissue cultures, cell and microbial cultures, and animal tissue cultures with regard to operational considerations (moisture, temperature, minerals, gaseous atmosphere) and design of apparati. PMID:14540802

  8. Evaluating standard operating procedures to mitigate off-flavor from Atlantic salmon Salmo salar cultured in a semi-commercial scale recirculating aquaculture system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fish cultured within water recirculating aquaculture systems (RAS) can acquire “earthy” or “musty” off-flavors due to bioaccumulation of the compounds geosmin and 2-methylisoborneol (MIB), respectively, which are produced by certain bacterial species present in RAS biosolids and microbial biofilms. ...

  9. Conversion of methane-derived carbon and microbial community in enrichment cultures in response to O2 availability.

    PubMed

    Wei, Xiao-Meng; He, Ruo; Chen, Min; Su, Yao; Ma, Ruo-Chan

    2016-04-01

    Methanotrophs not only play an important role in mitigating CH4 emissions from the environment, but also provide a large quantity of CH4-derived carbon to their habitats. In this study, the distribution of CH4-derived carbon and microbial community was investigated in a consortium enriched at three O2 tensions, i.e., the initial O2 concentrations of 2.5 % (LO-2), 5 % (LO-1), and 21 % (v/v) (HO). The results showed that compared with the O2-limiting environments (2.5 and 5 %), more CH4-derived carbon was converted into CO2 and biomass under the O2 sufficient condition (21 %). Besides biomass and CO2, a high conversion efficiency of CH4-derived carbon to dissolved organic carbon was detected in the cultures, especially in LO-2. Quantitative PCR and Miseq sequencing both showed that the abundance of methanotroph increased with the increasing O2 concentrations. Type II methanotroph Methylocystis dominated in the enrichment cultures, accounting for 54.8, 48.1, and 36.9 % of the total bacterial 16S rRNA gene sequencing reads in HO, LO-1, and LO-2, respectively. Methylotrophs, mainly including Methylophilus, Methylovorus, Hyphomicrobium, and Methylobacillus, were also abundant in the cultures. Compared with the O2 sufficient condition (21 %), higher microbial biodiversity (i.e., higher Simpson and lower Shannon indexes) was detected in LO-2 enriched at the initial O2 concentration of 2.5 %. These findings indicated that compared with the O2 sufficient condition, more CH4-derived carbon was exuded into the environments and promoted the growth of non-methanotrophic microbes in O2-limiting environments. PMID:26728286

  10. Radioisotopic, Culture-Based, and Oligonucleotide Microchip Analyses of Thermophilic Microbial Communities in a Continental High-Temperature Petroleum Reservoir†

    PubMed Central

    Bonch-Osmolovskaya, Elizaveta A.; Miroshnichenko, Margarita L.; Lebedinsky, Alexander V.; Chernyh, Nikolai A.; Nazina, Tamara N.; Ivoilov, Valery S.; Belyaev, Sergey S.; Boulygina, Eugenia S.; Lysov, Yury P.; Perov, Alexander N.; Mirzabekov , Andrei D.; Hippe, Hans; Stackebrandt, Erko; L'Haridon, Stéphane; Jeanthon, Christian

    2003-01-01

    Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H2S liter−1 day−1 occurred at 60 and 80°C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH4 liter−1 day−1. Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected. PMID:14532074

  11. Radioisotopic, culture-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir.

    PubMed

    Bonch-Osmolovskaya, Elizaveta A; Miroshnichenko, Margarita L; Lebedinsky, Alexander V; Chernyh, Nikolai A; Nazina, Tamara N; Ivoilov, Valery S; Belyaev, Sergey S; Boulygina, Eugenia S; Lysov, Yury P; Perov, Alexander N; Mirzabekov, Andrei D; Hippe, Hans; Stackebrandt, Erko; L'Haridon, Stéphane; Jeanthon, Christian

    2003-10-01

    Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H(2)S liter(-1) day(-1) occurred at 60 and 80 degrees C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH(4) liter(-1) day(-1). Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected. PMID:14532074

  12. Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation.

    PubMed

    Sutton, Nora B; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H M

    2015-01-01

    While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2-4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose

  13. Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

    PubMed Central

    Sutton, Nora B.; Atashgahi, Siavash; Saccenti, Edoardo; Grotenhuis, Tim; Smidt, Hauke; Rijnaarts, Huub H. M.

    2015-01-01

    While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose

  14. Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity.

    PubMed

    Velmourougane, Kulandaivelu

    2016-01-01

    A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system.

  15. Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity

    PubMed Central

    2016-01-01

    A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system. PMID:27042378

  16. How Commercial and "Violent" Video Games Can Promote Culturally Sensitive Science Learning: Some Questions and Challenges

    ERIC Educational Resources Information Center

    Kwah, Helen

    2012-01-01

    In their paper, Munoz and El-Hani propose to bring video games into science classrooms to promote culturally sensitive ethics and citizenship education. Instead of bringing "educational" games, Munoz and El-Hani take a more creative route and include games such as Fallout 3[R] precisely because they are popular and they reproduce ideological and…

  17. TV Commercials as Authentic Materials to Teach Communication, Culture and Critical Thinking

    ERIC Educational Resources Information Center

    Erkaya, Odilea Rocha

    2005-01-01

    This article discusses the importance of using authentic materials to teach foreign students to communicate in English in a natural way, teach them about the target culture, and help them to engage in critical thinking. Since authentic materials have been defined in various ways, this researcher has chosen for this article two definitions which…

  18. Effects of added chelated trace minerals, organic selenium, yeast culture, direct-fed microbials, and Yucca schidigera extract in horses. Part I: Blood nutrient concentration and digestibility.

    PubMed

    Gordon, M E; Edwards, M S; Sweeney, C R; Jerina, M L

    2013-08-01

    The objective of this study was to test the hypothesis that feed additives such as chelated minerals, organic Se, yeast culture, direct-fed microbials, and Yucca schidigera extract would improve nutrient digestibility when included in an equine diet. Horses (Quarter Horse geldings 4.5 to 16 yr of age; mean BW 522 kg ± 46 kg) were acclimated to 100% pelleted diets formulated with (ADD) and without (CTRL) commercially available sources of the aforementioned additives followed by a 14-d collection period of feces and urine. Chelated sources of Cu, Zn, Mn and Co were utilized versus sulfated forms, at a 100% replacement rate. No significant differences among apparent the digestibility of DM, ADF, or NDF (P= 0.665, P = 0.866, P = 0.747, respectively) were detected between dietary treatments. Likewise, no differences in apparent digestibility of Cu (P = 0.724), Zn (P = 0.256), Mn (P = 0.888), Co (P = 0.71), or Se (P = 0.588) were observed. No differences were observed in serum Cu, Mn, or Co concentrations between ADD and CTRL at acclimation or collection time points (P > 0.05). While no difference in serum Zn concentrations were observed between ADD and CTRL groups at acclimation (P > 0.05), they were statistically higher at the collection time period for horses consuming CTRL (P < 0.0001). Whole blood Se concentration was greater in the CTRL group versus the ADD group both at acclimation (P = 0.041) and collection (P = 0.005) time periods. In reference to time, serum Cu concentrations increased (P = 0.012) for animals consuming CTRL, but not ADD (P > 0.05). Serum Zn concentrations of horses consuming both ADD (P = 0.021) and CTRL (P < 0.0001) increased over time from acclimation to collection time points. No time differences (P > 0.05) were observed in serum Mn concentrations. Serum Co concentrations increased over time in horses consuming both ADD (P = 0.001) and CTRL (P = 0.021). From acclimation to collection, whole blood Se concentration increased for horses

  19. A novel approach to recycle bacterial culture waste for fermentation reuse via a microbial fuel cell-membrane bioreactor system.

    PubMed

    Li, Jian; Zhu, Yuan; Zhuang, Liangpeng; Otsuka, Yuichiro; Nakamura, Masaya; Goodell, Barry; Sonoki, Tomonori; He, Zhen

    2015-09-01

    Biochemical production processes require water and nutrient resources for culture media preparation, but aqueous waste is generated after the target products are extracted. In this study, culture waste (including cells) produced from a lab-scale fermenter was fed into a microbial fuel cell-membrane bioreactor (MFC-MBR) system. Electrical energy was generated via the interaction between the microbial consortia and the solid electrode in the MFC. The treated wastewater was reclaimed in this process which was reused as a solvent and a nutrient source in subsequent fermentation. Polarization testing showed that the MFC produced a maximum current density of 37.53 A m(-3) with a maximum power density of 5.49 W m(-3). The MFC was able to generate 0.04 kWh of energy per cubic meter of culture waste treated. The lab-scale fermenters containing pure cultures of an engineered Pseudomonas spp. were used to generate 2-pyrone-4,6-dicarboxylic acid (PDC), a high value platform chemical. When the MFC-MBR-treated wastewater was used for the fermenter culture medium, a specific bacterial growth rate of 1.00 ± 0.05 h(-1) was obtained with a PDC production rate of 708.11 ± 64.70 mg PDC L(-1) h(-1). Comparable values for controls using pure water were 0.95 ± 0.06 h(-1) and 621.01 ± 22.09 mg PDC L(-1) h(-1) (P > 0.05), respectively. The results provide insight on a new approach for more sustainable bio-material production while at the same time generating energy, and suggest that the treated wastewater can be used as a solvent and a nutrient source for the fermentation production of high value platform chemicals. PMID:26013992

  20. Detection of Biosignatures in Natural and Microbial Cultured Jarosites Using Laser- Desorption Fourier Transform Mass Spectrometry: Implications for Astrobiology

    NASA Astrophysics Data System (ADS)

    Kotler, J.; Hinman, N. W.; Yan, B.; Stoner, D. L.; Scott, J. R.

    2006-12-01

    The jarosite group minerals have received increasing attention since the discovery by the Mars Exploration Rover-Opportunity of jarosite on the Martian surface. The general chemical formula for jarosite is XFe3(SO4)2(OH)6 where the X represents both monovalent and divalent cations that can occupy the axial positions in the crystal structure. Commonly found ions include K+, Na+, H3O+, NH4+, and Pb2+ with reports of other large ions occupying this position in the literature. Modeling efforts have been performed to confirm that jarosite has the ability to incorporate a variety of "foreign" cations. The minerals unique ability to incorporate various large ions in its structure and its association with biological activity in terrestrial environments has lead to investigations regarding its use as an indicator of aqueous and/or biological activity. The use of laser desorption Fourier transform mass spectrometry (LD-FTMS) has revealed the presence of organic matter including the amino acid, glycine, in several jarosite samples from various worldwide locations. Iron precipitates derived from acidophilic microbial cultures were also analyzed. Using attenuated total reflectance infrared spectroscopy (ATR-IR), signals indicative of microbes or microbial exudates were weak and ambiguous. In contrast, LD-FTMS clearly detected bioorganic constituents in some desorption spots. However, the signals were sporadic and required the laser scanning/imaging capability of our laboratory built system to locate the microbial signatures in the heterogeneous samples. The ability to observe these bioorganic signatures in jarosite samples using the instrumental technique employed in this study furthers the goals of planetary geologists to determine whether signs of life (e.g., presence of biomolecules or biomolecule precursors) can be detected in the rock record of terrestrial and extraterrestrial samples.

  1. Microbial communities in uranium mine tailings and mine water sediment from Jaduguda U mine, India: A culture independent analysis.

    PubMed

    Dhal, Paltu Kumar; Sar, Pinaki

    2014-01-01

    Microbial diversity within uranium mine tailings and mine water sediment from the Jaduguda uranium mine, India was characterized by metagenome-derived 16S rRNA gene clone libraries. Samples from fresh tailings (JFT244), abandoned (vegetated) tailings (JOT245) and mine water sediment (J1-5) having wide ranges of pH (5.7 to 10.4), nitrogen, phosphorus and organic carbon [150-5700 ppm, 800-9100 ppm and 0.18-6.5% (w/w)] and elevated metals (Ni, Cu, Zn and U) were used to explore the inhabitant bacterial and archaeal community structures. Consistent to the sample's physicochemical properties, up to four orders of magnitude variation in bacterial CFU counts was observed. The data showed that with increasing metal and decreasing nutrient (organic C, N, P, etc.) contents, microbial diversity indices decrease within the samples. Culture-independent analyses revealed predominance of phyla Proteobacteria and/or Acidobacteria within the samples along with members of Actinobacteria, Cyanobacteria, Chloroflexi, Genera incertae sedis OP10, Firmicutes and Planctomycete as relatively minor groups. Abundance of Crenarchaeota in tailings samples and Euryachaeota in mine water sediment was noted. Diversity of dissimilatory sulfate reductase gene (dsr) was studied. Putative metabolic properties as derived from taxonomy and phylogenetic lineages indicated presence of chemolithotrophic and heteotrophic aerobic and anaerobic organisms capable of nitrogen fixation, nitrate reduction and biogeochemical cycling of metals, sulfur and methane. The data indicated that indigenous microbial populations are capable of maintaining self-sustenance in these highly hazardous environments and possess catalytic potential for their use in in situ bioremediation.

  2. Commercial Lysogeny Broth culture media and oxidative stress: a cautious tale.

    PubMed

    Ezraty, Benjamin; Henry, Camille; Hérisse, Marion; Denamur, Erick; Barras, Frédéric

    2014-09-01

    Lysogeny Broth (LB), most often misnamed Luria-Bertani medium, ranks among the most commonly used growth media in microbiology. Surprisingly, we observed that oxidative levels vary with the commercial origin of the LB ready to use powder. Indeed, growth on solid media of Escherichia coli and Salmonella derivatives lacking antioxidative stress defenses, such as oxyR mutant devoid of the H2O2-sensing transcriptional activator or Hpx(-) strains lacking catalases and peroxidases, exhibit different phenotypes on LB-Sigma or LB-Difco. Using gene fusion and exogenously added catalase, we found that LB-Sigma contains higher levels of H2O2 than LB-Difco. Also we observed differences in population counts of 82 clinical and environmental isolates of E. coli, depending on the LB used. Further investigations revealed a significant influence of the commercial origin of agar as well. Besides being a warning to the wide population of LB users, our observations provide researchers in the oxidative stress field with a tool to appreciate the severity of mutations in antioxidative stress defenses.

  3. Development of a mixed mode adsorption process for the direct product sequestration of an extracellular protease from microbial batch cultures.

    PubMed

    Hamilton, G E; Luechau, F; Burton, S C; Lyddiatt, A

    2000-04-28

    Direct product sequestration of extracellular proteins from microbial batch cultures can be achieved by continuous or intermittent broth recycle through an external extractive loop. Here, we describe the development of a fluidisable, mixed mode adsorbent, designed to tolerate increasing ionic strength (synonymous with extended productive batch cultures). This facilitated operations for the integrated recovery of an extracellular acid protease from cultures of Yarrowia lipolytica. Mixed mode adsorbents were prepared using chemistries containing hydrophobic and ionic groups. Matrix hydrophobicity and titration ranges were matched to the requirements of integrated protease adsorption. A single expanded bed was able to service the productive phase of growth without recourse to the pH adjustment of the broth previously required for ion exchange adsorption. This resulted in increased yields of product, accompanied by further increases in enzyme specific activity. A step change from pH 4.5 to 2.6, across the isoelectric point of the protease, enabled high resolution fixed bed elution induced by electrostatic repulsion. The generic application of mixed mode chemistries, which combine the physical robustness of ion-exchange ligands in sanitisation and sterilisation procedures with a selectivity, which approaches that of affinity interactions, is discussed.

  4. Microbial xanthophylls.

    PubMed

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

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

  5. Methods for Facilitating Microbial Growth on Pulp Mill Waste Streams and Characterization of the Biodegradation Potential of Cultured Microbes

    PubMed Central

    Mathews, Stephanie L.; Ayoub, Ali S.; Pawlak, Joel; Grunden, Amy M.

    2013-01-01

    The kraft process is applied to wood chips for separation of lignin from the polysaccharides within lignocellulose for pulp that will produce a high quality paper. Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. However, the recalcitrant nature of the lignocellulose resources, its chemical derivatives that constitute the majority of available organic carbon within black liquor, and its basic pH present challenges to microbial biodegradation of this waste material. Methods for the collection and modification of black liquor for microbial growth are aimed at utilization of this pulp waste to convert the lignin, organic acids, and polysaccharide degradation byproducts into valuable chemicals. The lignocellulose extraction techniques presented provide a reproducible method for preparation of lignocellulose growth substrates for understanding metabolic capacities of cultured microorganisms. Use of gas chromatography-mass spectrometry enables the identification and quantification of the fermentation products resulting from the growth of microorganisms on pulping waste. These methods when used together can facilitate the determination of the metabolic activity of microorganisms with potential to produce fermentation products that would provide greater value to the pulping system and reduce effluent waste, thereby increasing potential paper milling profits and offering additional uses for black liquor. PMID:24378616

  6. High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

    PubMed Central

    2013-01-01

    Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described. PMID:23475615

  7. High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.

    PubMed

    Ercolini, Danilo

    2013-05-01

    Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

  8. Contribution of oocyte source and culture conditions to phenotypic and transcriptomic variation in commercially produced bovine blastocysts.

    PubMed

    Plourde, Dany; Vigneault, Christian; Lemay, Alexandra; Breton, Lévéke; Gagné, Dominic; Laflamme, Isabelle; Blondin, Patrick; Robert, Claude

    2012-07-01

    Bovine embryo production is practiced worldwide for commercial purposes. A major concern of embryo suppliers is the impact of in vitro production systems on embryo quality. In the present study, we compared Buffalo Rat Liver cell coculture with semidefined, medium-based culture, oocytes recovered postmortem with those obtained from live animals, and in vitro with in vivo embryo development. Gene expression levels in expanded blastocysts were measured using microarray and quantitative RT-PCR. The systems were similar in terms of blastocyst yield and rate of development, whereas embryo productivity was greater for immature oocytes collected in vivo. Although immature oocytes collected in vivo had greater developmental competence, they yielded blastocysts that were indistinguishable (in terms of level of gene expression) from embryos derived from immature oocytes recovered postmortem. Culture conditions had a significant impact on gene expression, particularly among genes involved in lipid metabolism. Numerous uncharacterized novel transcript regions were also influenced by in vitro treatments. In conclusion, ovum pick-up combined with in vitro culture in semidefined medium provided a high blastocyst yield, without the deleterious effects associated with coculture.

  9. Kinetics of nitrate and sulfate removal using a mixed microbial culture with or without limited-oxygen fed.

    PubMed

    Xu, Xi-Jun; Chen, Chuan; Wang, Ai-Jie; Guo, Hong-Liang; Yuan, Ye; Lee, Duu-Jong; Ren, Nan-Qi

    2014-07-01

    The biological degradation of nitrate and sulfate was investigated using a mixed microbial culture and lactate as the carbon source, with or without limited-oxygen fed. It was found that sulfate reduction was slightly inhibited by nitrate, since after nitrate depletion the sulfate reduction rate increased from 0.37 mg SO4 (2-)/mg VSS d to 0.71 mg SO4 (2-)/mg VSS d, and the maximum rate of sulfate reduction in the presence of nitrate corresponded to 56 % of the non-inhibited sulfate reduction rate determined after nitrate depleted. However, simultaneous but not sequential reduction of both oxy-anions was observed in this study, unlike some literature reports in which sulfate reduction starts only after depletion of nitrate, and this case might be due to the fact that lactate was always kept above the limiting conditions. At limited oxygen, the inhibited effect on sulfate reduction by nitrate was relieved, and the sulfate reduction rate seemed relatively higher than that obtained without limited-oxygen fed, whereas kept almost constant (0.86-0.89 mg SO4 (2-)/mg VSS d) cross the six ROS states. In contrast, nitrate reduction rates decreased substantially with the increase in the initial limited-oxygen fed, showing an inhibited effect on nitrate reduction by oxygen. Kinetic parameters determined for the mixed microbial culture showed that the maximum specific sulfate utilization rate obtained (0.098 ± 0.022 mg SO4 (2-)/(mg VSS h)) was similar to the reported typical value (0.1 mg SO4 (2-)/(mg VSS h)), also indicating a moderate inhibited effect by nitrate.

  10. A commercial rapid optical immunoassay detects Streptococcus agalactiae from aquatic cultures and clinical specimens.

    PubMed

    Evans, Joyce J; Pasnik, David J; Klesius, Phillip H

    2010-08-26

    The BioStar STREP B Optical ImmunoAssay (STREP B OIA) (BioStar OIA Strep B Assay Kit; BioStar Incorporation, Louisville, CO, USA), commonly used for diagnosis of human maternal group B streptococcus (GBS) colonization, was evaluated for its diagnostic and analytical sensitivity and specificity to aquatic animal GBS isolates, cross-reactivity, and diagnosis and recovery of GBS directly from clinically- infected fish swabs. STREP B OIA identified 25 known fish and dolphin GBS isolates. Thirteen non-GBS negative control isolates from fish and other animals were negative, giving 100% analytical specificity and no cross-reactivity. Three groups of 6 Nile tilapia (Oreochromis niloticus) (mean weight of 40.60+/-1.70 g) each were inoculated intraperitoneally with either 10(6) colony-forming units (cfu) GBS/fish, 10(6) cfu Streptococcus iniae/fish or 100 microL of tryptic soy broth (TSB) and observed for mortality for 7 days. The nare and brain of all fish were swabbed and subjected to the STREP B OIA for detection of GBS antigen immediately after swabbing (0 h) or 24, 48 and 72 h post-swabbing and compared to conventional culture on trypticase soy agar with 5% sheep blood. The STREP B OIA method demonstrated a diagnostic sensitivity of 75.0% and a diagnostic specificity of 69.2% compared to direct TSA. The percent agreement between OIA and culture was 100%. GBS antigen could be retrieved by OIA following 72-h storage of swabs. These results demonstrate the utility of the STREP B OIA to identify GBS from culture and directly from swabs of clinically- infected fish. PMID:20430538

  11. Egypt's Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites

    PubMed Central

    Mustafa, Ghada A.; Abd-Elgawad, Amr; Abdel-Haleem, Alyaa M.; Siam, Rania

    2014-01-01

    The Red Sea possesses a unique geography, and its shores are rich in mangrove, macro-algal and coral reef ecosystems. Various sources of pollution affect Red Sea biota, including microbial life. We assessed the effects of industrialization on microbes along the Egyptian Red Sea coast at eight coastal sites and two lakes. The bacterial communities of sediment samples were analyzed using bacterial 16S rDNA pyrosequencing of V6-V4 hypervariable regions. The taxonomic assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). Further analysis revealed distinct bacterial consortia that primarily included (1) marine Vibrio spp.—suggesting a “marine Vibrio phenomenon”; (2) potential human pathogens; and (3) oil-degrading bacteria. We discuss two divergent microbial consortia that were sampled from Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; these consortia contained the highest abundance of human pathogens and no pathogens, respectively. Our results draw attention to the effects of industrialization on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites. PMID:25157243

  12. Chronic impact of sulfamethoxazole on the metabolic activity and composition of enriched nitrifying microbial culture.

    PubMed

    Katipoglu-Yazan, Tugce; Merlin, Christophe; Pons, Marie-Noëlle; Ubay-Cokgor, Emine; Orhon, Derin

    2016-09-01

    This study investigated the chronic impact of sulfamethoxazole (SMX) on activated sludge sustaining an enriched nitrifying biomass. For this purpose, a laboratory scale fill and draw reactor was operated with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia at a sludge age of 15 days. Additionally, the biomass was exposed to a daily SMX dose of 50 mg/L once the reactor reached steady-state conditions. The reactor performance and microbial composition were monitored for 37 days with conventional parameters and molecular techniques based on the gene for ammonia monooxygenase subunit A (amoA) and the prokaryotic 16S rRNA gene. Denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene cloning analyses suggested a microbial community change concurrent with the addition of SMX. Specifically, quantitative polymerase chain reaction analyses (qPCR/RT-qPCR) revealed a significant reduction in the levels and activity of ammonia oxidizing bacteria (AOB). However, the acclimation period ended with high amoA mRNA levels and improved nitrification efficiency. Partial degradation of SMX by heterotrophic bacteria was also observed.

  13. Chronic impact of sulfamethoxazole on the metabolic activity and composition of enriched nitrifying microbial culture.

    PubMed

    Katipoglu-Yazan, Tugce; Merlin, Christophe; Pons, Marie-Noëlle; Ubay-Cokgor, Emine; Orhon, Derin

    2016-09-01

    This study investigated the chronic impact of sulfamethoxazole (SMX) on activated sludge sustaining an enriched nitrifying biomass. For this purpose, a laboratory scale fill and draw reactor was operated with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia at a sludge age of 15 days. Additionally, the biomass was exposed to a daily SMX dose of 50 mg/L once the reactor reached steady-state conditions. The reactor performance and microbial composition were monitored for 37 days with conventional parameters and molecular techniques based on the gene for ammonia monooxygenase subunit A (amoA) and the prokaryotic 16S rRNA gene. Denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene cloning analyses suggested a microbial community change concurrent with the addition of SMX. Specifically, quantitative polymerase chain reaction analyses (qPCR/RT-qPCR) revealed a significant reduction in the levels and activity of ammonia oxidizing bacteria (AOB). However, the acclimation period ended with high amoA mRNA levels and improved nitrification efficiency. Partial degradation of SMX by heterotrophic bacteria was also observed. PMID:27235775

  14. Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house.

    PubMed

    Brooks, J P; McLaughlin, M R; Scheffler, B; Miles, D M

    2010-09-15

    Poultry are known to harbor antibiotic resistant and pathogenic bacteria, and as such poultry litter and poultry house air can be contaminated with these bacteria. However, the presence of antibiotic resistant bacteria in biological aerosols and litter is largely not understood. The purpose of this study was to determine the amount of aerosolized bacteria and endotoxin, particularly fecal indicators, staphylococci, and enterococci, associated with poultry house and outdoor air. Aerosol samples were collected at multiple locations on the farm and in the house. Antibiotic resistance was investigated using the Kirby Bauer method on selected isolates using twelve different antibiotics spanning both narrow to broad spectrums of effectiveness. Overall there was a cyclical increase in bacterial concentrations as flocks progressed from pre-flock to late-flock, with >2 orders magnitude lower concentration during pre-flock periods (no chickens), in both the litter and aerosol samples. The house environment provided for significantly concentrated bacterial and endotoxin levels. It was estimated that Staphylococcus bacteria accounted for at least 90% of cultured aerobic bacteria and culture-independent 16S rRNA analyses demonstrated that significant population changes occurred from pre- to late-flock. Rarely was an isolate resistant to more than 4 antibiotic classes; however there was a trend upwards in overall resistance of enterococci as the flock cycle progressed. It appears that although levels of antibiotic resistant bacteria were highly concentrated within the house, levels were much lower outside of the house, and very little house escape occurred.

  15. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    PubMed

    Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

  16. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

    PubMed

    Park, Si Hong; Lee, Sang In; Ricke, Steven C

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. PMID:26992104

  17. Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform

    PubMed Central

    Park, Si Hong; Lee, Sang In; Ricke, Steven C.

    2016-01-01

    Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. PMID:26992104

  18. Batch fermentative hydrogen production by enriched mixed culture: Combination strategy and their microbial composition.

    PubMed

    Sivagurunathan, Periyasamy; Sen, Biswarup; Lin, Chiu-Yue

    2014-02-01

    The effect of individual and combined mixed culture on dark fermentative hydrogen production performance was investigated. Mixed cultures from cow dung (C1), sewage sludge (C2), and pig slurry (C3) were enriched under strict anaerobic conditions at 37°C with glucose as the sole carbon source. Biochemical hydrogen production test in peptone-yeast-glucose (PYG) and basal medium was performed for individual mixed cultures (C1, C2 and C3) and their combinations (C1-C2, C2-C3, C1-C3 and C1-C2-C3) at a glucose concentration of 10 g/L, 37°C and initial pH 7. Maximum hydrogen yields (HY) of 2.0 and 1.86 [Formula: see text] by C2, and 1.98 and 1.95 mol(H2)/mol(glucose) by C2-C3 were obtained in PYG and basal medium, respectively. Butyrate and acetate were the major soluble metabolites produced by all the cultures, and the ratio of butyrate to acetate was ∼2 fold higher in basal medium than PYG medium, indicating strong influence of media formulation on glucose catabolism. The major hydrogen-producing bacterial strains, observed in all mixed cultures, belonged to Clostridium butyricum, C. saccharobutylicum, C. tertium and C. perfringens. The hydrogen production performance of the combined mixed culture (C2-C3) was further evaluated on beverage wastewater (10 g/L) at pH 7 and 37°C. The results showed an HY of 1.92 mol(H2)/mol(glucose-equivalent). Experimental evidence suggests that hydrogen fermentation by mixed culture combination could be a novel strategy to improve the HY from industrial wastewater.

  19. Data correction pre-processing for electronically stored blood culture results: Implications on microbial spectrum and empiric antibiotic therapy

    PubMed Central

    2009-01-01

    Background The outcome of patients with bacteraemia is influenced by the initial selection of adequate antimicrobial therapy. The objective of our study was to clarify the influence of different crude data correction methods on a) microbial spectrum and ranking of pathogens, and b) cumulative antimicrobial susceptibility pattern of blood culture isolates obtained from patients from intensive care units (ICUs) using a computer based tool, MONI. Methods Analysis of 13 ICUs over a period of 7 years yielded 1427 microorganisms from positive results. Three different data correction methods were applied. Raw data method (RDM): Data without further correction, including all positive blood culture results. Duplicate-free method (DFM): Correction of raw data for consecutive patient's results yielding same microorganism with similar antibiogram within a two-week period. Contaminant-free method (CFM): Bacteraemia caused by possible contaminants was only assumed as true bloodstream infection, if an organism of the same species was isolated from > 2 sets of blood cultures within 5 days. Results Our study demonstrates that different approaches towards raw data correction – none (RDM), duplicate-free (DFM), and a contaminant-free method (CFM) – show different results in analysis of positive blood cultures. Regarding the spectrum of microorganisms, RDM and DFM yielded almost similar results in ranking of microorganisms, whereas using the CFM resulted in a clinically and epidemiologically more plausible spectrum. Conclusion For possible skin contaminants, the proportion of microorganisms in terms of number of episodes is most influenced by the CFM, followed by the DFM. However, with exception of fusidic acid for gram-positive organisms, none of the evaluated correction methods would have changed advice for empiric therapy on the selected ICUs. PMID:19500418

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

    PubMed

    Fujikawa, Hiroshi; Sakha, Mohammad Z

    2014-01-01

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

  1. Culture-Dependent and Culture-Independent Characterization of Microbial Assemblages Associated with High-Temperature Petroleum Reservoirs

    PubMed Central

    Orphan, V. J.; Taylor, L. T.; Hafenbradl, D.; Delong, E. F.

    2000-01-01

    Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90°C. Heterotrophic enrichments from all sites yielded sheathed rods (Thermotogales), pleomorphic rods resembling Thermoanaerobacter, and Thermococcus-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H2, acetate, and CO2 as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium, Methanococcus, and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included Thermoanaerobacter, Thermococcus, Desulfothiovibrio, Aminobacterium, Acidaminococcus, Pseudomonas, Halomonas, Acinetobacter, Sphingomonas, Methylobacterium, and Desulfomicrobium. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ. PMID:10653739

  2. Increased mesquite gum formation in nodal explants cultures after treatment with a microbial biomass preparation.

    PubMed

    Orozco-Villafuerte, Juan; Buendía-González, Leticia; Cruz-Sosa, Francisco; Vernon-Carter, Eduardo J

    2005-08-01

    Prosopis laevigata nodal explants cultures were established in Murashige and Skoog medium. Simultaneously these cultures were subjected to stress with biotic elicitors and an environmental factor (temperature increase to promote heat stress) in order to promote and increase exuded mesquite gum production. The biotic elicitors were: Aspergillus nidulans and Pseudomonas pseudoalcaligenes both used in concentrations of 10, 20 and 30 mg, whereas the environmental condition was different incubation temperatures (25, 35 and 40 degrees C). The greatest gum production (approximately 13 mg of pooled gum from 100 explants after 14 days incubation) took place when the culture medium was added 10, 20 and 30 mg of autoclaved fungal mycelium of A. nidulans or 30 mg of autoclaved bacterial biomass of P. pseudoalcaligenes in combination with an incubation temperature of 35 degrees C. These treatments were non-significantly different among themselves (P < 0.05), but were significantly different to the rest of the treatments (P > 0.05).

  3. Changing the academic culture: Valuing patents and commercialization toward tenure and career advancement

    PubMed Central

    Sanberg, Paul R.; Gharib, Morteza; Harker, Patrick T.; Kaler, Eric W.; Marchase, Richard B.; Sands, Timothy D.; Arshadi, Nasser; Sarkar, Sudeep

    2014-01-01

    There is national and international recognition of the importance of innovation, technology transfer, and entrepreneurship for sustained economic revival. With the decline of industrial research laboratories in the United States, research universities are being asked to play a central role in our knowledge-centered economy by the technology transfer of their discoveries, innovations, and inventions. In response to this challenge, innovation ecologies at and around universities are starting to change. However, the change has been slow and limited. The authors believe this can be attributed partially to a lack of change in incentives for the central stakeholder, the faculty member. The authors have taken the position that universities should expand their criteria to treat patents, licensing, and commercialization activity by faculty as an important consideration for merit, tenure, and career advancement, along with publishing, teaching, and service. This position is placed in a historical context with a look at the history of tenure in the United States, patents, and licensing at universities, the current status of university tenure and career advancement processes, and models for the future. PMID:24778248

  4. Flux balance analysis of mixed microbial cultures: application to the production of polyhydroxyalkanoates from complex mixtures of volatile fatty acids.

    PubMed

    Pardelha, Filipa; Albuquerque, Maria G E; Reis, Maria A M; Dias, João M L; Oliveira, Rui

    2012-12-31

    Fermented agro-industrial wastes are potential low cost substrates for polyhydroxyalkanoates (PHA) production by mixed microbial cultures (MMC). The use of complex substrates has however profound implications in the PHA metabolism. In this paper we investigate PHA accumulation using a lumped metabolic model that describes PHA storage from arbitrary mixtures of volatile fatty acids (VFA). Experiments were conducted using synthetic and complex VFA mixtures obtained from the fermentation of sugar cane molasses. Metabolic flux analysis (MFA) and flux balance analysis (FBA) were performed at different stages of culture enrichment in order to investigate the effect of VFA composition and time of enrichment in PHA storage efficiency. Substrate uptake and PHA storage fluxes increased over enrichment time by 70% and 73%, respectively. MFA calculations show that higher PHA storage fluxes are associated to an increase in the uptake of VFA with even number of carbon atoms and a more effective synthesis of hydroxyvalerate (HV) precursors from VFA with odd number of carbons. Furthermore, FBA shows that the key metabolic objective of a MMC subjected to the feast and famine regimen is the minimization of the tricarboxylic acid cycle fluxes. The PHA flux and biopolymer composition (hydroxybutyrate (HB): HV) could be accurately predicted in several independent experiments.

  5. The Influence of Staphylococcus aureus on Gut Microbial Ecology in an In Vitro Continuous Culture Human Colonic Model System

    PubMed Central

    Sannasiddappa, Thippeswamy H.; Costabile, Adele; Gibson, Glenn R.; Clarke, Simon R.

    2011-01-01

    An anaerobic three-stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine, was used to study the effect of S. aureus infection of the gut on the resident faecal microbiota. Studies on the development of the microbiota in the three vessels were performed and bacteria identified by culture independent fluorescence in situ hybridization (FISH). Furtheremore, short chain fatty acids (SCFA), as principal end products of gut bacterial metabolism, were measured along with a quantitative assessment of the predominant microbiota. During steady state conditions, numbers of S. aureus cells stabilised until they were washed out, but populations of indigenous bacteria were transiently altered; thus S. aureus was able to compromise colonisation resistance by the colonic microbiota. Furthermore, the concentration of butyric acid in the vessel representing the proximal colon was significantly decreased by infection. Thus infection by S. aureus appears to be able to alter the overall structure of the human colonic microbiota and the microbial metabolic profiles. This work provides an initial in vitro model to analyse interactions with pathogens. PMID:21858036

  6. Model-based data evaluation of polyhydroxybutyrate producing mixed microbial cultures in aerobic sequencing batch and fed-batch reactors.

    PubMed

    Johnson, Katja; Kleerebezem, Robbert; van Loosdrecht, Mark C M

    2009-09-01

    The production of polyhydroxyalkanoates (PHAs) with mixed microbial cultures is a promising approach for the sustainable production of bioplastics. Usually a two-step process is employed consisting of (i) the enrichment of a PHA producing mixed culture in a sequencing batch reactor (SBR) and (ii) the subsequent PHA production in a fed-batch reactor. Both reactors are highly dynamic systems, particularly if the SBR is working at low sludge residence times (SRTs) or if growth is (partly) permitted in fed-batch systems. Under these conditions the concentrations of substrate, PHA and biomass change rapidly, complicating the identification of biomass specific conversion rates as required for process characterization. We developed a structured approach for the evaluation of such SBR and fed-batch experiments consisting of five steps: (1) Measurement of a sufficiently large set of parameters including off-gas concentrations, (2) Corrections of measurements for effects of sampling and addition of liquids (pH control, substrate), (3) Calculation of oxygen uptake and carbon dioxide evolution rates, the latter including inorganic carbon dissolved in the liquid phase, (4) Balancing of the measured conversions, (5) Evaluation of the measurements by means of a metabolic model. This approach has been successfully applied to a large number of data sets. Steps 1-4 ensured that data sets of high quality were obtained. Step 5 allowed to find the best estimates for all conversions and biomass specific rates for the measured data sets, while complying with material balances. Conversions of the substrate acetate, the nitrogen source ammonia and of the storage polymer PHA (here polyhydroxybutyrate (PHB)) were described very accurately by the model. Modeled off-gas conversions often deviated somewhat from measured conversions, which might be partly due to an inaccurate model stoichiometry. Nonetheless, the described approach proved to be a very useful tool for the evaluation and

  7. Studies on microbial chromate reduction by Pseudomonas sp. in aerobic continuous suspended growth cultures

    SciTech Connect

    Gopalan, R.; Veeramani, H. . Centre for Environmental Science and Engineering)

    1994-03-15

    Reduction of hexavalent chromium was studied in three bench-scale continuous stirred tank reactors. The inoculum was a culture of Pseudomonas sp., capable of giving 83% to 87% chromate reduction in 72-h batch assays with 60 mg Cr(6) L[sup [minus]1] in synthetic medium. The continuous culture studies were conducted for about 100 days using synthetic feed containing different levels of chromate at 28 to 30 C and pH 6.8. The feed rate was varied over the range 0.5 to 1 L d[sup [minus]1] to obtain hydraulic retention time of 36 to 72 h. Chromate reduction efficiency was 81% to 91% and 100% for influent (Cr(6)) concentrations of 15 to 124 and 5 mg L[sup [minus]1], respectively, with a hydraulic retention time of 72 h.

  8. Removal of hydrocarbon from refinery tank bottom sludge employing microbial culture.

    PubMed

    Saikia, Rashmi Rekha; Deka, Suresh

    2013-12-01

    Accumulation of oily sludge is becoming a serious environmental threat, and there has not been much work reported for the removal of hydrocarbon from refinery tank bottom sludge. Effort has been made in this study to investigate the removal of hydrocarbon from refinery sludge by isolated biosurfactant-producing Pseudomonas aeruginosa RS29 strain and explore the biosurfactant for its composition and stability. Laboratory investigation was carried out with this strain to observe its efficacy of removing hydrocarbon from refinery sludge employing whole bacterial culture and culture supernatant to various concentrations of sand-sludge mixture. Removal of hydrocarbon was recorded after 20 days. Analysis of the produced biosurfactant was carried out to get the idea about its stability and composition. The strain could remove up to 85 ± 3 and 55 ± 4.5 % of hydrocarbon from refinery sludge when whole bacterial culture and culture supernatant were used, respectively. Maximum surface tension reduction (26.3 mN m(-1)) was achieved with the strain in just 24 h of time. Emulsification index (E24) was recorded as 100 and 80 % with crude oil and n-hexadecane, respectively. The biosurfactant was confirmed as rhamnolipid containing C8 and C10 fatty acid components and having more mono-rhamnolipid congeners than the di-rhamnolipid ones. The biosurfactant was stable up to 121 °C, pH 2-10, and up to a salinity value of 2-10 % w/v. To our knowledge, this is the first report showing the potentiality of a native strain from the northeast region of India for the efficient removal of hydrocarbon from refinery sludge.

  9. Persistence of pentolite (PETN and TNT) in soil microcosms and microbial enrichment cultures.

    PubMed

    Arbeli, Ziv; Garcia-Bonilla, Erika; Pardo, Cindy; Hidalgo, Kelly; Velásquez, Trigal; Peña, Luis; C, Eliana Ramos; Avila-Arias, Helena; Molano-Gonzalez, Nicolás; Brandão, Pedro F B; Roldan, Fabio

    2016-05-01

    Pentolite is a mixture (1:1) of 2,4,6-trinitrotoluene (TNT) and pentaerythritol tetranitrate (PETN), and little is known about its fate in the environment. This study was aimed to determine the dissipation of pentolite in soils under laboratory conditions. Microcosm experiments conducted with two soils demonstrated that dissipation rate of PETN was significantly slower than that of TNT. Interestingly, the dissipation of PETN was enhanced by the presence of TNT, while PETN did not enhanced the dissipation of TNT. Pentolite dissipation rate was significantly faster under biostimulation treatment (addition of carbon source) in soil from the artificial wetland, while no such stimulation was observed in soil from detonation field. In addition, the dissipation rate of TNT and PETN in soil from artificial wetland under biostimulation was significantly faster than the equivalent abiotic control, although it seems that non-biological processes might also be important for the dissipation of TNT and PETN. Transformation of PETN was also slower during establishment of enrichment culture using pentolite as the sole nitrogen source. In addition, transformation of these explosives was gradually reduced and practically stopped after the forth cultures transfer (80 days). DGGE analysis of bacterial communities from these cultures indicates that all consortia were dominated by bacteria from the order Burkholderiales and Rhodanobacter. In conclusion, our results suggest that PETN might be more persistent than TNT. PMID:26832872

  10. Persistence of pentolite (PETN and TNT) in soil microcosms and microbial enrichment cultures.

    PubMed

    Arbeli, Ziv; Garcia-Bonilla, Erika; Pardo, Cindy; Hidalgo, Kelly; Velásquez, Trigal; Peña, Luis; C, Eliana Ramos; Avila-Arias, Helena; Molano-Gonzalez, Nicolás; Brandão, Pedro F B; Roldan, Fabio

    2016-05-01

    Pentolite is a mixture (1:1) of 2,4,6-trinitrotoluene (TNT) and pentaerythritol tetranitrate (PETN), and little is known about its fate in the environment. This study was aimed to determine the dissipation of pentolite in soils under laboratory conditions. Microcosm experiments conducted with two soils demonstrated that dissipation rate of PETN was significantly slower than that of TNT. Interestingly, the dissipation of PETN was enhanced by the presence of TNT, while PETN did not enhanced the dissipation of TNT. Pentolite dissipation rate was significantly faster under biostimulation treatment (addition of carbon source) in soil from the artificial wetland, while no such stimulation was observed in soil from detonation field. In addition, the dissipation rate of TNT and PETN in soil from artificial wetland under biostimulation was significantly faster than the equivalent abiotic control, although it seems that non-biological processes might also be important for the dissipation of TNT and PETN. Transformation of PETN was also slower during establishment of enrichment culture using pentolite as the sole nitrogen source. In addition, transformation of these explosives was gradually reduced and practically stopped after the forth cultures transfer (80 days). DGGE analysis of bacterial communities from these cultures indicates that all consortia were dominated by bacteria from the order Burkholderiales and Rhodanobacter. In conclusion, our results suggest that PETN might be more persistent than TNT.

  11. Microbial deterioration of cultural heritage and works of art--tilting at windmills?

    PubMed

    Sterflinger, Katja; Piñar, Guadalupe

    2013-11-01

    Microorganisms (bacteria, archaea and fungi), in addition to lichens and insect pests, cause problems in the conservation of cultural heritage because of their biodeteriorative potential. This holds true for all types of historic artefacts, and even for art made of modern materials, in public buildings, museums and private art collections. The variety of biodeterioration phenomena observed on materials of cultural heritage is determined by several factors, such as the chemical composition and nature of the material itself, the climate and exposure of the object, in addition to the manner and frequency of surface cleaning and housekeeping in museums. This study offers a review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials. The decontamination of infected artefacts, exhibition rooms and depots incurs high expenditure for museums. Nevertheless, the question has to be raised: whether the process of biodeterioration of cultural heritage can or should be stopped under all circumstances, or whether we have to accept it as a natural and an implicit consecution of its creation. This study also highlights critically the pros and cons of biocide treatments and gives some prominent examples of successful and unsuccessful conservation treatments. Furthermore, an outlook on the future research needs and developments in this highly interesting field is given.

  12. Microbial reduction and precipitation of vanadium (V) in groundwater by immobilized mixed anaerobic culture.

    PubMed

    Zhang, Baogang; Hao, Liting; Tian, Caixing; Yuan, Songhu; Feng, Chuanping; Ni, Jinren; Borthwick, Alistair G L

    2015-09-01

    Vanadium is an important contaminant impacted by natural and industrial activities. Vanadium (V) reduction efficiency as high as 87.0% was achieved by employing immobilized mixed anaerobic sludge as inoculated seed within 12h operation, while V(IV) was the main reduction product which precipitated instantly. Increasing initial V(V) concentration resulted in the decrease of V(V) removal efficiency, while this index increased first and then decreased with the increase of initial COD concentration, pH and conductivity. High-throughput 16S rRNA gene pyrosequencing analysis indicated the decreased microbial diversity. V(V) reduction was realized through dissimilatory reduction process by significantly enhanced Lactococcus and Enterobacter with oxidation of lactic and acetic acids from fermentative microorganisms such as the enriched Paludibacter and the newly appeared Acetobacterium, Oscillibacter. This study is helpful to detect new functional species for V(V) reduction and constitutes a step ahead in developing in situ bioremediations of vanadium contamination.

  13. X-ray spectroscopic studies of uranium transformations in microbial cultures

    SciTech Connect

    Dodge, C.J.; Francis, A.J.; Clayton, C.R.

    1995-12-31

    Microbial transformations of uranyl nitrate, U:citric acid, and mixed metal U:Fe:citric acid complex were investigated. X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure (XANES) analyses showed that soluble U{sup 6+} was reduced to insoluble U{sup 4+} by Clostridium sp. and was associated with the bacterial surface, whereas U{sup 3+} was observed within the biomass. Uranium forms a binuclear complex with citric acid involving two carboxylic acid groups and the hydroxyl group. Biodegradation studies of U:citric acid and U:Fe:citric acid complexes using Pseudomonas fluorescens showed they were recalcitrant. The lack of biodegradation was due to the nature of the metal-citrate complex species and not due to toxicity. Characterization of the mixed metal U:Fe:citric acid complex by extended X-ray absorption fine structure (EXAFS) indicated that Fe was associated with the U and citric acid, resulting in formation of a bionuclear mixed metal citrate complex.

  14. Effect of different levels of phosphorus on rumen microbial fermentation and synthesis determined using a continuous culture technique.

    PubMed

    Komisarczuk, S; Merry, R J; McAllan, A B

    1987-03-01

    A continuous culture technique was used to study the phosphorus requirements of rumen micro-organisms. Solutions of artificial saliva containing 120, 80, 40 and 0 mg inorganic phosphorus (Pi)/l were infused into the reaction vessels previously inoculated with rumen contents, resulting in Pi concentrations in the vessel contents of 48, 28, 4 and less than 1 mg/l respectively. Various fermentative and synthetic characteristics were examined. In the vessel contents, concentrations of protozoa (about 0.9 X 10(5)/ml) were not significantly affected by Pi concentration. Total volatile fatty acids (VFA) produced averaged about 6.83 mmol/h with Pi levels of 48 and 28 mg/l. Reduction in Pi concentrations to 4 and less than 1 mg/l resulted in significant reductions in total VFA to approximately 6.25 and 3.75 mmol/h respectively, accompanied by a rise in pH from 6.5 to 7.3. Ammonia-nitrogen values, which averaged about 131 mg/l at the higher Pi concentrations, also increased with the lowest level of Pi to about 240 mg/l. ATP concentrations averaged about 14 mumol/l at the highest Pi concentration and fell progressively with each reduction in Pi concentration to a final value of 2.5 mumol/l with the Pi level less than 1 mg/l. At Pi concentrations of 48 and 28 mg/l, the digestibilities of xylose, arabinose and cellulose-glucose were maintained at about 0.90, 0.62 and 0.70 g/g input respectively. At lower Pi concentrations these digestibilities fell significantly and corresponding values at Pi less than 1 mg/l were 0.73, 0.41 and 0.31 respectively. Starch digestion was unaffected by Pi concentration and remained at about 0.90 g/g input. The amount of microbial-N synthesized averaged 0.48 g/d and was maintained with Pi concentrations down to 4 mg/l. There was, however, a significant reduction to 0.26 g/d with Pi concentrations of less than 1 mg/l. The efficiency of microbial protein synthesis was variable but averaged approximately 25 g N/kg total carbohydrate fermented. It was

  15. Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

    NASA Technical Reports Server (NTRS)

    Ward, D. M.; Santegoeds, C. M.; Nold, S. C.; Ramsing, N. B.; Ferris, M. J.; Bateson, M. M.

    1997-01-01

    We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

  16. Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

    PubMed

    Hamet, Maria Fernanda; Londero, Alejandra; Medrano, Micaela; Vercammen, Elisabeth; Van Hoorde, Koenraad; Garrote, Graciela L; Huys, Geert; Vandamme, Peter; Abraham, Analía G

    2013-12-01

    The biological and technological characteristics of kefiran as well as its importance in grain integrity led us to analyze the microbial kefir grain consortium with focus on Lactobacillus kefiranofaciens. The presence of L. kefiranofaciens in the nine kefir grains studied was demonstrated by denaturing gradient gel electrophoresis. By culture dependent methods applying a methodology focused on the search of this species, 22 isolates with typical morphology were obtained and identified applying a combination of SDS-PAGE of whole cell proteins, (GTG)5-PCR and sequence analysis of the housekeeping gene encoding the α-subunit of bacterial phenylalanyl-tRNA synthase (pheS). This polyphasic approach allowed the reliable identification of 11 L. kefiranofaciens, 5 Lactobacillus paracasei, 4 Lactobacillus kefiri and 2 Lactobacillus parakefiri isolates. Isolated L. kefiranofaciens strains produced polysaccharide in strain-dependent concentrations and EPS produced by them also differed in the degree of polymerization. The isolation and accurate identification of L. kefiranofaciens is relevant taking into account the important role of this microorganism in the grain ecosystem as well as its potential application as starter in food fermentations.

  17. Microbial dormancy in batch cultures as a function of substrate-dependent mortality.

    PubMed

    Ayati, Bruce P

    2012-01-21

    We present models and computational studies of dormancy in batch cultures to try to understand the relationship between reculturing time and death penalty for low substrate and the relative advantage of fast versus slow reawakening on the part of the bacteria. We find that the advantage goes to the faster waker for shorter reculturing times and lower mortality under low substrate, and moves to the slower waker as reculturing times and death penalty increase. The advantage returns again to the fast waker for very high death penalties. We use an explicit, continuous structure variable to represent dormancy so as to allow for flexibility in substrate usage on the part of dormant cells, and for a more mechanistic representation of the reawakening process.

  18. Microbial dormancy in batch cultures as a function of substrate-dependent mortality.

    PubMed

    Ayati, Bruce P

    2012-01-21

    We present models and computational studies of dormancy in batch cultures to try to understand the relationship between reculturing time and death penalty for low substrate and the relative advantage of fast versus slow reawakening on the part of the bacteria. We find that the advantage goes to the faster waker for shorter reculturing times and lower mortality under low substrate, and moves to the slower waker as reculturing times and death penalty increase. The advantage returns again to the fast waker for very high death penalties. We use an explicit, continuous structure variable to represent dormancy so as to allow for flexibility in substrate usage on the part of dormant cells, and for a more mechanistic representation of the reawakening process. PMID:22004996

  19. Biodegradation kinetics of the nitramine explosive CL-20 in soil and microbial cultures.

    PubMed

    Panikov, N S; Sizova, M V; Ros, D; Christodoulatos, C; Balas, W; Nicolich, S

    2007-06-01

    The cyclic nitramine explosive CL-20 (C(6)H(6)N(12)O(12), 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12 -hexaazaisowurtzitane) is a relatively new energetic compound which could be a persistent organic pollutant. To follow its biodegradation dynamics, CL-20 was added to soil alone or together with organic co-substrates and N-source and incubated under oxic and anoxic conditions. Without co-substrates, the CL-20 degradation was detectable only under anoxic conditions. The highest degradation rate was found under aerobic conditions and with the addition of co-substrates, succinate and pyruvate being more efficient than acetate, glucose, starch or yeast extract. When added to intact soil, CL-20 degradation was not affected by the N content, but in soil serially diluted with N-free succinate-mineral medium, the process became N-limited. About 40% of randomly selected bacterial colonies grown on succinate agar medium were able to decompose CL-20. Based on 16S rDNA gene sequence and cell morphology, they were affiliated to Pseudomonas, Rhodococcus, Ochrobactrum, Mycobacterium and Ralstonia. In the pure culture of Pseudomonas sp. MS-P grown on the succinate-mineral N(+) medium, the degradation kinetics were first order with the same apparent kinetic constant throughout growth and decline phases of the batch culture. The observed kinetics agreed with the model that supposes co-metabolic transformation of CL-20 uncoupled from cell growth, which can be carried out by several constitutive cellular enzymes with wide substrate specificity. PMID:17091356

  20. Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Bolster, C. H.; Mills, A. L.

    2001-01-01

    A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

  1. A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community

    PubMed Central

    Wang, Yun; Chen, Yin; Zhou, Qian; Huang, Shi; Ning, Kang; Xu, Jian; Kalin, Robert M.; Rolfe, Stephen; Huang, Wei E.

    2012-01-01

    Most microorganisms in nature are uncultured with unknown functionality. Sequence-based metagenomics alone answers ‘who/what are there?’ but not ‘what are they doing and who is doing it and how?’. Function-based metagenomics reveals gene function but is usually limited by the specificity and sensitivity of screening strategies, especially the identification of clones whose functional gene expression has no distinguishable activity or phenotypes. A ‘biosensor-based genetic transducer’ (BGT) technique, which employs a whole-cell biosensor to quantitatively detect expression of inserted genes encoding designated functions, is able to screen for functionality of unknown genes from uncultured microorganisms. In this study, BGT was integrated with Stable isotope probing (SIP)-enabled Metagenomics to form a culture-independent SMB toolbox. The utility of this approach was demonstrated in the discovery of a novel functional gene cluster in naphthalene contaminated groundwater. Specifically, metagenomic sequencing of the 13C-DNA fraction obtained by SIP indicated that an uncultured Acidovorax sp. was the dominant key naphthalene degrader in-situ, although three culturable Pseudomonas sp. degraders were also present in the same groundwater. BGT verified the functionality of a new nag2 operon which co-existed with two other nag and two nah operons for naphthalene biodegradation in the same microbial community. Pyrosequencing analysis showed that the nag2 operon was the key functional operon in naphthalene degradation in-situ, and shared homology with both nag operons in Ralstonia sp. U2 and Polaromonas naphthalenivorans CJ2. The SMB toolbox will be useful in providing deep insights into uncultured microorganisms and unravelling their ecological roles in natural environments. PMID:23082176

  2. Microbial production of low molecular weight hyaluronic acid by adding hydrogen peroxide and ascorbate in batch culture of Streptococcus zooepidemicus.

    PubMed

    Liu, Long; Du, Guocheng; Chen, Jian; Zhu, Yang; Wang, Miao; Sun, Jun

    2009-01-01

    Microbial production of low molecular weight hyaluronic acid (HA) by the addition of hydrogen peroxide and ascorbate during the batch culture of Streptococcus zooepidemicus was investigated. Hydrogen peroxide (1.0 mmol/g HA) and ascorbate (0.5 mmol/g HA) were added at 8h and 12h to degrade HA. With the redox depolymerization of HA, the HA molecular weight decreased from 1,300 kDa for the control to 80 kDa, and the average broth viscosity during 8-16 h decreased from 360 mPa s for the control to 290 mPa s. The average oxygen mass transfer coefficient K(L)a increased from 10h(-1) for the control to 35 h(-1) and the average dissolved oxygen level increased from 1% of air saturation in the control to 10%. HA production increased from 5.0 g/L for the control to 6.5 g/L, and contributed to the increased redox potential and energy charge. This novel process not only significantly enhanced production of low molecular weight HA, but also improved purification efficiency due to a decreased broth viscosity. Low molecular weight HA finds applications in biomedical and healthcare fields.

  3. Polyhydroxyalkanoate granules quantification in mixed microbial cultures using image analysis: Sudan Black B versus Nile Blue A staining.

    PubMed

    Mesquita, Daniela P; Amaral, A Luís; Leal, Cristiano; Oehmen, Adrian; Reis, Maria A M; Ferreira, Eugénio C

    2015-03-20

    Polyhydroxyalkanoates (PHA) can be produced and intracellularly accumulated as inclusions by mixed microbial cultures (MMC) for bioplastic production and in enhanced biological phosphorus removal (EBPR) systems. Classical methods for PHA quantification use a digestion step prior to chromatography analysis, rendering them labor intensive and time-consuming. The present work investigates the use of two quantitative image analysis (QIA) procedures specifically developed for PHA inclusions identification and quantification. MMC obtained from an EBPR system were visualized by bright-field and fluorescence microscopy for PHA inclusions detection, upon Sudan Black B (SBB) and Nile Blue A (NBA) staining, respectively. The captured color images were processed by QIA techniques and the image analysis data were further treated using multivariate statistical analysis. Partial least squares (PLS) regression coefficients of 0.90 and 0.86 were obtained between QIA parameters and PHA concentrations using SBB and NBA, respectively. It was found that both staining procedures might be seen as alternative methodologies to classical PHA determination.

  4. Microbial protein production in activated suspension tanks manipulating C:N ratio in feed and the implications for fish culture.

    PubMed

    Azim, M E; Little, D C; Bron, J E

    2008-06-01

    The present experiment investigated the possibility of microbial protein production in 250 l indoor tanks by manipulating C:N ratio in fish feed applied. Two different levels of protein feed (35% and 22% CP) resulting in C:N ratio of 8.4 and 11.6, respectively, were applied at 25 g daily in each tank. Tanks were aerated and agitated continuously using a dome diffuser. The experiment was carried out for eight weeks. The biofloc development in terms of VSS and BOD5 was better in the low protein fed tanks than in the high protein fed tanks. An estimated biofloc productivity ranged 3-5 g Cm(-3)day(-1). A 3-D image stained with DAPI indicates that the biofloc is comprised of hundreds of bacterial nuclei, size being ranged from 100 to 200 microm. Biofloc quality was independent of the quality of feed applied and contained more than 50% crude protein, 2.5% crude lipid, 4% fibre, 7% ash and 22 kJ g(-1) energy on dry matter basis. The dietary composition and size of biofloc can be considered as appropriate for all omnivorous fish species. The underlying ecological processes are explained through factor analysis. The potential of using biofloc in fish culture is also discussed. PMID:17869097

  5. Segregated flux balance analysis constrained by population structure/function data: the case of PHA production by mixed microbial cultures.

    PubMed

    Pardelha, F; Albuquerque, M G E; Carvalho, G; Reis, M A M; Dias, J M L; Oliveira, R

    2013-08-01

    In this study we developed a segregated flux balance analysis (FBA) method to calculate metabolic flux distributions of the individual populations present in a mixed microbial culture (MMC). Population specific flux data constraints were derived from the raw data typically obtained by the fluorescence in situ hybridization (FISH) and microautoradiography (MAR)-FISH techniques. This method was applied to study the metabolic heterogeneity of a MMC that produces polyhydroxyalkanoates (PHA) from fermented sugar cane molasses. Three populations were identified by FISH, namely Paracoccus sp., Thauera sp., and Azoarcus sp. The segregated FBA method predicts a flux distribution for each of the identified populations. The method is shown to predict with high accuracy the average PHA storage flux and the respective monomeric composition for 16 independent experiments. Moreover, flux predictions by segregated FBA were slightly better than those obtained by nonsegregated FBA, and also highly concordant with metabolic flux analysis (MFA) estimated fluxes. The segregated FBA method can be of high value to assess metabolic heterogeneity in MMC systems and to derive more efficient eco-engineering strategies. For the case of PHA-producing MMC considered in this work, it becomes apparent that the PHA average monomeric composition might be controlled not only by the volatile fatty acids (VFA) feeding profile but also by the population composition present in the MMC. PMID:23475571

  6. Polyhydroxyalkanoate granules quantification in mixed microbial cultures using image analysis: Sudan Black B versus Nile Blue A staining.

    PubMed

    Mesquita, Daniela P; Amaral, A Luís; Leal, Cristiano; Oehmen, Adrian; Reis, Maria A M; Ferreira, Eugénio C

    2015-03-20

    Polyhydroxyalkanoates (PHA) can be produced and intracellularly accumulated as inclusions by mixed microbial cultures (MMC) for bioplastic production and in enhanced biological phosphorus removal (EBPR) systems. Classical methods for PHA quantification use a digestion step prior to chromatography analysis, rendering them labor intensive and time-consuming. The present work investigates the use of two quantitative image analysis (QIA) procedures specifically developed for PHA inclusions identification and quantification. MMC obtained from an EBPR system were visualized by bright-field and fluorescence microscopy for PHA inclusions detection, upon Sudan Black B (SBB) and Nile Blue A (NBA) staining, respectively. The captured color images were processed by QIA techniques and the image analysis data were further treated using multivariate statistical analysis. Partial least squares (PLS) regression coefficients of 0.90 and 0.86 were obtained between QIA parameters and PHA concentrations using SBB and NBA, respectively. It was found that both staining procedures might be seen as alternative methodologies to classical PHA determination. PMID:25732579

  7. Numerical Modeling Analysis of Hydrodynamic and Microbial Controls on DNAPL Pool Dissolution and Detoxification: Dehalorespirers in Co-culture

    SciTech Connect

    Wesseldyke, Eric S.; Becker, Jennifer G.; Seagren, Eric A.; Mayer, Alex S.; Zhang, Changyong

    2015-04-01

    Dissolution of dense non-aqueous phase liquid (DNAPL) contaminants like tetrachloroethene (PCE) can be “bioenhanced” via biodegradation, which increases the concentration gradient at the DNAPL–water interface. Model simulations were used to evaluate the impact of ecological interactions between different dehalorespiring strains and hydrodynamics on the bioenhancement effect and the extent of PCE dechlorination. Simulations were performed using a two-dimensional coupled flow-transport model, with a DNAPL pool source and two microbial species, Dehalococcoides mccartyi 195 and Desulfuromonas michiganensis, which compete for electron acceptors (e.g., PCE), but not for their electron donors. Under biostimulation, low vx conditions, D. michiganensis alone significantly enhanced dissolution by rapidly utilizing aqueous-phase PCE. In co-culture under these conditions, D. mccartyi 195 increased this bioenhancement modestly and greatly increased the extent of PCE transformation. Although D. michiganensis was the dominant population under low velocity conditions, D. mccartyi 195 dominated under high velocity conditions due to bioclogging effects.

  8. Microbial protein production in activated suspension tanks manipulating C:N ratio in feed and the implications for fish culture.

    PubMed

    Azim, M E; Little, D C; Bron, J E

    2008-06-01

    The present experiment investigated the possibility of microbial protein production in 250 l indoor tanks by manipulating C:N ratio in fish feed applied. Two different levels of protein feed (35% and 22% CP) resulting in C:N ratio of 8.4 and 11.6, respectively, were applied at 25 g daily in each tank. Tanks were aerated and agitated continuously using a dome diffuser. The experiment was carried out for eight weeks. The biofloc development in terms of VSS and BOD5 was better in the low protein fed tanks than in the high protein fed tanks. An estimated biofloc productivity ranged 3-5 g Cm(-3)day(-1). A 3-D image stained with DAPI indicates that the biofloc is comprised of hundreds of bacterial nuclei, size being ranged from 100 to 200 microm. Biofloc quality was independent of the quality of feed applied and contained more than 50% crude protein, 2.5% crude lipid, 4% fibre, 7% ash and 22 kJ g(-1) energy on dry matter basis. The dietary composition and size of biofloc can be considered as appropriate for all omnivorous fish species. The underlying ecological processes are explained through factor analysis. The potential of using biofloc in fish culture is also discussed.

  9. Persistence of the tissue culture origin vaccine for infectious laryngotracheitis virus in commercial chicken flocks in Brazil.

    PubMed

    Parra, Silvana H Santander; Nuñez, Luis F; Astolfi-Ferreira, Claudete S; Ferreira, Antonio J Piantino

    2015-11-01

    Infectious laryngotracheitis (ILT) is a respiratory disease of great importance that causes serious economic losses in the poultry industry. Its control is based on biosecurity procedures and vaccination programs that use live attenuated vaccines such as tissue culture origin (TCO), chicken embryo origin (CEO), and vectored vaccines. However, problems have been reported, such as the reversion of virulence, virus latency, and field virus outbreaks. Several molecular techniques have been developed to differentiate between the field and vaccine strains. This study was conducted to determine the presence of infectious laryngotracheitis virus (ILTV) in Brazil from 2012 to 2014. PCR-RFLP (restriction fragment length polymorphism) was used to detect and differentiate ILTV strains; DNA sequencing and predictive RFLP analysis were also used for this purpose. Molecular analysis detected the presence of ILTV in 15 samples that were characterized as strains of TCO vaccine origin. This study showed that the ILTV TCO vaccine strain has been circulating in commercial chicken flocks in Brazil since its introduction during the 2002 outbreak.

  10. Efficacy of a vaccine and a direct-fed microbial against fecal shedding of Escherichia coli O157:H7 in a randomized pen-level field trial of commercial feedlot cattle.

    PubMed

    Cull, Charley A; Paddock, Zachary D; Nagaraja, T G; Bello, Nora M; Babcock, Abram H; Renter, David G

    2012-09-21

    Our primary objective was to determine the efficacy of a siderophore receptor and porin proteins-based vaccine (VAC) and a Lactobacillus acidophilus-based direct-fed microbial (DFM) against fecal shedding of Escherichia coli O157:H7 in commercial feedlot cattle fed a corn grain-based diet with 25% distiller's grains. Cattle projected to be on a finishing diet during the summer were randomly allocated into 40 study pens within ten blocks based on allocation dates. Blocks were complete; each of the four pens within a block was randomly assigned one treatment: control, VAC, DFM, or VAC+DFM. The DFM was fed (10⁶CFU/animal/day of Lactobacillus) throughout the study periods (84-88 days) and cattle were vaccinated at enrollment and again three weeks later. Fresh fecal samples (30/pen) from pen floors were collected weekly for four consecutive weeks (study days 52-77). Two concurrent culture procedures were used to enable estimates of E. coli O157:H7 shedding prevalence and prevalence of high shedders. From 4800 total samples, 1522 (31.7%) were positive for E. coli O157:H7 and 169 (3.5%) were considered high shedders. Pen-level linear mixed models were used for data analyses. There were no significant interactions among treatments and time of sampling. However, vaccinated pens had lower (P<0.01) overall prevalence of E. coli O157:H7 (model-adjusted mean ± SEM=17.4 ± 3.95%) and lower (P<0.01) prevalence of high shedders (0.95 ± 0.26%) than unvaccinated pens (37.0 ± 6.32% and 4.19 ± 0.81%, respectively). There was no evidence of a DFM effect on either measure of E. coli O157:H7 shedding. Results indicate that a two-dose regimen of the vaccine significantly reduces fecal prevalence of E. coli O157:H7 (vaccine efficacy of 53.0%) and prevalence of E. coli O157:H7 high shedders (vaccine efficacy of 77.3%) in commercial feedlot cattle reared in the summer on a finishing diet with 25% distiller's grains.

  11. The potential of autochthonous microbial culture encapsulation in a confined environment for phenol biodegradation.

    PubMed

    Azaizeh, Hassan; Kurzbaum, Eyal; Said, Ons; Jaradat, Husain; Menashe, Ofir

    2015-10-01

    Olive mill wastewater (OMWW) is claimed to be one of the most polluting effluents produced by agro-food industries, providing high contaminants load that encase cytotoxic agents such as phenolic and polyphenolic compounds. Therefore, a significant and continuous stress episode is induced once the mixed liquor of the wastewater treatment plants (WWTP's) is being exposed to OMWW. The use of bio-augmentation treatment procedures can be useful to eliminate or reduce such stress episodes. In this study, we have estimated the use of autochthonous biomass implementation within small bioreactor platform (SBP) particles as a bio-augmentation method to challenge against WWTPs stress episodes. Our results showed that SBP particles significantly reduced the presence of various phenolics: tannic, gallic and caffeic acid in a synthetic medium and in crude OMWW matrix. Moreover, the SBP particles succeeded to biodegrade a very high concentration of phenol blend (3000 mg L(-1)). Our findings indicated that the presence of the SBP microfiltration membrane has reduced the phenol biodegradation rate by 50 % compared to the same suspended culture. Despite the observed reduction in biodegradation rate, encapsulation in a confined environment can offer significant values such as overcoming the grazing forcers and dilution, thus achieving a long-term sufficient biomass. The potential for reducing stress episodes caused by cytotoxic agents through bio-augmentation treatment procedure using the SBP technology is discussed. PMID:26250809

  12. Bioelectricity production from microbial fuel cell using mixed bacterial culture isolated from distillery wastewater.

    PubMed

    Samsudeen, N; Radhakrishnan, T K; Matheswaran, Manickam

    2015-11-01

    The effect of various system parameters such as wastewater Chemical Oxygen Demand (COD) concentration, pH, conductivity, membrane size and thickness on efficient energy production using mixed isolated culture from the distillery wastewater in the MFC was studied. The power density increased with increase in the anolyte pH from 6 to 8. The peak power density and COD removal efficiency was observed as 63.8±0.65 mW/m(2) and 63.5±1.5% at pH 8, respectively. The MFC performance increased with increasing COD concentration (800-3200 mg/l), conductivity (1.1-9.7 mS/cm) and membrane area (8-24 cm(2)). The MFC operating with wastewater COD concentration of 3200 mg/l and its conductivity of 9.7 mS/cm produced the highest power density of 202±6 mW/m(2) with a corresponding current density of 412±12 mA/m(2). The results showed that the efficient electricity generation and simultaneous treatment of distillery wastewater can be attained in the MFC.

  13. The potential of autochthonous microbial culture encapsulation in a confined environment for phenol biodegradation.

    PubMed

    Azaizeh, Hassan; Kurzbaum, Eyal; Said, Ons; Jaradat, Husain; Menashe, Ofir

    2015-10-01

    Olive mill wastewater (OMWW) is claimed to be one of the most polluting effluents produced by agro-food industries, providing high contaminants load that encase cytotoxic agents such as phenolic and polyphenolic compounds. Therefore, a significant and continuous stress episode is induced once the mixed liquor of the wastewater treatment plants (WWTP's) is being exposed to OMWW. The use of bio-augmentation treatment procedures can be useful to eliminate or reduce such stress episodes. In this study, we have estimated the use of autochthonous biomass implementation within small bioreactor platform (SBP) particles as a bio-augmentation method to challenge against WWTPs stress episodes. Our results showed that SBP particles significantly reduced the presence of various phenolics: tannic, gallic and caffeic acid in a synthetic medium and in crude OMWW matrix. Moreover, the SBP particles succeeded to biodegrade a very high concentration of phenol blend (3000 mg L(-1)). Our findings indicated that the presence of the SBP microfiltration membrane has reduced the phenol biodegradation rate by 50 % compared to the same suspended culture. Despite the observed reduction in biodegradation rate, encapsulation in a confined environment can offer significant values such as overcoming the grazing forcers and dilution, thus achieving a long-term sufficient biomass. The potential for reducing stress episodes caused by cytotoxic agents through bio-augmentation treatment procedure using the SBP technology is discussed.

  14. Effects of enzyme supplementation of a total mixed ration on microbial fermentation in continuous culture, maintained at high and low pH.

    PubMed

    Colombatto, D; Hervás, G; Yang, W Z; Beauchemin, K A

    2003-10-01

    A dual-flow continuous culture system was used to investigate the effects of pH and addition of an enzyme mixture to a total mixed ration (TMR) on fermentation, nutrient digestion, and microbial protein synthesis. A 4 x 4 Latin square design with a factorial arrangement of treatments was used, with four 9-d periods consisting of 6 d for adaptation and 3 d for measurements. Treatments were as follows: 1) high pH with control TMR, 2) high pH with TMR treated with enzyme, 3) low pH with control TMR, and 4) low pH with TMR treated with enzyme. Ranges of pH were 6.0 to 6.6 and 5.4 to 6.0 for high and low, respectively. Fermenters were fed twice daily a TMR consisting of 30% alfalfa hay, 30% corn silage, and 40% rolled corn (DM basis). The silage was milled fresh and the TMR was fed to the fermenters in fresh form (64% DM). The enzyme mixture was a commercial product of almost exclusive protease activity; it was applied daily to the fresh TMR and stored at 4 degrees C for at least 12 h before feeding. Degradability of OM, NDF, ADF, and cellulose was decreased (P < 0.05) by low pH. Hemicellulose and protein degradation were not affected by pH. Enzyme addition increased (P < 0.01) NDF degradability (by 43% and 25% at high and low pH, respectively), largely as a result of an increase in hemicellulose degradation (by 79% and 51% at high and low pH, respectively). This improvement was supported by an increase (P < 0.05) in the xylanase and cellulase activities in the liquid phase of the fermenter contents. Total VFA were decreased (P < 0.05) by low pH, but were not affected by enzyme addition. Total bacterial numbers were increased (P < 0.03) at low pH and tended (P < 0.13) to increase with enzyme addition. Cellulolytic bacteria in effluent fluid were decreased (P < 0.02) at low pH but were unaffected by enzyme addition. Despite a large increase (P < 0.001) in protease activity, protein degradation was only numerically increased by enzyme addition. Microbial protein synthesis

  15. Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars.

    PubMed

    Dutta, Jintu; Handique, Pratap J; Thakur, Debajit

    2015-01-01

    In the present study, 217 rhizobacterial isolates were obtained from six different tea estates of Assam, India and subjected to preliminary in vitro plant growth promotion (PGP) screening for indole acetic acid (IAA) production, phosphate solubilization, siderophore production and ammonia production. Fifty isolates showed all the PGP traits and five isolates did not exhibit any PGP traits. These 50 potential isolates were further analyzed for quantitative estimation of the PGP traits along with the aminocyclopropane-1-carboxylate (ACC) deaminase, protease and cellulose production. After several rounds of screening, four rhizobacteria were selected based on their maximum ability to produce in vitro PGP traits and their partial 16S rRNA gene sequence analysis revealed that they belong to Enterobacter lignolyticus strain TG1, Burkholderia sp. stain TT6, Bacillus pseudomycoides strain SN29 and Pseudomonas aeruginosa strain KH45. To evaluate the efficacy of these four rhizobacteria as plant growth promoters, three different commercially important tea clones TV1, TV19, and TV20 plants were inoculated with these rhizobacteria in greenhouse condition and compared to the uninoculated control plants. Though, all the rhizobacterial treatments showed an increase in plant growth compared to control but the multivariate PCA analysis confirmed more growth promotion by TG1 and SN29 strains than the other treatments in all three clones. To validate this result, the fold change analysis was performed and it revealed that the tea clone TV19 plants inoculated with the E. lignolyticus strain TG1 showed maximum root biomass production with an increase in 4.3-fold, shoot biomass with increase in 3.1-fold, root length by 2.2-fold and shoot length by 1.6-fold. Moreover, two way ANOVA analysis also revealed that rhizobacterial treatment in different tea clones showed the significant increase (P < 0.05) in growth promotion compared to the control. Thus, this study indicates that the

  16. Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars

    PubMed Central

    Dutta, Jintu; Handique, Pratap J.; Thakur, Debajit

    2015-01-01

    In the present study, 217 rhizobacterial isolates were obtained from six different tea estates of Assam, India and subjected to preliminary in vitro plant growth promotion (PGP) screening for indole acetic acid (IAA) production, phosphate solubilization, siderophore production and ammonia production. Fifty isolates showed all the PGP traits and five isolates did not exhibit any PGP traits. These 50 potential isolates were further analyzed for quantitative estimation of the PGP traits along with the aminocyclopropane-1-carboxylate (ACC) deaminase, protease and cellulose production. After several rounds of screening, four rhizobacteria were selected based on their maximum ability to produce in vitro PGP traits and their partial 16S rRNA gene sequence analysis revealed that they belong to Enterobacter lignolyticus strain TG1, Burkholderia sp. stain TT6, Bacillus pseudomycoides strain SN29 and Pseudomonas aeruginosa strain KH45. To evaluate the efficacy of these four rhizobacteria as plant growth promoters, three different commercially important tea clones TV1, TV19, and TV20 plants were inoculated with these rhizobacteria in greenhouse condition and compared to the uninoculated control plants. Though, all the rhizobacterial treatments showed an increase in plant growth compared to control but the multivariate PCA analysis confirmed more growth promotion by TG1 and SN29 strains than the other treatments in all three clones. To validate this result, the fold change analysis was performed and it revealed that the tea clone TV19 plants inoculated with the E. lignolyticus strain TG1 showed maximum root biomass production with an increase in 4.3-fold, shoot biomass with increase in 3.1-fold, root length by 2.2-fold and shoot length by 1.6-fold. Moreover, two way ANOVA analysis also revealed that rhizobacterial treatment in different tea clones showed the significant increase (P < 0.05) in growth promotion compared to the control. Thus, this study indicates that the

  17. Inflight Microbial Monitoring - An Alternative Method to Culture Based Detection Currently Used on the International Space Station

    NASA Technical Reports Server (NTRS)

    Khodadad, Christina L.; Birmele, Michele N.; Hummerick, Mary E.; Roman, Monsi; Smith, David J.

    2015-01-01

    Microorganisms including potential human pathogens have been detected on the International Space Station (ISS). The potential to introduce new microorganisms occurs with every exchange of crew or addition of equipment or supplies. Current microbial monitoring methods require enrichment of microorganisms and a 48-hour incubation time resulting in an increase in microbial load, detecting a limited number of unidentified microorganisms. An expedient, low-cost, in-flight method of microbial detection, identification, and enumeration is warranted.

  18. Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona.

    PubMed

    Ikner, Luisa A; Toomey, Rickard S; Nolan, Ginger; Neilson, Julia W; Pryor, Barry M; Maier, Raina M

    2007-01-01

    Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year-1) and compared to samples taken from areas designated as having medium (30-40 visitors year-1) and low (2-3 visitors year-1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations. PMID:17186153

  19. Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona.

    PubMed

    Ikner, Luisa A; Toomey, Rickard S; Nolan, Ginger; Neilson, Julia W; Pryor, Barry M; Maier, Raina M

    2007-01-01

    Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year-1) and compared to samples taken from areas designated as having medium (30-40 visitors year-1) and low (2-3 visitors year-1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations.

  20. Kinetics of microbial methionine metabolism in continuous cultures administered different methionine sources.

    PubMed

    Firkins, J L; Fowler, C M; Devillard, E; Bequette, B J

    2015-02-01

    The Met precursor 2-hydroxy-4-(methylthio) butanoic acid (HMB) is expected to be more extensively degraded in the rumen than its isopropyl ester (HMBi). A control and 3 isomolar treatments-0.097% dl-methionine, 0.11% HMBi (HMBi), and 0.055% HMBi plus 0.048% Met (Met + HMBi)-were dosed every 8h simultaneously with 3-times-daily feeding into continuous cultures. Starting on d 9, for 6 consecutive doses, both [1-(13)C]-l-Met and [methyl-(2)H3]-l-Met replaced part of the unlabeled dl-Met, [(13)C5]-dl-HMBi replaced a portion of the unlabeled dl-HMBi, and [1-(13)C]-l-Met plus [(13)C5]-dl-HMBi replaced a portion of the respective unlabeled doses for the Met + HMBi treatment. After the sixth dose (d 11), unlabeled Met or HMBi provided 100% of the doses to follow elimination kinetics of the labels in HMBi, free Met, and bacterial Met compartments. The free [1-(13)C]-l-Met recycled more and was recovered in bacterial Met to a lesser extent than was the free [methyl-(2)H3]-l-Met recycling and that was recovered in bacterial Met. Increasing HMBi inclusion (0, 50, and 100% substitution of the exogenously dosed Met on a molar equivalent basis) tended to increase HMBi escape from 54.7 to 71.3% for the 50 and 100% HMBi treatments, respectively. Despite HMBi substituting for and decreasing the dosage of Met, increasing HMBi increased accumulation of free Met in fermenter fluid. The HMBi (after de-esterification of the isopropyl group) presumably produces Met through the intermediate α-ketomethylthyiobutyrate with an aminotransferase that also has high affinity for branched-chain AA. We provide evidence that the HMBi-derived Met is likely released from bacterial cells and accumulates rather than being degraded, potentially as a result of lagging d-stereoisomer metabolism. More research is needed to evaluate racemization and metabolism of stereoisomers of HMBi, Met, and other AA in ruminal microbes.

  1. Family fun or cultural free-for-all? A critique of the 2015 National Football League Super Bowl commercials

    PubMed Central

    Basch, Corey H.; Kernan, William D; Reeves, Rachel

    2016-01-01

    Background: The purpose of this cross-sectional study was to enumerate and describe violent and risky behaviors as well as other general health behaviors exhibited in the advertisements during the National Football League (NFL) Super Bowl 2015. Methods: Commercials during the NFL Super Bowl 2015 were assessed for violent and risky behaviors. Additional health behaviors were indicated such as the advertisement of unhealthy food, promotion of physical activity, and sexual content. Results: A total of 110 commercials were documented, accounting for 64 minutes of broadcast time. Commercials promoting automobiles, television shows, food, and movies were the most prevalent, representing just over half (53.7%) of all of the advertisements featured. Depictions of unsafe driving were found in 10.9% (n = 12) of the commercials. All 12 commercials contained some sort of risky or wild driving behavior, and speeding was observed in 11 of the 12 commercials. A total of 32 (29.1%) of the commercials were coded as including violent content.Physical activity behavior was present in 3 (2.7%) of the commercials. Conversely, substance use was observed in 3 (2.7%) of the commercials, none of which included health promotion messaging. Of the 110 commercials aired during the 2015 Super Bowl, 12.7% (n = 14) included sexual content. Conclusion: Parents should consider the possibility that their children may observe acts of violence or conflicting safety messages during commercial breaks. PMID:27123435

  2. Establishment of microbial eukaryotic enrichment cultures from a chemically stratified antarctic lake and assessment of carbon fixation potential.

    PubMed

    Dolhi, Jenna M; Ketchum, Nicholas; Morgan-Kiss, Rachael M

    2012-01-01

    Lake Bonney is one of numerous permanently ice-covered lakes located in the McMurdo Dry Valleys, Antarctica. The perennial ice cover maintains a chemically stratified water column and unlike other inland bodies of water, largely prevents external input of carbon and nutrients from streams. Biota are exposed to numerous environmental stresses, including year-round severe nutrient deficiency, low temperatures, extreme shade, hypersalinity, and 24-hour darkness during the winter (1). These extreme environmental conditions limit the biota in Lake Bonney almost exclusively to microorganisms (2). Single-celled microbial eukaryotes (called "protists") are important players in global biogeochemical cycling (3) and play important ecological roles in the cycling of carbon in the dry valley lakes, occupying both primary and tertiary roles in the aquatic food web. In the dry valley aquatic food web, protists that fix inorganic carbon (autotrophy) are the major producers of organic carbon for organotrophic organisms (4, 2). Phagotrophic or heterotrophic protists capable of ingesting bacteria and smaller protists act as the top predators in the food web (5). Last, an unknown proportion of the protist population is capable of combined mixotrophic metabolism (6, 7). Mixotrophy in protists involves the ability to combine photosynthetic capability with phagotrophic ingestion of prey microorganisms. This form of mixotrophy differs from mixotrophic metabolism in bacterial species, which generally involves uptake dissolved carbon molecules. There are currently very few protist isolates from permanently ice-capped polar lakes, and studies of protist diversity and ecology in this extreme environment have been limited (8, 4, 9, 10, 5). A better understanding of protist metabolic versatility in the simple dry valley lake food web will aid in the development of models for the role of protists in the global carbon cycle. We employed an enrichment culture approach to isolate potentially

  3. Culture-dependent comparison of microbial diversity in deep granitic groundwater from two sites considered for a Swedish final repository of spent nuclear fuel.

    PubMed

    Hallbeck, Lotta; Pedersen, Karsten

    2012-07-01

    Site selection for a spent nuclear fuel (SNF) repository required analysis of microbial abundance and diversity at two Swedish sites, Forsmark and Laxemar-Simpevarp. Information about sulphate-reducing bacteria (SRB) was required, as sulphide could corrode copper SNF canisters. Total number of cells (TNC) and ATP were analysed, and plate counts and most probable number (MPN) analyses were conducted using eight media based on different electron donors and acceptors for specific microorganism physiological groups. Groundwater chemical composition and E(h) were analysed; sampling depths were 112-978 m below sea level. TNC was 5.5 × 10(3) to 4.7 × 10(5) cells mL(-1), correlating with ATP concentrations. Culturability in TNC percentage was 0.01-35.9, averaging 5.12. Culturable numbers varied greatly between sample positions and uncorrelated with depth. SRB were found in 29 samples and were below detection in three; the MPN of SRB correlated negatively with E(h), as did the MPN of acetogens. Data indicated that microbial sulphate reduction was ongoing in many sampled aquifers; published stable isotope data and modelling results supported this observation. The sites did not differ significantly, but the large data range suggested that analysis of more samples would enable detailed evaluation of microbial processes and their relationship with geochemical information.

  4. Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

    SciTech Connect

    Boaro, Amy A.; Kim, Young-Mo; Konopka, Allan; Callister, Stephen J.; Ahring, Birgitte K.

    2014-12-01

    Integrated ‘omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated ‘omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function such as cellulose degradation. However, 16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes two days after the perturbation followed by increased protein abundances six days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing two days after the perturbation and increasing after six days. This study demonstrated that community ‘omics data provides valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.

  5. Integrated 'omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture.

    PubMed

    Boaro, Amy A; Kim, Young-Mo; Konopka, Allan E; Callister, Stephen J; Ahring, Birgitte K

    2014-12-01

    Integrated 'omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated 'omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function in terms of cellulose degradation. However, 16S rDNA gene pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes 2 days after the perturbation followed by increased protein abundances 6 days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing 2 days after the perturbation and increasing after 6 days. This study demonstrated that community 'omics data provide valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.

  6. Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques.

    PubMed

    Ryssel, Mia; Johansen, Pernille; Al-Soud, Waleed Abu; Sørensen, Søren; Arneborg, Nils; Jespersen, Lene

    2015-12-23

    Microbial successions on the surface and in the interior of surface ripened semi-hard Danish Danbo cheeses were investigated by culture-dependent and -independent techniques. Culture-independent detection of microorganisms was obtained by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture-independent techniques correlated, a higher number of genera were detected by pyrosequencing compared to DGGE. Additionally, minor parts of the microbiota, i.e. comprising <10.0% of the operational taxonomic units (OTUs), were detected by pyrosequencing, resulting in more detailed information on the microbial succession. As expected, microbial profiles of the surface and the interior of the cheeses diverged. During cheese production pyrosequencing determined Lactococcus as the dominating genus on cheese surfaces, representing on average 94.7%±2.1% of the OTUs. At day 6 Lactococcus spp. declined to 10.0% of the OTUs, whereas Staphylococcus spp. went from 0.0% during cheese production to 75.5% of the OTUs at smearing. During ripening, i.e. from 4 to 18 weeks, Corynebacterium was the dominant genus on the cheese surface (55.1%±9.8% of the OTUs), with Staphylococcus (17.9%±11.2% of the OTUs) and Brevibacterium (10.4%±8.3% of the OTUs) being the second and third most abundant genera. Other detected bacterial genera included Clostridiisalibacter (5.0%±4.0% of the OTUs), as well as Pseudoclavibacter, Alkalibacterium and Marinilactibacillus, which represented <2% of the OTUs. At smearing, yeast counts were low with Debaryomyces being the dominant genus accounting for 46.5% of the OTUs. During ripening the yeast counts increased significantly with Debaryomyces being the predominant genus

  7. Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques.

    PubMed

    Ryssel, Mia; Johansen, Pernille; Al-Soud, Waleed Abu; Sørensen, Søren; Arneborg, Nils; Jespersen, Lene

    2015-12-23

    Microbial successions on the surface and in the interior of surface ripened semi-hard Danish Danbo cheeses were investigated by culture-dependent and -independent techniques. Culture-independent detection of microorganisms was obtained by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture-independent techniques correlated, a higher number of genera were detected by pyrosequencing compared to DGGE. Additionally, minor parts of the microbiota, i.e. comprising <10.0% of the operational taxonomic units (OTUs), were detected by pyrosequencing, resulting in more detailed information on the microbial succession. As expected, microbial profiles of the surface and the interior of the cheeses diverged. During cheese production pyrosequencing determined Lactococcus as the dominating genus on cheese surfaces, representing on average 94.7%±2.1% of the OTUs. At day 6 Lactococcus spp. declined to 10.0% of the OTUs, whereas Staphylococcus spp. went from 0.0% during cheese production to 75.5% of the OTUs at smearing. During ripening, i.e. from 4 to 18 weeks, Corynebacterium was the dominant genus on the cheese surface (55.1%±9.8% of the OTUs), with Staphylococcus (17.9%±11.2% of the OTUs) and Brevibacterium (10.4%±8.3% of the OTUs) being the second and third most abundant genera. Other detected bacterial genera included Clostridiisalibacter (5.0%±4.0% of the OTUs), as well as Pseudoclavibacter, Alkalibacterium and Marinilactibacillus, which represented <2% of the OTUs. At smearing, yeast counts were low with Debaryomyces being the dominant genus accounting for 46.5% of the OTUs. During ripening the yeast counts increased significantly with Debaryomyces being the predominant genus

  8. What they eat is how they fractionate: controls on sulfur isotope fractionations during microbial sulfate reduction in culture and nature (Invited)

    NASA Astrophysics Data System (ADS)

    Bosak, T.; Sim, M.; Donovan, K.; Grabenstatter, J. D.; Ono, S.

    2010-12-01

    Some of the largest sulfur isotope effects are produced by microbial dissimilatory sulfate reduction. This biological signature is used to reconstruct the oxygenation of Earth’s surface, the coupled cycling of carbon and sulfur through geologic time and to constrain the evolution of sulfur-based metabolisms. However, mechanistic links between the isotopic signatures of sedimentary sulfides and sulfates and microbial physiologies and growth conditions are poorly understood. To address this, we investigate the fractionation of sulfur isotopes by marine sulfate reducing bacteria as a function of the type and the availability of the electron donors. DMSS-1, a bacterium that is unable to completely oxidize acetate to CO2, produces isotope effects between 5-46 ‰ during active growth on various electron donors in batch and continuous cultures. Overall, the largest isotope effects are produced at very slow dilution and growth rates, but appear to correlate best with the rate at which cells release free energy. Maximum sulfur isotope effects in continuous cultures are produced during very slow growth, when the physiology of the organism is visibly altered. Because the same genetic and enzymatic machinery can yield fractionations from ~ 5 to 46 ‰, we conclude that the upper range of sulfur isotope effects during microbial sulfate reduction depends primarily on the coupling between the intracellular processes coupling the oxidation of carbon to the reduction of sulfur. Future work will attempt to identify these processes and the underlying enzymatic machinery by identifying the changes in the expression of genes during microbial growth under conditions that yield low and high sulfur isotope effects.

  9. In-Flight Microbial Monitor

    NASA Technical Reports Server (NTRS)

    Zeitlin, Nancy; Mullenix, Pamela; Wheeler, Raymond M.; Ruby, Anna Maria

    2015-01-01

    Previous research has shown that potential human pathogens have been detected on the International Space Station (ISS). New microorganisms are introduced with every exchange of crew and cargo. Microorganisms introduced to the ISS are readily transferred between crew and subsystems (i.e., ECLSS, environmental control and life support systems). Current microbial characterization methods require a culture-based enrichment of microorganisms and at least a 48-hour incubation time. This increases the microbial load while detecting only a limited number of microorganisms. The culture-based method detects approximately 1-10% of the total organisms present and provides no identification. To identify and enumerate ISS samples requires that the microbes be returned to Earth for complete analysis. Therefore, a more expedient, low-cost, inflight method of microbial detection, identification, and enumeration is needed. The RAZOR EX, a ruggedized, commercial off the shelf, real-time PCR field instrument was tested for its ability to detect microorganisms at low concentrations within one hour. Escherichia coli, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa were detected at low levels using real-time DNA amplification. Total heterotrophic counts could also be detected using a 16S gene marker that can identify up to 98% of all bacteria. To reflect viable cells found in the samples, RNA was also detectable using a modified, single-step reverse transcription reaction.

  10. Investigating unsaturated fat, monensin, or bromoethanesulfonate in continuous cultures retaining ruminal protozoa. I. Fermentation, biohydrogenation, and microbial protein synthesis.

    PubMed

    Karnati, S K R; Sylvester, J T; Ribeiro, C V D M; Gilligan, L E; Firkins, J L

    2009-08-01

    Methane is an end product of ruminal fermentation that is energetically wasteful and contributes to global climate change. Bromoethanesulfonate, animal-vegetable fat, and monensin were compared with a control treatment to suppress different functional groups of ruminal prokaryotes in the presence or absence of protozoa to evaluate changes in fermentation, digestibility, and microbial N outflow. Four dual-flow continuous culture fermenter systems were used in 4 periods in a 4 x 4 Latin square design split into 2 subperiods. In subperiod 1, a multistage filter system (50-microm smallest pore size) retained most protozoa. At the start of subperiod 2, conventional filters (300-microm pore size) were substituted to efflux protozoa via filtrate pumps over 3 d; after a further 7 d of adaptation, the fermenters were sampled for 3 d. Treatments were retained during both subperiods. Flow of total N and digestibilities of NDF and OM were 18, 16, and 9% higher, respectively, for the defaunated subperiod but were not different among treatments. Ammonia concentration was 33% higher in the faunated fermenters but was not affected by treatment. Defaunation increased the flow of nonammonia N and bacterial N from the fermenters. Protozoal counts were not different among treatments, but bromoethanesulfonate increased the generation time from 43.2 to 55.6 h. Methanogenesis was unaffected by defaunation but tended to be increased by unsaturated fat. Defaunation did not affect total volatile fatty acid production but decreased the acetate:propionate ratio; monensin increased production of isovalerate and valerate. Biohydrogenation of unsaturated fatty acids was impaired in the defaunated fermenters because effluent flows of oleic, linoleic, and linolenic acids were 60, 77, and 69% higher, and the ratio of vaccenic acid:unsaturated FA ratio was decreased by 34% in the effluent. This ratio was increased in both subperiods with the added fat diet, indicating an accumulation of

  11. Changes in microbial communities, including both uncultured and culturable bacteria, with mid-ocean ballast-water exchange during a voyage from Japan to Australia.

    PubMed

    Tomaru, Akiko; Kawachi, Masanobu; Demura, Mikihide; Fukuyo, Yasuwo

    2014-01-01

    We assessed changes in the microbial communities in ballast water during a trans-Pacific voyage from Japan to Australia that included a mid-ocean ballast-water exchange. Uncultured (i.e., total) and culturable bacteria were counted and were characterized by using denaturing gradient gel electrophoresis (DGGE). There was a clear decrease over time in numbers of uncultured microorganisms, except for heterotrophic nanoflagellates, whereas the abundance of culturable bacteria initially decreased after the ballast-water exchange but then increased. The increase, however, was only up to 5.34% of the total number of uncultured bacteria. Cluster analysis showed that the DGGE profiles of uncultured bacteria clearly changed after the exchange. In contrast, there was no clear change in the DGGE profiles of culturable bacteria after the exchange. Multidimensional scaling analysis showed changes in microbial communities over the course of the voyage. Although indicator microbes as defined by the International Convention for the Control and Management of Ships' Ballast Water and Sediments were occasionally detected, no coliform bacteria were detected after the exchange.

  12. Changes in Microbial Communities, Including both Uncultured and Culturable Bacteria, with Mid-Ocean Ballast-Water Exchange during a Voyage from Japan to Australia

    PubMed Central

    Tomaru, Akiko; Kawachi, Masanobu; Demura, Mikihide; Fukuyo, Yasuwo

    2014-01-01

    We assessed changes in the microbial communities in ballast water during a trans-Pacific voyage from Japan to Australia that included a mid-ocean ballast-water exchange. Uncultured (i.e., total) and culturable bacteria were counted and were characterized by using denaturing gradient gel electrophoresis (DGGE). There was a clear decrease over time in numbers of uncultured microorganisms, except for heterotrophic nanoflagellates, whereas the abundance of culturable bacteria initially decreased after the ballast-water exchange but then increased. The increase, however, was only up to 5.34% of the total number of uncultured bacteria. Cluster analysis showed that the DGGE profiles of uncultured bacteria clearly changed after the exchange. In contrast, there was no clear change in the DGGE profiles of culturable bacteria after the exchange. Multidimensional scaling analysis showed changes in microbial communities over the course of the voyage. Although indicator microbes as defined by the International Convention for the Control and Management of Ships' Ballast Water and Sediments were occasionally detected, no coliform bacteria were detected after the exchange. PMID:24817212

  13. From genetic improvement to commercial-scale mass culture of a Chilean strain of the green microalga Haematococcus pluvialis with enhanced productivity of the red ketocarotenoid astaxanthin

    PubMed Central

    Gómez, Patricia I.; Inostroza, Ingrid; Pizarro, Mario; Pérez, Jorge

    2013-01-01

    Astaxanthin is a red ketocarotenoid, widely used as a natural red colourant in marine fish aquaculture and poultry and, recently, as an antioxidant supplement for humans and animals. The green microalga Haematococcus pluvialis is one of the richest natural sources of this pigment. However, its slow growth rate and complex life cycle make mass culture difficult for commercial purposes. The aims of this research were (i) to standardize and apply a genetic improvement programme to a Chilean strain of H. pluvialis in order to improve its carotenogenic capacity and (ii) to evaluate the performance of a selected mutant strain in commercial-sized (125 000 L) open ponds in the north of Chile. Haematococcus pluvialis strain 114 was mutated by ethyl methanesulfonate. The level of mutagen dose (exposure time and concentration) was one that induced at least 90 % mortality. Surviving colonies were screened for resistance to the carotenoid biosynthesis inhibitor diphenylamine (25 µM). Resistant mutants were grown in a 30-mL volume for 30 days, after which the total carotenoid content was determined by spectrophotometry. Tens of mutants with improved carotenogenic capacity compared with the wild-type strain were isolated by the application of these standardized protocols. Some mutants exhibited curious morphological features such as spontaneous release of astaxanthin and loss of flagella. One of the mutants was grown outdoors in commercial-sized open ponds of 125 000 L in the north of Chile. Grown under similar conditions, the mutant strain accumulated 30 % more astaxanthin than the wild-type strain on a per dry weight basis and 72 % more on a per culture volume basis. We show that random mutagenesis/selection is an effective strategy for genetically improving strains of H. pluvialis and that improved carotenogenic capacity is maintained when the volume of the cultures is scaled up to a commercial size. PMID:23789055

  14. Evaluation of microbial stability, bioactive compounds, physicochemical properties, and consumer acceptance of pomegranate juice processed in a commercial scale pulsed electric field system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper investigated the feasibility for pasteurizing raw pomegranate juice in a commercial scale pulsed electric field (PEF) system. The juice was processed in a commercial scale PEF processing system at 35 and 38 kV/cm for 281 µs at 55 degree C with a flow rate of 100 L/h. Effect of PEF process...

  15. Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

    PubMed Central

    Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

    2016-01-01

    Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types. PMID:27485896

  16. Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process

    NASA Astrophysics Data System (ADS)

    Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

    2016-08-01

    Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types.

  17. Effects of carbon sources on the enrichment of halophilic polyhydroxyalkanoate-storing mixed microbial culture in an aerobic dynamic feeding process.

    PubMed

    Cui, You-Wei; Zhang, Hong-Yu; Lu, Peng-Fei; Peng, Yong-Zhen

    2016-01-01

    Microbial polyhydroxyalkanoate (PHA) production serves as a substitute for petroleum-based plastics. Enriching mixed microbial cultures (MMCs) with the capacity to store PHA is a key precursor for low-cost PHA production. This study investigated the impact of carbon types on enrichment outcomes. Three MMCs were separately fed by acetate sodium, glucose, and starch as an enriching carbon source, and were exposed to long-term aerobic dynamic feeding (ADF) periods. The PHA production capacity, kinetics and stoichiometry of the enrichments, the PHA composition, and the microbial diversity and community composition were explored to determine carbon and enrichment correlations. After 350-cycle enriching periods under feast-famine (F-F) regimes, the MMCs enriched by acetate sodium and glucose contained a maximum PHA content of 64.7% and 60.5% cell dry weight (CDW). The starch-enriched MMC only had 27.3% CDW of PHA. High-throughput sequencing revealed that non-PHA bacteria survived alongside PHA storing bacteria, even under severe F-F selective pressure. Genus of Pseudomonas and Stappia were the possible PHA accumulating bacteria in acetate-enriched MMC. Genus of Oceanicella, Piscicoccus and Vibrio were found as PHA accumulating bacteria in glucose-enriched MMC. Vibrio genus was the only PHA accumulating bacteria in starch-enriched MMC. The community diversity and composition were regulated by the substrate types. PMID:27485896

  18. Nitrogen availability of grape juice limits killer yeast growth and fermentation activity during mixed-culture fermentation with sensitive commercial yeast strains.

    PubMed Central

    Medina, K; Carrau, F M; Gioia, O; Bracesco, N

    1997-01-01

    The competition between selected or commercial killer strains of type K2 and sensitive commercial strains of Saccharomyces cerevisiae was studied under various conditions in sterile grape juice fermentations. The focus of this study was the effect of yeast inoculation levels and the role of assimilable nitrogen nutrition on killer activity. A study of the consumption of free amino nitrogen (FAN) by pure and mixed cultures of killer and sensitive cells showed no differences between the profiles of nitrogen assimilation in all cases, and FAN was practically depleted in the first 2 days of fermentation. The effect of the addition of assimilable nitrogen and the size of inoculum was examined in mixed killer and sensitive strain competitions. Stuck and sluggish wine fermentations were observed to depend on nitrogen availability when the ratio of killer to sensitive cells was low (1:10 to 1:100). A relationship between the initial assimilable nitrogen content of must and the proportion of killer cells during fermentation was shown. An indirect relationship was found between inoculum size and the percentage of killer cells: a smaller inoculum resulted in a higher proportion of killer cells in grape juice fermentations. In all cases, wines obtained with pure-culture fermentations were preferred to mixed-culture fermentations by sensory analysis. The reasons why killer cells do not finish fermentation under competitive conditions with sensitive cells are discussed. PMID:9212430

  19. RELATIONSHIPS BETWEEN CULTURABLE SOIL MICROBIAL POPULATIONS AND GROSS NITROGEN TRANSFORMATION PROCESSES IN A CLAY LOAM SOIL ACROSS ECOSYSTEMS

    EPA Science Inventory

    The size and quality of soil organic matter (SOM) pool can vary between ecosystems and can affect many soil properties. The objective of this study was to examine the relationship between gross N transformation rates and microbial populations and to investigate the role that SOM...

  20. Production of polyol oils from soybean oil by bioprocess: results of microbial screening and identification of positive cultures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recently we reported methods for microbial screening and production of polyol oils from soybean oil through bioprocessing (Hou and Lin, 2013). Soy-polyol oils (oxygenated acylglycerols) are important starting materials for the manufacture of polymers such as polyurethane. Currently, they are produce...

  1. Kako zapakirati islam: kulturalna politika u krajoliku komercijalne televizije (Packaging Islam: Cultural Politics on the Landscape of Commercial Television).

    ERIC Educational Resources Information Center

    Oncu, Ayse

    1995-01-01

    Considers the change in the media presentation of Islam in Turkey after the ascent of commercial television. Discusses the image of Islam and of Turkish politicians as presented in different contexts on TV--the "issuetization" of Islam for the consumption of the mainstream audience. (PA)

  2. Electroactive mixed culture biofilms in microbial bioelectrochemical systems: the role of temperature for biofilm formation and performance.

    PubMed

    Patil, Sunil A; Harnisch, Falk; Kapadnis, Balasaheb; Schröder, Uwe

    2010-10-15

    In this paper we investigate the temperature dependence and temperature limits of waste water derived anodic microbial biofilms. We demonstrate that these biofilms are active in a temperature range between 5°C and 45°C. Elevated temperatures during initial biofilm growth not only accelerate the biofilm formation process, they also influence the bioelectrocatalytic performance of these biofilms when measured at identical operation temperatures. For example, the time required for biofilm formation decreases from above 40 days at 15°C to 3.5 days at 35°C. Biofilms grown at elevated temperatures are more electrochemically active at these temperatures than those grown at lower incubation temperature. Thus, at 30°C current densities of 520 μA cm(-2) and 881 μA cm(-2) are achieved by biofilms grown at 22°C and 35°C, respectively. Vice versa, and of great practical relevance for waste water treatment plants in areas of moderate climate, at low operation temperatures, biofilms grown at lower temperatures outperform those grown at higher temperatures. We further demonstrate that all biofilms possess similar lower (0°C) and upper (50°C) temperature limits--defining the operational limits of a respective microbial fuel cell or microbial biosensor--as well as similar electrochemical electron transfer characteristics.

  3. Surface-to-surface biofilm transfer: a quick and reliable startup strategy for mixed culture microbial fuel cells.

    PubMed

    Vogl, Andreas; Bischof, Franz; Wichern, Marc

    2016-01-01

    The startup of microbial fuel cells (MFCs) is known to be prone to failure or result in erratic performance impeding the research. The aim of this study was to advise a quick launch strategy for laboratory-scale MFCs that ensures steady operation performance in a short period of time. Different startup strategies were investigated and compared with membraneless single chamber MFCs. A direct surface-to-surface biofilm transfer (BFT) in an operating MFC proved to be the most efficient method. It provided steady power densities of 163 ± 13 mWm(-2) 4 days after inoculation compared to 58 ± 15 mWm(-2) after 30 days following a conventional inoculation approach. The in situ BFT eliminates the need for microbial acclimation during startup and reduces performance fluctuations caused by shifts in microbial biodiversity. Anaerobic pretreatment of the substrate and addition of suspended enzymes from an operating MFC into the new MFC proved to have a beneficial effect on startup and subsequent operation. Polarization methods were applied to characterize the startup phase and the steady state operation in terms of power densities, internal resistance and power overshoot during biofilm maturation. Applying this method a well-working MFC can be multiplied into an array of identically performing MFCs. PMID:27120629

  4. Microbial diversity in methanogenic hydrocarbon-degrading enrichment cultures isolated from a water-flooded oil reservoir (Dagang oil field, China)

    NASA Astrophysics Data System (ADS)

    Jiménez, Núria; Cai, Minmin; Straaten, Nontje; Yao, Jun; Richnow, Hans H.; Krüger, Martin

    2015-04-01

    Microbial transformation of oil to methane is one of the main degradation processes taking place in oil reservoirs, and it has important consequences as it negatively affects the quality and economic value of the oil. Nevertheless, methane could constitute a recovery method of carbon from exhausted reservoirs. Previous studies combining geochemical and isotopic analysis with molecular methods showed evidence for in situ methanogenic oil degradation in the Dagang oil field, China (Jiménez et al., 2012). However, the main key microbial players and the underlying mechanisms are still relatively unknown. In order to better characterize these processes and identify the main microorganisms involved, laboratory biodegradation experiments under methanogenic conditions were performed. Microcosms were inoculated with production and injection waters from the reservoir, and oil or 13C-labelled single hydrocarbons (e.g. n-hexadecane or 2-methylnaphthalene) were added as sole substrates. Indigenous microbiota were able to extensively degrade oil within months, depleting most of the n-alkanes in 200 days, and producing methane at a rate of 76 ± 6 µmol day-1 g-1 oil added. They could also produce heavy methane from 13C-labeled 2-methylnaphthalene, suggesting that further methanogenesis may occur from the aromatic and polyaromatic fractions of Dagang reservoir fluids. Microbial communities from oil and 2-methyl-naphthalene enrichment cultures were slightly different. Although, in both cases Deltaproteobacteria, mainly belonging to Syntrophobacterales (e.g. Syntrophobacter, Smithella or Syntrophus) and Clostridia, mostly Clostridiales, were among the most represented taxa, Gammaproteobacteria could be only identified in oil-degrading cultures. The proportion of Chloroflexi, exclusively belonging to Anaerolineales (e.g. Leptolinea, Bellilinea) was considerably higher in 2-methyl-naphthalene degrading cultures. Archaeal communities consisted almost exclusively of representatives of

  5. Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan.

    PubMed

    Hirayama, Hisako; Sunamura, Michinari; Takai, Ken; Nunoura, Takuro; Noguchi, Takuro; Oida, Hanako; Furushima, Yasuo; Yamamoto, Hiroyuki; Oomori, Tamotsu; Horikoshi, Koki

    2007-12-01

    Microbial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52 degrees C) contained 175 microM H2S and gas bubbles mainly composed of CH4 (69%) and N2 (29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilic Thiomicrospira spp. and thermophilic Sulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37 degrees C, and another novel type I methanotroph exhibited optimum growth at 45 degrees C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of the Epsilonproteobacteria was isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducing Desulfovibrio spp., iron-reducing Deferribacter sp., and sulfur-reducing Thermococcus spp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community, S. caldicuralii was identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic

  6. Selection of an actinobacteria mixed culture for chlordane remediation. Pesticide effects on microbial morphology and bioemulsifier production.

    PubMed

    Fuentes, María S; Colin, Verónica L; Amoroso, María J; Benimeli, Claudia S

    2016-02-01

    Chlordane bioremediation using actinobacteria mixed culture is an attractive clean-up technique. Their ability to produce bioemulsifiers could increase the bioavailability of this pesticide. In order to select a defined actinobacteria mixed culture for chlordane remediation, compatibility assays were performed among six Streptomyces strains. The strains did not show growth inhibition, and they were assayed for chlordane removal, either as pure or as mixed cultures. In pure cultures, all of the strains showed specific dechlorination activity (1.42-24.20 EU mg(-1)) and chlordane removal abilities (91.3-95.5%). The specific dechlorination activity was mainly improved with cultures of three or four microorganisms. The mixed culture consisting of Streptomyces sp. A2-A5-A13 was selected. Their ability to produce bioemulsifiers in the presence of glucose or chlordane was tested, but no significant differences were observed (p > 0.05). However, the stability of the emulsions formed was linked to the carbon source used. Only in chlordane presence the emulsions retained 100% of their initial height. Finally, the selected consortium showed a high degree of sporulation in the pesticide presence. This is the first study on the effects that chlordane exerts on microbe morphology and emulsifier production for a defined mixed culture of Streptomyces with ability to remediate the pesticide. PMID:26554742

  7. Selection of an actinobacteria mixed culture for chlordane remediation. Pesticide effects on microbial morphology and bioemulsifier production.

    PubMed

    Fuentes, María S; Colin, Verónica L; Amoroso, María J; Benimeli, Claudia S

    2016-02-01

    Chlordane bioremediation using actinobacteria mixed culture is an attractive clean-up technique. Their ability to produce bioemulsifiers could increase the bioavailability of this pesticide. In order to select a defined actinobacteria mixed culture for chlordane remediation, compatibility assays were performed among six Streptomyces strains. The strains did not show growth inhibition, and they were assayed for chlordane removal, either as pure or as mixed cultures. In pure cultures, all of the strains showed specific dechlorination activity (1.42-24.20 EU mg(-1)) and chlordane removal abilities (91.3-95.5%). The specific dechlorination activity was mainly improved with cultures of three or four microorganisms. The mixed culture consisting of Streptomyces sp. A2-A5-A13 was selected. Their ability to produce bioemulsifiers in the presence of glucose or chlordane was tested, but no significant differences were observed (p > 0.05). However, the stability of the emulsions formed was linked to the carbon source used. Only in chlordane presence the emulsions retained 100% of their initial height. Finally, the selected consortium showed a high degree of sporulation in the pesticide presence. This is the first study on the effects that chlordane exerts on microbe morphology and emulsifier production for a defined mixed culture of Streptomyces with ability to remediate the pesticide.

  8. Carbon dioxide reduction by mixed and pure cultures in microbial electrosynthesis using an assembly of graphite felt and stainless steel as a cathode.

    PubMed

    Bajracharya, Suman; ter Heijne, Annemiek; Dominguez Benetton, Xochitl; Vanbroekhoven, Karolien; Buisman, Cees J N; Strik, David P B T B; Pant, Deepak

    2015-11-01

    Carbon dioxide (CO2) reduction to multi-carbon compounds at the cathode using chemolithoautotrophs is an emerging application of microbial electrosynthesis (MES). In this study, CO2 reduction in MES was investigated at hydrogen evolving potentials, separately by a mixed culture and Clostridium ljungdahlii, using a graphite felt and stainless steel assembly as cathode. The mixed culture reactor produced acetate at the maximum rate of 1.3 mM d(-1), along with methane and hydrogen at -1.1 V/Ag/AgCl. Over 160 days of run-time in four fed-batches, 26% of bicarbonate was converted to acetate between day 28 and 41, whereas in the late batches, methane production prevailed. Out of 45 days of run-time in the C. ljungdahlii reactor, 2.4 mM d(-1) acetate production was achieved at -0.9 V/Ag/AgCl in Batch 1. Simultaneous product degradation occurred when the mixed culture was not selectively enriched. Hydrogen evolution is potentially the rapid way of transferring electrons to the biocatalysts for higher bioproduction rates.

  9. The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture.

    PubMed

    Hagen, Live Heldal; Vivekanand, Vivekanand; Pope, Phillip B; Eijsink, Vincent G H; Horn, Svein J

    2015-07-01

    A new biogas process is initiated by adding a microbial community, typically in the form of a sample collected from a functional biogas plant. This inoculum has considerable impact on the initial performance of a biogas reactor, affecting parameters such as stability, biogas production yields and the overall efficiency of the anaerobic digestion process. In this study, we have analyzed changes in the microbial composition and performance of an inoculum during storage using barcoded pyrosequencing of bacterial and archaeal 16S ribosomal RNA (rRNA) genes, and determination of the biomethane potential, respectively. The inoculum was stored at room temperature, 4 and -20 °C for up to 11 months and cellulose was used as a standard substrate to test the biomethane potential. Storage up to 1 month resulted in similar final methane yields, but the rate of methane production was reduced by storage at -20 °C. Longer storage times resulted in reduced methane yields and slower production kinetics for all storage conditions, with room temperature and frozen samples consistently giving the best and worst performance, respectively. Both storage time and temperature affected the microbial community composition and methanogenic activity. In particular, fluctuations in the relative abundance of Bacteroidetes were observed. Interestingly, a shift from hydrogenotrophic methanogens to methanogens with the capacity to perform acetoclastic methanogensis was observed upon prolonged storage. In conclusion, this study suggests that biogas inocula may be stored up to 1 month with low loss of methanogenic activity, and identifies bacterial and archaeal species that are affected by the storage.

  10. Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members.

    PubMed

    Tan, Boonfei; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia

    2013-10-01

    A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6-C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic-fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO(2) fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction. PMID:24237341

  11. Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel.

    PubMed

    Varrone, C; Heggeset, T M B; Le, S B; Haugen, T; Markussen, S; Skiadas, I V; Gavala, H N

    2015-01-01

    Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs), able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable and stable MMC, trying to overcome inhibition problems and enhance substrate degradation efficiency, as well as generation of soluble fermentation products. Repeated transfers in small batches and fed-batch conditions have been applied, comparing the use of different inoculum, growth media, and Kinetic Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h) and different dominant metabolic products were obtained, depending on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate). On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1,3-propanediol and butyrate production. Changes in microbial composition were monitored by means of Next Generation Sequencing, revealing a dominance of glycerol consuming species, such as Clostridium, Klebsiella, and Escherichia.

  12. Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel

    PubMed Central

    Varrone, C.; Heggeset, T. M. B.; Le, S. B.; Haugen, T.; Markussen, S.; Skiadas, I. V.; Gavala, H. N.

    2015-01-01

    Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs), able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable and stable MMC, trying to overcome inhibition problems and enhance substrate degradation efficiency, as well as generation of soluble fermentation products. Repeated transfers in small batches and fed-batch conditions have been applied, comparing the use of different inoculum, growth media, and Kinetic Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h) and different dominant metabolic products were obtained, depending on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate). On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1,3-propanediol and butyrate production. Changes in microbial composition were monitored by means of Next Generation Sequencing, revealing a dominance of glycerol consuming species, such as Clostridium, Klebsiella, and Escherichia. PMID:26509171

  13. Fate of β-hexachlorocyclohexane in the mixed microbial cultures (MMCs) three-stage polyhydroxyalkanoates (PHA) production process from cheese whey.

    PubMed

    Valentino, Francesco; Riccardi, Carmela; Campanari, Sabrina; Pomata, Donatella; Majone, Mauro

    2015-09-01

    This work aimed to study the fate and effect of β-hexachlorocyclohexane (β-HCH) during several steps of PHA production and purification, by using an artificially contaminated cheese whey (CW) as the feedstock. Most of β-HCH (around 90%) was adsorbed on CW solids and it was removed after the acidogenic fermentation step, when residual CW solids are separated along with anaerobic biomass from the liquid-phase. Purification steps also contributed strongly to the removal of residual β-HCH; overall, the PHA production process removed about 99.9% of initial β-HCH content. Moreover, it has been shown that β-HCH has neither detrimental effect on acidogenic fermentation nor on PHA accumulation, that were performed by using unacclimated mixed microbial cultures. PMID:26048084

  14. Fate of β-hexachlorocyclohexane in the mixed microbial cultures (MMCs) three-stage polyhydroxyalkanoates (PHA) production process from cheese whey.

    PubMed

    Valentino, Francesco; Riccardi, Carmela; Campanari, Sabrina; Pomata, Donatella; Majone, Mauro

    2015-09-01

    This work aimed to study the fate and effect of β-hexachlorocyclohexane (β-HCH) during several steps of PHA production and purification, by using an artificially contaminated cheese whey (CW) as the feedstock. Most of β-HCH (around 90%) was adsorbed on CW solids and it was removed after the acidogenic fermentation step, when residual CW solids are separated along with anaerobic biomass from the liquid-phase. Purification steps also contributed strongly to the removal of residual β-HCH; overall, the PHA production process removed about 99.9% of initial β-HCH content. Moreover, it has been shown that β-HCH has neither detrimental effect on acidogenic fermentation nor on PHA accumulation, that were performed by using unacclimated mixed microbial cultures.

  15. Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture.

    PubMed

    Lee, Duu-Jong; Lee, Chin-Yu; Chang, Jo-Shu

    2012-12-01

    Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

  16. Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

    NASA Technical Reports Server (NTRS)

    Jahnke, L. L.; Eder, W.; Huber, Robert; Hinrichs, K-U.; Hayes, J. M.; DesMarais, D. J.; Cady, S. L.; Hope, J. M.; Summons, R. E.

    2001-01-01

    This paper describes a study of lipid biomarker composition and carbon isotopic fractionation in cultured Aquificales and natural analogues from Yellowstone National Park. Additional information is contained in the original extended abstract.

  17. Electron Microscopy Studies, Surface Analysis and Microbial Culturing Experiments on a Depth Profile Through Martian Meteorite Nakhla

    NASA Technical Reports Server (NTRS)

    Toporski, J. K. W.; Steele, A.; Westall, F.; Griffin, C.; Whitby, C.; Avci, R.; McKay, D. S.

    2000-01-01

    Combined electron microscopy studies and culturing experiments have shown that Nakhla became contaminated with recent terrestrial microorganisms. Additional surface analysis detected an as yet unknown organic species which may represent a biomarker.

  18. Determination of alachlor and its metabolite 2,6-diethylaniline in microbial culture medium using online microdialysis enriched-sampling coupled to high-performance liquid chromatography.

    PubMed

    Chen, Chi-Zen; Yan, Cheing-Tong; Kumar, Ponnusamy Vinoth; Huang, Jenn-Wen; Jen, Jen-Fon

    2011-08-10

    In this study, a simple and novel microdialysis sampling technique incorporating hollow fiber liquid phase microextraction (HF-LPME) coupled online to high-performance liquid chromatography (HPLC) for the one-step sample pretreatment and direct determination of alachlor (2-chloro-2',6'-diethyl-N -(methoxymethyl)acetanilide) and its metabolite 2,6-diethylaniline (2,6-DEA) in microbial culture medium has been developed. A reversed-phase C-18 column was utilized to separate alachlor and 2,6-DEA from other species using an acetonitrile/water mixture (1:1) containing 0.1 M phosphate buffer solution at pH 7.0 as the mobile phase. Detection was carried out with a UV detector operated at 210 nm. Parameters that influenced the enrichment efficiency of online HF-LPME sampling, including the length of the hollow fiber, the perfusion solvent and its flow rate, the pH, and the salt added in sample solution, as well as chromatographic conditions were thoroughly optimized. Under optimal conditions, excellent enrichment efficiency was achieved by the microdialysis of a sample solution (pH 7.0) using hexane as perfusate at the flow rate of 4 μL/min. Detection limits were 72 and 14 ng/mL for alachlor and 2,6-DEA, respectively. The enrichment factors were 403 and 386 (RSD < 5%) for alachlor and 2,6-DEA, respectively, when extraction was performed by using a 40 cm regenerated cellulose hollow fiber and hexane as perfusion solvent at the flow rate of 0.1 μL/min. The proposed method provides a sensitive, flexible, fast, and eco-friendly procedure to enrich and determine alachlor and its metabolite (2,6-DEA) in microbial culture medium. PMID:21707080

  19. Validation of the BacT/ALERT®3D automated culture system for the detection of microbial contamination of epithelial cell culture medium.

    PubMed

    Plantamura, E; Huyghe, G; Panterne, B; Delesalle, N; Thépot, A; Reverdy, M E; Damour, O; Auxenfans, Céline

    2012-08-01

    Living tissue engineering for regenerative therapy cannot withstand the usual pharmacopoeia methods of purification and terminal sterilization. Consequently, these products must be manufactured under aseptic conditions at microbiologically controlled environment facilities. This study was proposed to validate BacT/ALERT(®)3D automated culture system for microbiological control of epithelial cell culture medium (ECCM). Suspensions of the nine microorganisms recommended by the European Pharmacopoeia (Chap. 2.6.27: "Microbiological control of cellular products"), plus one species from oral mucosa and two negative controls with no microorganisms were prepared in ECCM. They were inoculated in FA (anaerobic) and SN (aerobic) culture bottles (Biomérieux, Lyon, France) and incubated in a BacT/ALERT(®)3D automated culture system. For each species, five sets of bottles were inoculated for reproducibility testing: one sample was incubated at the French Health Products Agency laboratory (reference) and the four others at Cell and Tissue Bank of Lyon, France. The specificity of the positive culture bottles was verified by Gram staining and then subcultured to identify the microorganism grown. The BacT/ALERT(®)3D system detected all the inoculated microorganisms in less than 2 days except Propionibacterium acnes which was detected in 3 days. In conclusion, this study demonstrates that the BacT/ALERT(®)3D system can detect both aerobic and anaerobic bacterial and fungal contamination of an epithelial cell culture medium consistent with the European Pharmacopoeia chapter 2.6.27 recommendations. It showed the specificity, sensitivity, and precision of the BacT/ALERT(®)3D method, since all the microorganisms seeded were detected in both sites and the uncontaminated medium ECCM remained negative at 7 days. PMID:22160810

  20. Effects of Phytoecdysteroids (PEDS) Extracted from Cyanotis arachnoidea on Rumen Fermentation, Enzyme Activity and Microbial Efficiency in a Continuous-Culture System

    PubMed Central

    Li, Deyong; Zhang, Yawei; Cui, Zhenliang; He, Liwen; Chen, Wanbao; Meng, Qingxiang; Ren, Liping

    2016-01-01

    The objective of this study was to evaluate the effects of supplementation of phytoecdysteroids (PEDS) extracted from Cyanotis arachnoidea on rumen fermentation, enzymes activity and microbial efficiency in a dual flow continuous-culture system. A single-factor experimental design was used with twelve fermenters in 4 groups with 3 replicates each. Fermenters were incubated for a total of 7 days that included first 4 days for adaptation and last 3 days for sampling. PEDS was added at levels of zero (as control), 5, 10, and 15 mg/g of the substrate (DM). The results showed that increasing supplementation levels of PEDS resulted in incremental digestibility of dry matter (DMD) (quadratic, P = 0.001) and organic matter (OMD) (quadratic, P = 0.031), but unchanged digestibility of neutral detergent fiber (NDFD), crude protein (CPD) and acid detergent acid (ADFD). As supplementation levels of PEDS increased, there were decreased response in the concentration of ammonia nitrogen (NH3-N) (linear, P = 0.015) and increased response in molar proportions of butyrate (linear, P = 0.004), but unchanged response in total volatile fatty acid (TVFA) and the molar proportion of acetate and propionate, respectively. Increasing PEDS supplementation levels decreased the ratio of acetate to propionate (linear, P = 0.038), suggesting an alteration of rumen fermentation pattern occurring due to PEDS supplementation in the diet. Supplementation of PEDS significantly increased activities of glutamate dehydrogenase (quadratic, P = 0.001), alanine dehydrogenase (quadratic, P = 0.004), glutamate synthase (linear, P = 0.038), glutamine synthetase (quadratic, P = 0.011), respectively. There were no discernible differences in the activity of carboxymethyl cellulose (CMCase), xylanase and protease regardless of the treatments. The daily production of microbial nitrogen (linear, P = 0.002) and microbial efficiency (MOEEF) (linear, P = 0.001) increased linearly as supplementation levels of PEDS

  1. Effects of Phytoecdysteroids (PEDS) Extracted from Cyanotis arachnoidea on Rumen Fermentation, Enzyme Activity and Microbial Efficiency in a Continuous-Culture System.

    PubMed

    Li, Deyong; Zhang, Yawei; Cui, Zhenliang; He, Liwen; Chen, Wanbao; Meng, Qingxiang; Ren, Liping

    2016-01-01

    The objective of this study was to evaluate the effects of supplementation of phytoecdysteroids (PEDS) extracted from Cyanotis arachnoidea on rumen fermentation, enzymes activity and microbial efficiency in a dual flow continuous-culture system. A single-factor experimental design was used with twelve fermenters in 4 groups with 3 replicates each. Fermenters were incubated for a total of 7 days that included first 4 days for adaptation and last 3 days for sampling. PEDS was added at levels of zero (as control), 5, 10, and 15 mg/g of the substrate (DM). The results showed that increasing supplementation levels of PEDS resulted in incremental digestibility of dry matter (DMD) (quadratic, P = 0.001) and organic matter (OMD) (quadratic, P = 0.031), but unchanged digestibility of neutral detergent fiber (NDFD), crude protein (CPD) and acid detergent acid (ADFD). As supplementation levels of PEDS increased, there were decreased response in the concentration of ammonia nitrogen (NH3-N) (linear, P = 0.015) and increased response in molar proportions of butyrate (linear, P = 0.004), but unchanged response in total volatile fatty acid (TVFA) and the molar proportion of acetate and propionate, respectively. Increasing PEDS supplementation levels decreased the ratio of acetate to propionate (linear, P = 0.038), suggesting an alteration of rumen fermentation pattern occurring due to PEDS supplementation in the diet. Supplementation of PEDS significantly increased activities of glutamate dehydrogenase (quadratic, P = 0.001), alanine dehydrogenase (quadratic, P = 0.004), glutamate synthase (linear, P = 0.038), glutamine synthetase (quadratic, P = 0.011), respectively. There were no discernible differences in the activity of carboxymethyl cellulose (CMCase), xylanase and protease regardless of the treatments. The daily production of microbial nitrogen (linear, P = 0.002) and microbial efficiency (MOEEF) (linear, P = 0.001) increased linearly as supplementation levels of PEDS

  2. Effects of Phytoecdysteroids (PEDS) Extracted from Cyanotis arachnoidea on Rumen Fermentation, Enzyme Activity and Microbial Efficiency in a Continuous-Culture System.

    PubMed

    Li, Deyong; Zhang, Yawei; Cui, Zhenliang; He, Liwen; Chen, Wanbao; Meng, Qingxiang; Ren, Liping

    2016-01-01

    The objective of this study was to evaluate the effects of supplementation of phytoecdysteroids (PEDS) extracted from Cyanotis arachnoidea on rumen fermentation, enzymes activity and microbial efficiency in a dual flow continuous-culture system. A single-factor experimental design was used with twelve fermenters in 4 groups with 3 replicates each. Fermenters were incubated for a total of 7 days that included first 4 days for adaptation and last 3 days for sampling. PEDS was added at levels of zero (as control), 5, 10, and 15 mg/g of the substrate (DM). The results showed that increasing supplementation levels of PEDS resulted in incremental digestibility of dry matter (DMD) (quadratic, P = 0.001) and organic matter (OMD) (quadratic, P = 0.031), but unchanged digestibility of neutral detergent fiber (NDFD), crude protein (CPD) and acid detergent acid (ADFD). As supplementation levels of PEDS increased, there were decreased response in the concentration of ammonia nitrogen (NH3-N) (linear, P = 0.015) and increased response in molar proportions of butyrate (linear, P = 0.004), but unchanged response in total volatile fatty acid (TVFA) and the molar proportion of acetate and propionate, respectively. Increasing PEDS supplementation levels decreased the ratio of acetate to propionate (linear, P = 0.038), suggesting an alteration of rumen fermentation pattern occurring due to PEDS supplementation in the diet. Supplementation of PEDS significantly increased activities of glutamate dehydrogenase (quadratic, P = 0.001), alanine dehydrogenase (quadratic, P = 0.004), glutamate synthase (linear, P = 0.038), glutamine synthetase (quadratic, P = 0.011), respectively. There were no discernible differences in the activity of carboxymethyl cellulose (CMCase), xylanase and protease regardless of the treatments. The daily production of microbial nitrogen (linear, P = 0.002) and microbial efficiency (MOEEF) (linear, P = 0.001) increased linearly as supplementation levels of PEDS

  3. Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: Model validation and sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Chen, Mingjie; Abriola, Linda M.; Amos, Benjamin K.; Suchomel, Eric J.; Pennell, Kurt D.; Löffler, Frank E.; Christ, John A.

    2013-08-01

    Reductive dechlorination catalyzed by organohalide-respiring bacteria is often considered for remediation of non-aqueous phase liquid (NAPL) source zones due to cost savings, ease of implementation, regulatory acceptance, and sustainability. Despite knowledge of the key dechlorinators, an understanding of the processes and factors that control NAPL dissolution rates and detoxification (i.e., ethene formation) is lacking. A recent column study demonstrated a 5-fold cumulative enhancement in tetrachloroethene (PCE) dissolution and ethene formation (Amos et al., 2009). Spatial and temporal monitoring of key geochemical and microbial (i.e., Geobacter lovleyi and Dehalococcoides mccartyi strains) parameters in the column generated a data set used herein as the basis for refinement and testing of a multiphase, compositional transport model. The refined model is capable of simulating the reactive transport of multiple chemical constituents produced and consumed by organohalide-respiring bacteria and accounts for substrate limitations and competitive inhibition. Parameter estimation techniques were used to optimize the values of sensitive microbial kinetic parameters, including maximum utilization rates, biomass yield coefficients, and endogenous decay rates. Comparison and calibration of model simulations with the experimental data demonstrate that the model is able to accurately reproduce measured effluent concentrations, while delineating trends in dechlorinator growth and reductive dechlorination kinetics along the column. Sensitivity analyses performed on the optimized model parameters indicate that the rates of PCE and cis-1,2-dichloroethene (cis-DCE) transformation and Dehalococcoides growth govern bioenhanced dissolution, as long as electron donor (i.e., hydrogen flux) is not limiting. Dissolution enhancements were shown to be independent of cis-DCE accumulation; however, accumulation of cis-DCE, as well as column length and flow rate (i.e., column residence time

  4. Evaluation of a plastic nonvented aerobic blood culture bottle for use with the BacT/ALERT microbial detection system.

    PubMed

    Snyder, J W; Munier, G K; Bostic, G D; Bozigar, P S; Hanna, R

    2002-12-01

    The current BacT/ALERT SA (BTA SA) aerobic blood culture bottle is made from glass, does not require venting, and contains a liquid emulsion sensor (LES). Its performance has been shown to be equivalent to that of the vented standard aerobic culture bottle. A further-improved version of the BTA SA bottle, designated the BacT/ALERT plastic SA (BTA PSA) culture bottle, is made from clear plastic to prevent breakage, does not require venting, and contains a modified LES (LES 2) to reduce the possibility of false positives. The BTA PSA provides a practical alternative to the current glass version of this bottle. The plastic bottle is also comparable to the current glass bottle in transparency and growth performance and additionally minimizes the exposure to infectious agents due to glass bottle breakage.

  5. Mixed culture models for predicting intestinal microbial interactions between Escherichia coli and Lactobacillus in the presence of probiotic Bacillus subtilis.

    PubMed

    Yang, J J; Niu, C C; Guo, X H

    2015-01-01

    Bacillus has been proposed as a probiotic due to its in vivo effectiveness in the gastrointestinal tract through antimicrobial activities. The present study investigates the effects of Lactobacillus alone or in the presence of Bacillus subtilis MA139 on the inhibition of pathogenic Escherichia coli K88. Mixed cultures were used to predict the possible interactions among these bacteria within the intestinal tract of animals. B. subtilis MA139 was first assayed for its inhibition against E. coli K88 both under shaking and static culture conditions. A co-culture assay was employed under static conditions to test the inhibitory effects of Lactobacillus reuteri on E. coli K88, with or without addition of B. subtilis MA139. The results showed that B. subtilis MA139 had marked inhibition against E. coli K88 under shaking conditions and weak inhibition under static conditions. Lactobacillus alone as well as in combination with B. subtilis MA139 spores exerted strong inhibition against E. coli K88 under static conditions. However, the inhibition by Lactobacillus in combination with B. subilis spores was much higher than that by Lactobacillus alone (P<0.01). B. subtilis MA139 significantly decreased the pH and oxidation-reduction potential values of the co-culture broth compared to that of Lactobacillus alone (P<0.05). The viability of Lactobacillus increased when co-cultured with B. subtilis MA139 because of significantly higher Lactobacillus counts and lower pH values in the broth (P<0.05). The role of Bacillus in the mixed culture models suggests that Bacillus may produce beneficial effects by increasing the viability of lactobacilli and subsequently inhibiting the growth of pathogenic E. coli. Therefore, the combination of Bacillus and Lactobacillus species as a probiotic is recommended. PMID:26259891

  6. Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres.

    PubMed

    Smith, David; McCluskey, Kevin; Stackebrandt, Erko

    2014-01-01

    Through their long history of public service, diverse microbial Biological Resource Centres (mBRCs) have made myriad contributions to society and science. They have enabled the maintenance of specimens isolated before antibiotics, made available strains showing the development and change of pathogenicity toward animals, humans and plants, and have maintained and provided reference strains to ensure quality and reproducibility of science. However, this has not been achieved without considerable financial commitment. Different collections have unique histories and their support is often tied to their origins. However many collections have grown to serve large constituencies and need to develop novel funding mechanisms. Moreover, several international initiatives have described mBRCs as a factor in economic development and have led to the increased professionalism among mBRCs.

  7. Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains.

    PubMed

    Vararu, Florin; Moreno-García, Jaime; Zamfir, Cătălin-Ioan; Cotea, Valeriu V; Moreno, Juan

    2016-04-15

    Nine wines obtained by fermenting Aligoté musts with individual starter cultures of eight Saccharomyces cerevisiae yeast strains and with the indigenous microbiota were compared in terms of their composition in minor volatile aroma compounds. An easy handle methodology Stir-Bar-Sorptive-Adsorption, Gas Chromatography-Mass Spectrometry based, permits the identification of 49 aroma compounds. The rearrangement of these aroma compounds in six chemical families permits the establishment of a finger printing for each wine. Eighteen aroma compounds that exhibit a high differentiation power (p⩽0.05) were selected for chemometric analysis. The Principal Component Analysis carried out with these aroma compounds reveal that the first two principal components explain 53.8% and 17.2% of the total variance, respectively, allowing the establishment of nine different groups, in accordance with the wine types obtained. These results reveal analytical differences among the wines that are not recognized by sensorial analysis. PMID:26616963

  8. Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains.

    PubMed

    Vararu, Florin; Moreno-García, Jaime; Zamfir, Cătălin-Ioan; Cotea, Valeriu V; Moreno, Juan

    2016-04-15

    Nine wines obtained by fermenting Aligoté musts with individual starter cultures of eight Saccharomyces cerevisiae yeast strains and with the indigenous microbiota were compared in terms of their composition in minor volatile aroma compounds. An easy handle methodology Stir-Bar-Sorptive-Adsorption, Gas Chromatography-Mass Spectrometry based, permits the identification of 49 aroma compounds. The rearrangement of these aroma compounds in six chemical families permits the establishment of a finger printing for each wine. Eighteen aroma compounds that exhibit a high differentiation power (p⩽0.05) were selected for chemometric analysis. The Principal Component Analysis carried out with these aroma compounds reveal that the first two principal components explain 53.8% and 17.2% of the total variance, respectively, allowing the establishment of nine different groups, in accordance with the wine types obtained. These results reveal analytical differences among the wines that are not recognized by sensorial analysis.

  9. Culture.

    ERIC Educational Resources Information Center

    1997

    Twelve conference papers on cultural aspects of second language instruction include: "Towards True Multiculturalism: Ideas for Teachers" (Brian McVeigh); Comparing Cultures Through Critical Thinking: Development and Interpretations of Meaningful Observations" (Laurel D. Kamada); "Authority and Individualism in Japan and the USA" (Alisa Woodring);…

  10. MICROBIAL REDUCTIVE DECHLORINATION OF HEXACHLORO-1,3-BUTADIENE IN A METHANOGENIC ENRICHMENT CULTURE. (R825513C007)

    EPA Science Inventory

    Sequential reductive dechlorination of hexachloro-1,3-butadiene (HCBD) was achieved by a mixed, methanogenic culture enriched from a contaminated estuarine sediment. Both methanol and lactate served as carbon and electron sources. Methanol was stoichiometrically converted to m...

  11. Bioelectricity generation in microbial fuel cell using natural microflora and isolated pure culture bacteria from anaerobic palm oil mill effluent sludge.

    PubMed

    Nor, Muhamad Hanif Md; Mubarak, Mohd Fahmi Muhammad; Elmi, Hassan Sh Abdirahman; Ibrahim, Norahim; Wahab, Mohd Firdaus Abdul; Ibrahim, Zaharah

    2015-08-01

    A double-chambered membrane microbial fuel cell (MFC) was constructed to investigate the potential use of natural microflora anaerobic palm oil mill effluent (POME) sludge and pure culture bacteria isolated from anaerobic POME sludge as inoculum for electricity generation. Sterilized final discharge POME was used as the substrate with no addition of nutrients. MFC operation using natural microflora anaerobic POME sludge showed a maximum power density and current density of 85.11mW/m(2) and 91.12mA/m(2) respectively. Bacterial identification using 16S rRNA analysis of the pure culture isolated from the biofilm on the anode MFC was identified as Pseudomonas aeruginosa strain ZH1. The electricity generated in MFC using P. aeruginosa strain ZH1 showed maximum power density and current density of 451.26mW/m(2) and 654.90mA/m(2) respectively which were five times higher in power density and seven times higher in current density compared to that of MFC using anaerobic POME sludge.

  12. Bioelectricity generation in microbial fuel cell using natural microflora and isolated pure culture bacteria from anaerobic palm oil mill effluent sludge.

    PubMed

    Nor, Muhamad Hanif Md; Mubarak, Mohd Fahmi Muhammad; Elmi, Hassan Sh Abdirahman; Ibrahim, Norahim; Wahab, Mohd Firdaus Abdul; Ibrahim, Zaharah

    2015-08-01

    A double-chambered membrane microbial fuel cell (MFC) was constructed to investigate the potential use of natural microflora anaerobic palm oil mill effluent (POME) sludge and pure culture bacteria isolated from anaerobic POME sludge as inoculum for electricity generation. Sterilized final discharge POME was used as the substrate with no addition of nutrients. MFC operation using natural microflora anaerobic POME sludge showed a maximum power density and current density of 85.11mW/m(2) and 91.12mA/m(2) respectively. Bacterial identification using 16S rRNA analysis of the pure culture isolated from the biofilm on the anode MFC was identified as Pseudomonas aeruginosa strain ZH1. The electricity generated in MFC using P. aeruginosa strain ZH1 showed maximum power density and current density of 451.26mW/m(2) and 654.90mA/m(2) respectively which were five times higher in power density and seven times higher in current density compared to that of MFC using anaerobic POME sludge. PMID:25799955

  13. Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches.

    PubMed

    Suenaga, Hikaru; Mizuta, Shiori; Miyazaki, Kentaro; Yaoi, Katsuro

    2014-11-01

    Culture-dependent and culture-independent approaches were used for extensive retrieval of the extradiol dioxygenase (EDO) gene from the environment to investigate the relationship between the EDO genes from isolated bacteria and the metagenomic EDO genes from which they were isolated. In our previous study, we identified 91 fosmid clones showing EDO enzyme activity using a metagenomic approach. In the present study, we classified all these metagenome-derived EDOs and newly isolated 88 phenol-utilizing bacteria from the same sample and identified four EDO genes from them. Of these, two EDOs had amino acid sequences similar to those reported previously in aromatic-utilizing strains, and one EDO had a sequence almost identical to that of metagenomic EDOs identified in our previous study. Unexpectedly, one EDO showed no similarity to any class I EDOs and was categorized as class II, which has not been found in past metagenomic approaches. Quantitative polymerase chain reaction (PCR) assay indicated that the low-abundance class II EDO gene can be enriched by culturing approaches. We conclude that the combined use of the two approaches can explore the gene community more extensively than their individual use. PMID:25059259

  14. Effects of L- and iso-ascorbic acid on meat protein hydrolyzing activity of four commercial plant and three microbial protease preparations.

    PubMed

    Ha, Minh; Bekhit, Alaa El-Din; Carne, Alan

    2014-04-15

    The present study investigated the effects of both l- and iso-ascorbic acid (AA) on the activity of four plant proteases (papain, bromelain, actinidin and zingibain) and three microbial proteases (Bacterial Protease G, Fungal 31,000 and Fungal 60,000) preparations using fluorescent-labelled casein, meat myofibrillar and connective tissue extracts to explore their effects on meat structure components upon treatment with individual proteases. While l-AA in the range 0.8-3.2mM inhibited the activity of papain, bromelain and zingibain, iso-AA acted as an inhibitor of papain but as an activator of zingibain and had no significant effect on bromelain. Both AA isoforms acted as an activator of the actinidin protease and the concentration of AA isoforms appeared to affect the level of activation of the protease. The effect of the two AA isoforms on collagen and myofibrillar protein hydrolyzing activity varied depending on the concentration of the two AA isoforms. The results indicate the ability to up and down regulate the activity of the investigated proteases by using an appropriate concentration of the AA isoform.

  15. Effects of L- and iso-ascorbic acid on meat protein hydrolyzing activity of four commercial plant and three microbial protease preparations.

    PubMed

    Ha, Minh; Bekhit, Alaa El-Din; Carne, Alan

    2014-04-15

    The present study investigated the effects of both l- and iso-ascorbic acid (AA) on the activity of four plant proteases (papain, bromelain, actinidin and zingibain) and three microbial proteases (Bacterial Protease G, Fungal 31,000 and Fungal 60,000) preparations using fluorescent-labelled casein, meat myofibrillar and connective tissue extracts to explore their effects on meat structure components upon treatment with individual proteases. While l-AA in the range 0.8-3.2mM inhibited the activity of papain, bromelain and zingibain, iso-AA acted as an inhibitor of papain but as an activator of zingibain and had no significant effect on bromelain. Both AA isoforms acted as an activator of the actinidin protease and the concentration of AA isoforms appeared to affect the level of activation of the protease. The effect of the two AA isoforms on collagen and myofibrillar protein hydrolyzing activity varied depending on the concentration of the two AA isoforms. The results indicate the ability to up and down regulate the activity of the investigated proteases by using an appropriate concentration of the AA isoform. PMID:24295669

  16. Evaluation of the Punch-it™ NA-Sample kit for detecting microbial DNA in blood culture bottles using PCR-reverse blot hybridization assay.

    PubMed

    Kim, Jungho; Wang, Hye-Young; Kim, Seoyong; Park, Soon Deok; Yu, Kwangmin; Kim, Hyo Youl; Uh, Young; Lee, Hyeyoung

    2016-09-01

    DNA extraction efficiency affects the success of PCR-based method applications. The Punch-it™ NA-Sample kit for extracting DNA by using paper chromatography is technically easy to use and requires just two reagents and only 10min to complete. The Punch-it™ NA-Sample kit could be offered as a rapid, accurate, and convenient method for extracting bacterial and fungal DNA from blood culture bottles. We compared the efficiencies of the commercial kit (Punch-it™ NA-Sample kit) and an in-house conventional boiling method with Chelex-100 resin for DNA extraction from blood culture bottles. The efficiency of the two DNA extraction methods was assessed by PCR-reverse blot hybridization assay (PCR-REBA, REBA Sepsis-ID) for detecting Gram positive (GP) bacteria, Gram negative (GN) bacteria, and Candida species with 196 positive and 200 negative blood culture bottles. The detection limits of the two DNA extraction methods were 10(3)CFU/mL for GP bacteria, 10(3)CFU/mL for GN bacteria, and 10(4)CFU/mL for Candida. The sensitivity and specificity of the Punch-it™ NA-Sample kit by REBA Sepsis-ID were 95.4% (187/196) and 100% (200/200), respectively. The overall agreement of the two DNA extraction methods was 98.9% (392/396). Three of four samples showing discrepant results between the two extraction methods were more accurately matched up with the Punch-it™ NA-Sample kit based on conventional culture methods. The results indicated that the Punch-it™ NA-Sample kit extracted bacterial and fungal DNA in blood culture bottles and allowed extracted DNA to be used in molecular assay. PMID:27263831

  17. Evaluation of the 3D BacT/ALERT automated culture system for the detection of microbial contamination of platelet concentrates.

    PubMed

    McDonald, C P; Rogers, A; Cox, M; Smith, R; Roy, A; Robbins, S; Hartley, S; Barbara, J A J; Rothenberg, S; Stutzman, L; Widders, G

    2002-10-01

    Bacterial transmission remains the major component of morbidity and mortality associated with transfusion-transmitted infections. Platelet concentrates are the most common cause of bacterial transmission. The BacT/ALERT 3D automated blood culture system has the potential to screen platelet concentrates for the presence of bacteria. Evaluation of this system was performed by spiking day 2 apheresis platelet units with individual bacterial isolates at final concentrations of 10 and 100 colony-forming units (cfu) mL-1. Fifteen organisms were used which had been cited in platelet transmission and monitoring studies. BacT/ALERT times to detection were compared with thioglycollate broth cultures, and the performance of five types of BacT/ALERT culture bottles was evaluated. Sampling was performed immediately after the inoculation of the units, and 10 replicates were performed per organism concentration for each of the five types of BacT/ALERT bottles. The mean times for the detection of these 15 organisms by BacT/ALERT, with the exception of Propionibacterium acnes, ranged from 9.1 to 48.1 h (all 10 replicates were positive). In comparison, the time range found using thioglycollate was 12.0-32.3 h (all 10 replicates were positive). P. acnes' BacT/ALERT mean detection times ranged from 89.0 to 177.6 h compared with 75.6-86.4 h for the thioglycollate broth. BacT/ALERT, with the exception of P. acnes, which has dubious clinical significance, gave equivalent or shorter detection times when compared with the thioglycollate broth system. The BacT/ALERT system detected a range of organisms at levels of 10 and 100 cfu mL-1. This study validates the BacT/ALERT microbial detection system for screening platelets. Currently, the system is the only practically viable option available for routinely screening platelet concentrates to prevent bacterial transmission.

  18. Biohydrogen production based on the evaluation of kinetic parameters of a mixed microbial culture using glucose and fruit-vegetable waste as feedstocks.

    PubMed

    Garcia-Peña, E I; Canul-Chan, M; Chairez, I; Salgado-Manjarez, E; Aranda-Barradas, J

    2013-09-01

    Hydrogen (H2) production from the organic fraction of solid waste such as fruit and vegetable waste (FVW) is a novel and feasible energy technology. Continuous application of this process would allow for the simultaneous treatment of organic residues and energy production. In this study, batch experiments were conducted using glucose as substrate, and data of H2 production obtained were successfully adjusted by a logistic model. The kinetic parameters (μ max = 0.101 h(-1), K s = 2.56 g/L) of an H2-producing microbial culture determined by the Monod and Haldane-Andrews growth models were used to establish the continuous culture conditions. This strategy led to a productive steady state in continuous culture. Once the steady state was reached in the continuous reactor, a maximum H2 production of 700 mL was attained. The feasibility of producing H2 from the FVW obtained from a local market in Mexico City was also evaluated using batch conditions. The effect of the initial FVW concentration on the H2 production and waste organic material degradation was determined. The highest H2 production rate (1.7 mmol/day), the highest cumulative H2 volume (310 mL), and 25 % chemical oxygen demand (COD) removal were obtained with an initial substrate (FVW) concentration of 37 g COD/L. The lowest H2 production rates were obtained with relatively low initial substrate concentrations of 5 and 11 g COD/L. The H2 production rates with FVW were also characterized by the logistic model. Similar cumulative H2 production was obtained when glucose and FVW were used as substrates.

  19. Evaluation of the 3D BacT/ALERT automated culture system for the detection of microbial contamination of platelet concentrates.

    PubMed

    McDonald, C P; Rogers, A; Cox, M; Smith, R; Roy, A; Robbins, S; Hartley, S; Barbara, J A J; Rothenberg, S; Stutzman, L; Widders, G

    2002-10-01

    Bacterial transmission remains the major component of morbidity and mortality associated with transfusion-transmitted infections. Platelet concentrates are the most common cause of bacterial transmission. The BacT/ALERT 3D automated blood culture system has the potential to screen platelet concentrates for the presence of bacteria. Evaluation of this system was performed by spiking day 2 apheresis platelet units with individual bacterial isolates at final concentrations of 10 and 100 colony-forming units (cfu) mL-1. Fifteen organisms were used which had been cited in platelet transmission and monitoring studies. BacT/ALERT times to detection were compared with thioglycollate broth cultures, and the performance of five types of BacT/ALERT culture bottles was evaluated. Sampling was performed immediately after the inoculation of the units, and 10 replicates were performed per organism concentration for each of the five types of BacT/ALERT bottles. The mean times for the detection of these 15 organisms by BacT/ALERT, with the exception of Propionibacterium acnes, ranged from 9.1 to 48.1 h (all 10 replicates were positive). In comparison, the time range found using thioglycollate was 12.0-32.3 h (all 10 replicates were positive). P. acnes' BacT/ALERT mean detection times ranged from 89.0 to 177.6 h compared with 75.6-86.4 h for the thioglycollate broth. BacT/ALERT, with the exception of P. acnes, which has dubious clinical significance, gave equivalent or shorter detection times when compared with the thioglycollate broth system. The BacT/ALERT system detected a range of organisms at levels of 10 and 100 cfu mL-1. This study validates the BacT/ALERT microbial detection system for screening platelets. Currently, the system is the only practically viable option available for routinely screening platelet concentrates to prevent bacterial transmission. PMID:12383336

  20. Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments.

    PubMed

    Besaury, Ludovic; Marty, Florence; Buquet, Sylvaine; Mesnage, Valérie; Muyzer, Gerard; Quillet, Laurent

    2013-02-01

    Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments. PMID:22976340

  1. Effect of time of cutting and maceration on nutrient flow, microbial protein synthesis, and digestibility in dual-flow continuous culture.

    PubMed

    Kokko, C; Soder, K J; Brito, A F; Hovey, R C; Berthiaume, R

    2013-04-01

    Maceration and evening-cutting are 2 forage management techniques that have independently improved forage quality and nutrient utilization in ruminants, but have not been evaluated in combination. Using a dual-flow continuous culture fermenter system, this preliminary study was designed to evaluate the individual and combined effects of time of cutting and maceration on in vitro ruminal digestion, nutrient flows, and microbial protein synthesis. Forages were harvested as hay from a timothy (Phleum pratense L.)-birdsfoot trefoil (Lotus corniculatus L.) stand in the morning (AM) or evening (PM). Half of each morning- and evening-cut treatment was macerated (AM-M, PM-M). The chemical composition (DM, OM, CP, NDF, ADF), including nonstructural carbohydrates (NSC) and water-soluble carbohydrates (WSC), was determined for each of the 4 treatments (AM, AM-M, PM, PM-M). Forages were ground to 2 mm and allocated to separate fermenters at 60 g of DM/d in a 4 × 4 Latin square design. Fermenters were operated over four 10-d periods with the first 7 d for adaptation followed by 3 d of sampling. Evening-cutting enhanced the apparent digestibility of NDF (P = 0.02) and ADF (P = 0.006), with a tendency (P < 0.10) for improved true DM digestibility and microbial protein synthesis. Molar proportions of individual VFA were not affected (P > 0.10) by time of cutting, though evening-cutting increased (P = 0.02) total concentration of VFA. Maceration had no effect (P > 0.10) on true nutrient digestibility or microbial protein synthesis. An interaction of time of cutting and maceration (P < 0.05) was observed whereby maceration decreased true DM and OM digestibilities in evening-cut treatments, but had no effect in morning-cut treatments. Similarly, maceration reduced total N supply (P < 0.001) and molar proportions of acetate (P = 0.04) and increased molar proportions of propionate (P = 0.01) in evening-cut treatments with no effect on morning-cut treatments. These results indicate

  2. Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9.

    PubMed

    Kanitkar, Yogendra H; Stedtfeld, Robert D; Steffan, Robert J; Hashsham, Syed A; Cupples, Alison M

    2016-01-08

    Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures.

  3. Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9

    PubMed Central

    Kanitkar, Yogendra H.; Stedtfeld, Robert D.; Steffan, Robert J.; Hashsham, Syed A.

    2016-01-01

    Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures. PMID:26746711

  4. Loop-Mediated Isothermal Amplification (LAMP) for Rapid Detection and Quantification of Dehalococcoides Biomarker Genes in Commercial Reductive Dechlorinating Cultures KB-1 and SDC-9.

    PubMed

    Kanitkar, Yogendra H; Stedtfeld, Robert D; Steffan, Robert J; Hashsham, Syed A; Cupples, Alison M

    2016-03-01

    Real-time quantitative PCR (qPCR) protocols specific to the reductive dehalogenase (RDase) genes vcrA, bvcA, and tceA are commonly used to quantify Dehalococcoides spp. in groundwater from chlorinated solvent-contaminated sites. In this study, loop-mediated isothermal amplification (LAMP) was developed as an alternative approach for the quantification of these genes. LAMP does not require a real-time thermal cycler (i.e., amplification is isothermal), allowing the method to be performed using less-expensive and potentially field-deployable detection devices. Six LAMP primers were designed for each of three RDase genes (vcrA, bvcA, and tceA) using Primer Explorer V4. The LAMP assays were compared to conventional qPCR approaches using plasmid standards, two commercially available bioaugmentation cultures, KB-1 and SDC-9 (both contain Dehalococcoides species). DNA was extracted over a growth cycle from KB-1 and SDC-9 cultures amended with trichloroethene and vinyl chloride, respectively. All three genes were quantified for KB-1, whereas only vcrA was quantified for SDC-9. A comparison of LAMP and qPCR using standard plasmids indicated that quantification results were similar over a large range of gene concentrations. In addition, the quantitative increase in gene concentrations over one growth cycle of KB-1 and SDC-9 using LAMP was comparable to that of qPCR. The developed LAMP assays for vcrA and tceA genes were validated by comparing quantification on the Gene-Z handheld platform and a real-time thermal cycler using DNA isolated from eight groundwater samples obtained from an SDC-9-bioaugmented site (Tulsa, OK). These assays will be particularly useful at sites subject to bioaugmentation with these two commonly used Dehalococcoides species-containing cultures. PMID:26746711

  5. The U.S. Culture Collection Network Lays the Foundation for Progress in Preservation of Valuable Microbial Resources.

    PubMed

    McCluskey, Kevin; Alvarez, Anne; Bennett, Rick; Bokati, Deepak; Boundy-Mills, Kyria; Brown, Daniel; Bull, Carolee T; Coffey, Michael; Dreaden, Tyler; Duke, Clifford; Dye, Greg; Ehmke, Erin; Eversole, Kellye; Fenstermacher, Kristi; Geiser, David; Glaeser, Jessie A; Greene, Stephanie; Gribble, Lisa; Griffith, M Patrick; Hanser, Kathryn; Humber, Richard; Johnson, Barbara W; Kermode, Anthony; Krichevsky, Micah; Laudon, Matt; Leach, Jan; Leslie, John; May, Meghan; Melcher, Ulrich; Nobles, David; Fonseca, Natalia Risso; Robinson, Sara; Ryan, Matthew; Scott, James; Silflow, Carolyn; Vidaver, Anne; Webb, Kimberly M; Wertz, John E; Yentsch, Sara; Zehr, Sarah

    2016-06-01

    The U.S. Culture Collection Network was formed in 2012 by a group of culture collection scientists and stakeholders in order to continue the progress established previously through efforts of an ad hoc group. The network is supported by a Research Coordination Network grant from the U.S. National Science Foundation (NSF) and has the goals of promoting interaction among collections, encouraging the adoption of best practices, and protecting endangered or orphaned collections. After prior meetings to discuss best practices, shared data, and synergy with genome programs, the network held a meeting at the U.S. Department of Agriculture (USDA)-Agricultural Research Service (ARS) National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, Colorado in October 2015 specifically to discuss collections that are vulnerable because of changes in funding programs, or are at risk of loss because of retirement or lack of funding. The meeting allowed collection curators who had already backed up their resources at the USDA NCGRP to visit the site, and brought collection owners, managers, and stakeholders together. Eight formal collections have established off-site backups with the USDA-ARS, ensuring that key material will be preserved for future research. All of the collections with backup at the NCGRP are public distributing collections including U.S. NSF-supported genetic stock centers, USDA-ARS collections, and university-supported collections. Facing the retirement of several pioneering researchers, the community discussed the value of preserving personal research collections and agreed that a mechanism to preserve these valuable collections was essential to any future national culture collection system. Additional input from curators of plant and animal collections emphasized that collections of every kind face similar challenges in developing long-range plans for sustainability.

  6. The U.S. Culture Collection Network Lays the Foundation for Progress in Preservation of Valuable Microbial Resources.

    PubMed

    McCluskey, Kevin; Alvarez, Anne; Bennett, Rick; Bokati, Deepak; Boundy-Mills, Kyria; Brown, Daniel; Bull, Carolee T; Coffey, Michael; Dreaden, Tyler; Duke, Clifford; Dye, Greg; Ehmke, Erin; Eversole, Kellye; Fenstermacher, Kristi; Geiser, David; Glaeser, Jessie A; Greene, Stephanie; Gribble, Lisa; Griffith, M Patrick; Hanser, Kathryn; Humber, Richard; Johnson, Barbara W; Kermode, Anthony; Krichevsky, Micah; Laudon, Matt; Leach, Jan; Leslie, John; May, Meghan; Melcher, Ulrich; Nobles, David; Fonseca, Natalia Risso; Robinson, Sara; Ryan, Matthew; Scott, James; Silflow, Carolyn; Vidaver, Anne; Webb, Kimberly M; Wertz, John E; Yentsch, Sara; Zehr, Sarah

    2016-06-01

    The U.S. Culture Collection Network was formed in 2012 by a group of culture collection scientists and stakeholders in order to continue the progress established previously through efforts of an ad hoc group. The network is supported by a Research Coordination Network grant from the U.S. National Science Foundation (NSF) and has the goals of promoting interaction among collections, encouraging the adoption of best practices, and protecting endangered or orphaned collections. After prior meetings to discuss best practices, shared data, and synergy with genome programs, the network held a meeting at the U.S. Department of Agriculture (USDA)-Agricultural Research Service (ARS) National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, Colorado in October 2015 specifically to discuss collections that are vulnerable because of changes in funding programs, or are at risk of loss because of retirement or lack of funding. The meeting allowed collection curators who had already backed up their resources at the USDA NCGRP to visit the site, and brought collection owners, managers, and stakeholders together. Eight formal collections have established off-site backups with the USDA-ARS, ensuring that key material will be preserved for future research. All of the collections with backup at the NCGRP are public distributing collections including U.S. NSF-supported genetic stock centers, USDA-ARS collections, and university-supported collections. Facing the retirement of several pioneering researchers, the community discussed the value of preserving personal research collections and agreed that a mechanism to preserve these valuable collections was essential to any future national culture collection system. Additional input from curators of plant and animal collections emphasized that collections of every kind face similar challenges in developing long-range plans for sustainability. PMID:26976729

  7. Production Methods for Microbial Biocontrol Agents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A critical constraint to the commercial use of microbial biopesticides is the development of an economic production process. The production process must be cost-effective and yield a microbial propagule that is stable and efficacious under field conditions. Currently, the commercial production of ...

  8. Removal of the pharmaceuticals ibuprofen and iohexol by four wetland plant species in hydroponic culture: plant uptake and microbial degradation.

    PubMed

    Zhang, Yang; Lv, Tao; Carvalho, Pedro N; Arias, Carlos A; Chen, Zhanghe; Brix, Hans

    2016-02-01

    We aimed at assessing the effects of four wetland plant species commonly used in constructed wetland systems: Typha, Phragmites, Iris and Juncus for removing ibuprofen (IBU) and iohexol (IOH) from spiked culture solution and exploring the mechanisms responsible for the removal. IBU was nearly completely removed by all plant species during the 24-day experiment, whereas the IOH removal varied between 13 and 80 %. Typha and Phragmites were the most efficient in removing IBU and IOH, respectively, with first-order removal rate constants of 0.38 and 0.06 day(-1), respectively. The pharmaceuticals were taken up by the roots and translocated to the aerial tissues. However, at the end of the experiment, plant accumulation constituted only up to 1.1 and 5.7 % of the amount of IBU and IOH spiked initially. The data suggest that the plants mainly function by facilitating pharmaceutical degradation in the rhizosphere through release of root exudates. PMID:26490885

  9. Removal of the pharmaceuticals ibuprofen and iohexol by four wetland plant species in hydroponic culture: plant uptake and microbial degradation.

    PubMed

    Zhang, Yang; Lv, Tao; Carvalho, Pedro N; Arias, Carlos A; Chen, Zhanghe; Brix, Hans

    2016-02-01

    We aimed at assessing the effects of four wetland plant species commonly used in constructed wetland systems: Typha, Phragmites, Iris and Juncus for removing ibuprofen (IBU) and iohexol (IOH) from spiked culture solution and exploring the mechanisms responsible for the removal. IBU was nearly completely removed by all plant species during the 24-day experiment, whereas the IOH removal varied between 13 and 80 %. Typha and Phragmites were the most efficient in removing IBU and IOH, respectively, with first-order removal rate constants of 0.38 and 0.06 day(-1), respectively. The pharmaceuticals were taken up by the roots and translocated to the aerial tissues. However, at the end of the experiment, plant accumulation constituted only up to 1.1 and 5.7 % of the amount of IBU and IOH spiked initially. The data suggest that the plants mainly function by facilitating pharmaceutical degradation in the rhizosphere through release of root exudates.

  10. A critical assessment of marine aquarist biodiversity data and commercial aquaculture: identifying gaps in culture initiatives to inform local fisheries managers.

    PubMed

    Murray, Joanna M; Watson, Gordon J

    2014-01-01

    It is widely accepted that if well managed, the marine aquarium trade could provide socio-economic stability to local communities while incentivising the maintenance of coral reefs. However, the trade has also been implicated as having potentially widespread environmental impacts that has in part driven developments in aquaculture to relieve wild collection pressures. This study investigates the biodiversity in hobbyist aquaria (using an online survey) and those species currently available from an aquaculture source (commercial data and hobbyist initiatives) in the context of a traffic light system to highlight gaps in aquaculture effort and identify groups that require fisheries assessments. Two hundred and sixty nine species including clown fish, damsels, dotty backs, angelfish, gobies, sea horses and blennies, have reported breeding successes by hobbyists, a pattern mirrored by the European and US commercial organisations. However, there is a mismatch (high demand and low/non-existent aquaculture) for a number of groups including tangs, starfish, anemones and hermit crabs, which we recommend are priority candidates for local stock assessments. Hobbyist perception towards the concept of a sustainable aquarium trade is also explored with results demonstrating that only 40% of respondents were in agreement with industry and scientists who believe the trade could be an exemplar of a sustainable use of coral reefs. We believe that a more transparent evidence base, including the publication of the species collected and cultured, will go some way to align the concept of a sustainable trade across industry stakeholders and better inform the hobbyist when purchasing their aquaria stock. We conclude by proposing that a certification scheme established with government support is the most effective way to move towards a self-regulating industry. It would prevent industry "greenwashing" from multiple certification schemes, alleviate conservation concerns, and, ultimately

  11. A Critical Assessment of Marine Aquarist Biodiversity Data and Commercial Aquaculture: Identifying Gaps in Culture Initiatives to Inform Local Fisheries Managers

    PubMed Central

    Murray, Joanna M.; Watson, Gordon J.

    2014-01-01

    It is widely accepted that if well managed, the marine aquarium trade could provide socio-economic stability to local communities while incentivising the maintenance of coral reefs. However, the trade has also been implicated as having potentially widespread environmental impacts that has in part driven developments in aquaculture to relieve wild collection pressures. This study investigates the biodiversity in hobbyist aquaria (using an online survey) and those species currently available from an aquaculture source (commercial data and hobbyist initiatives) in the context of a traffic light system to highlight gaps in aquaculture effort and identify groups that require fisheries assessments. Two hundred and sixty nine species including clown fish, damsels, dotty backs, angelfish, gobies, sea horses and blennies, have reported breeding successes by hobbyists, a pattern mirrored by the European and US commercial organisations. However, there is a mismatch (high demand and low/non-existent aquaculture) for a number of groups including tangs, starfish, anemones and hermit crabs, which we recommend are priority candidates for local stock assessments. Hobbyist perception towards the concept of a sustainable aquarium trade is also explored with results demonstrating that only 40% of respondents were in agreement with industry and scientists who believe the trade could be an exemplar of a sustainable use of coral reefs. We believe that a more transparent evidence base, including the publication of the species collected and cultured, will go some way to align the concept of a sustainable trade across industry stakeholders and better inform the hobbyist when purchasing their aquaria stock. We conclude by proposing that a certification scheme established with government support is the most effective way to move towards a self-regulating industry. It would prevent industry “greenwashing” from multiple certification schemes, alleviate conservation concerns, and, ultimately

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

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

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

  13. Effect of Feeding a Mixed Microbial Culture Fortified with Trace Minerals on the Performance and Carcass Characteristics of Late-fattening Hanwoo Steers: A Field Study.

    PubMed

    Kwak, W S; Kim, Y I; Lee, S M; Lee, Y H; Choi, D Y

    2015-11-01

    This study was conducted to determine the effects of feeding a trace minerals-fortified microbial culture (TMC) on the performance and carcass characteristics of late-fattening Hanwoo steers. A mixture of microbes (0.6% [v/w] of Enterobacter sp., Bacillus sp., Lactobacillus sp., and Saccharomyces sp.) was cultured with 99% feedstuff for ensiling and 0.4% trace minerals (zinc, selenium, copper, and cobalt). Sixteen late-fattening steers (mean age, 21.8 months) were allocated to two diets: a control diet (concentrate mix and rice straw) and a treated diet (control diet+3.3% TMC). At a mean age of 31.1 months, all the steers were slaughtered. The addition of TMC to the diet did not affect the average daily weight gain of the late fattening steers, compared with that of control steers. Moreover, consuming the TMC-supplemented diet did not affect cold carcass weight, yield traits such as back fat thickness, longissimus muscle area, yield index or yield grade, or quality traits such as meat color, fat color, texture, maturity, marbling score, or quality grade. However, consumption of a TMC-supplemented diet increased the concentrations of zinc, selenium, and sulfur (p<0.05) in the longissimus muscle. With respect to amino acids, animals consuming TMC showed increased (p<0.05) concentrations of lysine, leucine, and valine among essential amino acids and a decreased (p<0.05) concentration of proline among non-essential amino acids. In conclusion, the consumption of a TMC-supplemented diet during the late-fattening period elevated the concentrations of certain trace minerals and essential amino acids in the longissimus muscle, without any deleterious effects on performance and other carcass characteristics of Hanwoo steers. PMID:26580283

  14. Effect of Feeding a Mixed Microbial Culture Fortified with Trace Minerals on the Performance and Carcass Characteristics of Late-fattening Hanwoo Steers: A Field Study

    PubMed Central

    Kwak, W. S.; Kim, Y. I.; Lee, S. M.; Lee, Y. H.; Choi, D. Y.

    2015-01-01

    This study was conducted to determine the effects of feeding a trace minerals-fortified microbial culture (TMC) on the performance and carcass characteristics of late-fattening Hanwoo steers. A mixture of microbes (0.6% [v/w] of Enterobacter sp., Bacillus sp., Lactobacillus sp., and Saccharomyces sp.) was cultured with 99% feedstuff for ensiling and 0.4% trace minerals (zinc, selenium, copper, and cobalt). Sixteen late-fattening steers (mean age, 21.8 months) were allocated to two diets: a control diet (concentrate mix and rice straw) and a treated diet (control diet+3.3% TMC). At a mean age of 31.1 months, all the steers were slaughtered. The addition of TMC to the diet did not affect the average daily weight gain of the late fattening steers, compared with that of control steers. Moreover, consuming the TMC-supplemented diet did not affect cold carcass weight, yield traits such as back fat thickness, longissimus muscle area, yield index or yield grade, or quality traits such as meat color, fat color, texture, maturity, marbling score, or quality grade. However, consumption of a TMC-supplemented diet increased the concentrations of zinc, selenium, and sulfur (p<0.05) in the longissimus muscle. With respect to amino acids, animals consuming TMC showed increased (p<0.05) concentrations of lysine, leucine, and valine among essential amino acids and a decreased (p<0.05) concentration of proline among non-essential amino acids. In conclusion, the consumption of a TMC-supplemented diet during the late-fattening period elevated the concentrations of certain trace minerals and essential amino acids in the longissimus muscle, without any deleterious effects on performance and other carcass characteristics of Hanwoo steers. PMID:26580283

  15. Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents.

    PubMed

    Pérez-Rodríguez, Ileana; Bohnert, Kenneth A; Cuebas, Mariola; Keddis, Ramaydalis; Vetriani, Costantino

    2013-11-01

    Over the past few years the relevance of nitrate respiration in microorganisms from deep-sea hydrothermal vents has become evident. In this study, we surveyed the membrane-bound nitrate reductase (Nar) encoding gene in three different deep-sea vent microbial communities from the East Pacific Rise and the Mid-Atlantic Ridge. Additionally, we tested pure cultures of vent strains for their ability to reduce nitrate and for the presence of the NarG-encoding gene in their genomes. By using the narG gene as a diagnostic marker for nitrate-reducing bacteria, we showed that nitrate reductases related to Gammaproteobacteria of the genus Marinobacter were numerically prevalent in the clone libraries derived from a black smoker and a diffuse flow vent. In contrast, NarG sequences retrieved from a community of filamentous bacteria located about 50 cm above a diffuse flow vent revealed the presence of a yet to be identified group of enzymes. 16S rRNA gene-inferred community compositions, in accordance with previous studies, showed a shift from Alpha- and Gammaproteobacteria to Epsilonproteobacteria as the vent fluids become warmer and more reducing. Based on these findings, we argue that Nar-catalyzed nitrate reduction is likely relevant in temperate and less reducing environments where Alpha- and Gammaproteobacteria are more abundant and where nitrate concentrations reflect that of background deep seawater.

  16. Current production in a microbial fuel cell using a pure culture of Cupriavidus basilensis growing in acetate or phenol as a carbon source

    PubMed Central

    Friman, Hen; Schechter, Alex; Ioffe, Yulia; Nitzan, Yeshayahu; Cahan, Rivka

    2013-01-01

    Summary A microbial fuel cell (MFC) was operated with a pure culture of Cupriavidus basilensis bacterial cells growing in the anode compartment in a defined medium containing acetate or phenol. Operating this mediator-less MFC under a constant external resistor of 1 kΩ with acetate or phenol led to current generation of 902 and 310 mA m−2 respectively. In the MFC which was operated using acetate or phenol, the current density measured from the plankton bacterial cells with a fresh electrode was 125 and 109 mA m−2, respectively, whereas the current obtained with biofilm-covered electrodes in sterile medium was 541 and 228 mA m−2 respectively. After 72 h in the MFC, 86% of the initial phenol concentration was removed, while only 64% was removed after the same time in the control MFC which was held at an open circuit potential (OCP). Furthermore, SEM and confocal microscopy analyses demonstrated a developed biofilm with a live C. basilensis population. In conclusion, in this study we demonstrated, for the first time, use of C. basilensis facultative aerobe bacterial cells in a MFC using acetate or phenol as the sole carbon source which led to electricity generation. PMID:23302470

  17. Evaluating the efficiency of a mixed culture biofilm for the treatment of black liquor and molasses in a mediator-less microbial fuel cell.

    PubMed

    Ali, Naeem; Yousaf, Sameen; Anam, Maira; Bangash, Zain; Maleeha, Sehrish

    2016-11-01

    A microbial fuel cell (MFC) is an emerging environment-friendly technology to recover the useful energy available in waste by using microorganisms as catalyst. In this study, double chamber mediator-less MFCs separated by proton exchange membrane (PEM; Nafion) were constructed to determine the efficiency of mixed culture in using complex substrates (molasses and black liquor). It was found that activated sludge can serve as efficient source of electricigens for biofilm development on an anode. Power density of 2.425 W/m² was generated from molasses with chemical oxygen demand (COD) removal efficiency of 67% as compared to power density of 3.55 W/m² produced from black liquor along with COD removal efficiency of 78%. Moreover, it was demonstrated that surface area of PEM has a significant effect on power generation. An almost 5- to 8-fold increase in voltage was observed as the size of PEM was increased from 6.5 to 25 cm².

  18. Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches.

    PubMed

    Nishiyama, Minako; Yamamoto, Shuichi; Kurosawa, Norio

    2013-08-01

    Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.

  19. Indirect microbial detection

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R. (Inventor)

    1981-01-01

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

  20. Indirect microbial detection

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R.

    1980-01-01

    Indirect method for detection of microbial growth utilizes flow of charged particles across barrier that physically separated growing cells from electrodes and measures resulting difference in potential between two platinum electrodes. Technique allows simplified noncontact monitoring of all growth in highly infectious cultures or in critical biochemical studies.

  1. Production of a highly potent epoxide through the microbial metabolism of 3β-acetoxyurs-11-en-13β,28-olide by Aspergillus niger culture.

    PubMed

    Ali, Sajid; Nisar, Muhammad; Gulab, Hussain

    2016-09-01

    Context 3β-Acetoxyurs-11-en-13β,28-olide (I), a triterpenoid, is found in most plant species. Pharmacologically triterpenes are very effective compounds with potent anticancer, anti-HIV and antimicrobial activities. Objectives Microbial transformation of 3β-acetoxyurs-11-en-13β,28-olide (I) was performed in order to obtain derivatives with improved pharmacological potential. Materials and methods Compound (I, 100 mg) was incubated with Aspergillus niger culture for 12 d. The metabolite formed was purified through column chromatography. Structure elucidation was performed through extensive spectroscopy (IR, MS and NMR). In vitro α- and β-glucosidase inhibitory, and antiglycation potentials of both substrate and metabolite were evaluated. Results Structure of metabolite II was characterized as 3β-acetoxyurs-11,12-epoxy-13β,28-olide (II). Metabolite II was found to be an oxidized product of compound I. In vitro α- and β-glucosidases revealed that metabolite II was a potent and selective inhibitor of α-glucosidase (IC50 value = 3.56 ± 0.38 μM), showing that the inhibitory effect of metabolite II was far better than compound I (IC50 value = 14.7 ± 1.3 μM) as well as acarbose (IC50 value = 545 ± 7.9 μM). Antiglycation potential of compound II was also high with 82.51 ± 1.2% inhibition. Thus, through oxidation, the biological potential of the substrate molecule can be enhanced. Conclusion Biotransformation can be used as a potential tool for the production of biologically potent molecules.

  2. Generation of High Current Densities by Pure Cultures of Anode-Respiring Geoalkalibacter spp. under Alkaline and Saline Conditions in Microbial Electrochemical Cells

    PubMed Central

    Badalamenti, Jonathan P.; Krajmalnik-Brown, Rosa; Torres, César I.

    2013-01-01

    ABSTRACT Anode-respiring bacteria (ARB) generate electric current in microbial electrochemical cells (MXCs) by channeling electrons from the oxidation of organic substrates to an electrode. Production of high current densities by monocultures in MXCs has resulted almost exclusively from the activity of Geobacter sulfurreducens, a neutrophilic freshwater Fe(III)-reducing bacterium and the highest-current-producing member documented for the Geobacteraceae family of the Deltaproteobacteria. Here we report high current densities generated by haloalkaliphilic Geoalkalibacter spp., thus broadening the capability for high anode respiration rates by including other genera within the Geobacteraceae. In this study, acetate-fed pure cultures of two related Geoalkalibacter spp. produced current densities of 5.0 to 8.3 and 2.4 to 3.3 A m−2 under alkaline (pH 9.3) and saline (1.7% NaCl) conditions, respectively. Chronoamperometric studies of halophilic Glk. subterraneus DSM 23483 and alkaliphilic Glk. ferrihydriticus DSM 17813 suggested that cells performed long-range electron transfer through electrode-attached biofilms and not through soluble electron shuttles. Glk. ferrihydriticus also oxidized ethanol directly to produce current, with maximum current densities of 5.7 to 7.1 A m−2 and coulombic efficiencies of 84 to 95%. Cyclic voltammetry (CV) elicited a sigmoidal response with characteristic onset, midpoint, and saturation potentials, while CV performed in the absence of an electron donor suggested the involvement of redox molecules in the biofilm that were limited by diffusion. These results matched those previously reported for actively respiring Gb. sulfurreducens biofilms producing similar current densities (~5 to 9 A m−2). PMID:23631915

  3. Production of a highly potent epoxide through the microbial metabolism of 3β-acetoxyurs-11-en-13β,28-olide by Aspergillus niger culture.

    PubMed

    Ali, Sajid; Nisar, Muhammad; Gulab, Hussain

    2016-09-01

    Context 3β-Acetoxyurs-11-en-13β,28-olide (I), a triterpenoid, is found in most plant species. Pharmacologically triterpenes are very effective compounds with potent anticancer, anti-HIV and antimicrobial activities. Objectives Microbial transformation of 3β-acetoxyurs-11-en-13β,28-olide (I) was performed in order to obtain derivatives with improved pharmacological potential. Materials and methods Compound (I, 100 mg) was incubated with Aspergillus niger culture for 12 d. The metabolite formed was purified through column chromatography. Structure elucidation was performed through extensive spectroscopy (IR, MS and NMR). In vitro α- and β-glucosidase inhibitory, and antiglycation potentials of both substrate and metabolite were evaluated. Results Structure of metabolite II was characterized as 3β-acetoxyurs-11,12-epoxy-13β,28-olide (II). Metabolite II was found to be an oxidized product of compound I. In vitro α- and β-glucosidases revealed that metabolite II was a potent and selective inhibitor of α-glucosidase (IC50 value = 3.56 ± 0.38 μM), showing that the inhibitory effect of metabolite II was far better than compound I (IC50 value = 14.7 ± 1.3 μM) as well as acarbose (IC50 value = 545 ± 7.9 μM). Antiglycation potential of compound II was also high with 82.51 ± 1.2% inhibition. Thus, through oxidation, the biological potential of the substrate molecule can be enhanced. Conclusion Biotransformation can be used as a potential tool for the production of biologically potent molecules. PMID:26736075

  4. [Effects of snow pack removal on soil microbial biomass carbon and nitrogen and the number of soil culturable microorganisms during wintertime in alpine Abies faxoniana forest of western Sichuan, Southwest China].

    PubMed

    Yang, Yu-Lian; Wu, Fu-Zhong; He, Zhen-Hua; Xu, Zhen-Feng; Liu, Yang; Yang, Wan-Qin; Tan, Bo

    2012-07-01

    To understand the effects of the lack of snow pack under global warming on the characteristics of soil microorganisms during wintertime, a snow-shading experiment was conducted in a primary fir (Abies faxoniana) forest after snow pack removal, with the soil microbial biomass carbon (MBC) and nitrogen (MBN) and soil culturable microorganisms (bacteria and fungi) at the stages of snow forming, snow covering, and snow melting investigated. Snow pack removal had significant effects on the soil MBC and MBN and the number of soil culturable bacteria and fungi, but the responses of the culturable microorganisms differed with the stages of snow-shading. Under the condition of snow pack removal, the MBC and MBN in soil organic layer decreased significantly at the early stages of snow forming and snow melting but increased significantly at snow covering stage and at the later stage of snow melting, and the number of culturable bacteria decreased significantly from the early stage of snow forming to the stage of snow covering while that of culturable fungi had a significant increase from the early stage of snow forming to the stage of snow melting. After snow melting, the MBC and the number of culturable fungi in soil organic layer had a significant decrease, the number of cultural bacteria was in adverse, but the MBN had less change. The MBC and MBN and the number of culturable microorganisms in soil mineral layer had the similar variation trends as those in soil organic layer, but the fluctuations were smaller. It was suggested that snow pack removal changed the ratio of culturable bacteria to culturable fungi, showing positive effects on the number of soil culturable fungi during wintertime in alpine Abies faxoniana forest of western Sichuan.

  5. Nanoporous microscale microbial incubators.

    PubMed

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

    2016-02-01

    Reconstruction of phylogenetic trees based on 16S rRNA gene sequencing reveals abundant microbial diversity that has not been cultured in the laboratory. Many attribute this so-called 'great plate count anomaly' to traditional microbial cultivation techniques, which largely facilitate the growth of a single species. Yet, it is widely recognized that bacteria in nature exist in complex communities. One technique to increase the pool of cultivated bacterial species is to co-culture multiple species in a simulated natural environment. Here, we present nanoporous microscale microbial incubators (NMMI) that enable high-throughput screening and real-time observation of multi-species co-culture. The key innovation in NMMI is that they facilitate inter-species communication while maintaining physical isolation between species, which is ideal for genomic analysis. Co-culture of a quorum sensing pair demonstrates that the NMMI can be used to culture multiple species in chemical communication while monitoring the growth dynamics of individual species. PMID:26584739

  6. Bayesian Integrated Microbial Forensics

    SciTech Connect

    Jarman, Kristin H.; Kreuzer-Martin, Helen W.; Wunschel, David S.; Valentine, Nancy B.; Cliff, John B.; Petersen, Catherine E.; Colburn, Heather A.; Wahl, Karen L.

    2008-06-01

    In the aftermath of the 2001 anthrax letters, researchers have been exploring ways to predict the production environment of unknown source microorganisms. Different mass spectral techniques are being developed to characterize components of a microbe’s culture medium including water, carbon and nitrogen sources, metal ions added, and the presence of agar. Individually, each technique has the potential to identify one or two ingredients in a culture medium recipe. However, by integrating data from multiple mass spectral techniques, a more complete characterization is possible. We present a Bayesian statistical approach to integrated microbial forensics and illustrate its application on spores grown in different culture media.

  7. Starter cultures for cereal based foods.

    PubMed

    Brandt, Markus J

    2014-02-01

    Fermented cereals play a significant role in human nutrition in all parts of the world where cereals grow. These fermentations are started spontaneously or there have been traditional techniques developed in order to keep starter cultures for these processes alive. With the growing impact of industrial microbiology during 20th century this traditional starter culture propagation was replaced often, especially in the dairy industry, by the use of pure, frozen or freeze-dried cultures grown on microbial media. In contrast to the production of ethanol from cereals, in sourdough a pasteurization step before inoculation is avoided due to gelatinization of starch and inactivation of endogenous enzymes. Therefore cultures must be competitive to the relatively high microbial load of the cereal raw materials and well adapted to the specific ecology determined by the kind of cereal and the process conditions. Less adapted cultures could be used, but then the process of back-slopping of cultures is limited. Although cereal fermentations take the biggest volume among fermented foods, only for sourdoughs commercial cultures are available.

  8. Effects of added chelated trace minerals, organic selenium, yeast culture, direct-fed microbials, and Yucca schidigera extract in horses: II. Nutrient excretion and potential environmental impact.

    PubMed

    Gordon, M E; Edwards, M S; Sweeney, C R; Jerina, M L

    2013-08-01

    The objective of this study was to test the hypothesis that an equine diet formulated with chelated trace minerals, organic selenium, yeast culture, direct-fed microbials (DFM) and Yucca schidigera extract would decrease excretion of nutrients that have potential for environmental impact. Horses were acclimated to 100% pelleted diets formulated with (ADD) and without (CTRL) the aforementioned additives. Chelated sources of Cu, Zn, Mn, and Co were included in the ADD diet at a 100% replacement rate of sulfate forms used in the CTRL diet. Additionally, the ADD diet included organic selenium yeast, DFM, and Yucca schidigera extract. Ten horses were fed the 2 experimental diets during two 42-d periods in a crossover design. Total fecal and urine collection occurred during the last 14 d of each period. Results indicate no significant differences between Cu, Zn, Mn, and Co concentrations excreted via urine (P > 0.05) due to dietary treatment. There was no difference between fecal Cu and Mn concentrations (P > 0.05) based on diet consumed. Mean fecal Zn and Co concentrations excreted by horses consuming ADD were greater than CTRL (P < 0.003). Differences due to diet were found for selenium fecal (P < 0.0001) and urine (P < 0.0001) excretions, with decreased concentrations found for horses consuming organic selenium yeast (ADD). In contrast, fecal K (%) was greater (P = 0.0421) for horses consuming ADD, whereas concentrations of fecal solids, total N, ammonia N, P, total ammonia, and fecal output did not differ between dietary treatments (P > 0.05). In feces stockpiled to simulate a crude composting method, no differences (P > 0.05) due to diet were detected for particle size, temperature, moisture, OM, total N, P, phosphate, K, moisture, potash, or ammonia N (P > 0.05). Although no difference (P = 0.2737) in feces stockpile temperature due to diet was found, temperature differences over time were documented (P < 0.0001). In conclusion, the addition of certain chelated

  9. Effect of varying the salt and fat content in Cheddar cheese on aspects of the performance of a commercial starter culture preparation during ripening.

    PubMed

    Yanachkina, Palina; McCarthy, Catherine; Guinee, Tim; Wilkinson, Martin

    2016-05-01

    Production of healthier reduced-fat and reduced-salt cheeses requires careful selection of starter bacteria, as any substantial alterations to cheese composition may prompt changes in the overall performance of starters during cheese ripening. Therefore, it is important to assess the effect of compositional alterations on the individual strain response during cheese ripening for each optimised cheese matrix. In the current study, the effect of varying fat and salt levels in Cheddar cheese on the performance of a commercial Lactococcus lactis culture preparation, containing one L. lactis subsp. lactis strain and one L. lactis subsp. cremoris strain was investigated. Compositional variations in fat or salt levels did not affect overall starter viability, yet reduction of fat by 50% significantly delayed non-starter lactic acid bacteria (NSLAB) populations at the initial ripening period. In comparison to starter viability, starter autolysis, as measured by release of intracellular lactate dehydrogenase (LDH) or post-proline dipeptidyl aminopeptidase (Pep X) into cheese juices, decreased significantly with lower salt addition levels in full-fat Cheddar. Conversely, reducing fat content of cheese resulted in a significantly higher release of intracellular Pep X, and to a lesser extent intracellular LDH, into juices over ripening. Flow cytometry (FCM) indicated that the permeabilised and dead cell sub-populations were generally lower in juices from cheeses with reduced salt content, however no significant differences were observed between different salt and fat treatments. Interestingly, fat reductions by 30 and 50% in cheeses with reduced or half added salt contents appeared to balance out the effect of salt, and enhanced cell permeabilisation, cell death, and also cell autolysis in these variants. Overall, this study has highlighted that alterations in both salt and fat levels in cheese influence certain aspects of starter performance during ripening, including

  10. Effect of varying the salt and fat content in Cheddar cheese on aspects of the performance of a commercial starter culture preparation during ripening.

    PubMed

    Yanachkina, Palina; McCarthy, Catherine; Guinee, Tim; Wilkinson, Martin

    2016-05-01

    Production of healthier reduced-fat and reduced-salt cheeses requires careful selection of starter bacteria, as any substantial alterations to cheese composition may prompt changes in the overall performance of starters during cheese ripening. Therefore, it is important to assess the effect of compositional alterations on the individual strain response during cheese ripening for each optimised cheese matrix. In the current study, the effect of varying fat and salt levels in Cheddar cheese on the performance of a commercial Lactococcus lactis culture preparation, containing one L. lactis subsp. lactis strain and one L. lactis subsp. cremoris strain was investigated. Compositional variations in fat or salt levels did not affect overall starter viability, yet reduction of fat by 50% significantly delayed non-starter lactic acid bacteria (NSLAB) populations at the initial ripening period. In comparison to starter viability, starter autolysis, as measured by release of intracellular lactate dehydrogenase (LDH) or post-proline dipeptidyl aminopeptidase (Pep X) into cheese juices, decreased significantly with lower salt addition levels in full-fat Cheddar. Conversely, reducing fat content of cheese resulted in a significantly higher release of intracellular Pep X, and to a lesser extent intracellular LDH, into juices over ripening. Flow cytometry (FCM) indicated that the permeabilised and dead cell sub-populations were generally lower in juices from cheeses with reduced salt content, however no significant differences were observed between different salt and fat treatments. Interestingly, fat reductions by 30 and 50% in cheeses with reduced or half added salt contents appeared to balance out the effect of salt, and enhanced cell permeabilisation, cell death, and also cell autolysis in these variants. Overall, this study has highlighted that alterations in both salt and fat levels in cheese influence certain aspects of starter performance during ripening, including

  11. Xanthan gum: an economical substitute for agar in plant tissue culture media.

    PubMed

    Jain, R; Babbar, S B

    2006-03-01

    Xanthan gum, a microbial desiccation-resistant polysaccharide prepared commercially by aerobic submerged fermentation from Xanthomonas campestris, has been successfully used as a solidifying agent for plant tissue culture media. Its suitability as a substitute to agar was demonstrated for in vitro seed germination, caulogenesis and rhizogenesis of Albizzia lebbeck, androgenesis in anther cultures of Datura innoxia, and somatic embryogenesis in callus cultures of Calliandra tweedii. Culture media used for eliciting these morphogenic responses were gelled with either 1% xanthan gum or 0.9% agar. Xanthan gum, like agar, supported all these responses.

  12. Microbial enhanced oil recovery research. [Peptides

    SciTech Connect

    Sharma, M.M.; Georgiou, G. )

    1992-01-01

    The surface active lipopeptide produced by Bacillus licheniformis JF-2 was isolated to near apparent homogeneity. NMR experiments revealed that this compound consists of a heptapeptide with an amino acid sequence similar to surfactin and a heterogeneous fatty acid consisting of the normal-, anteiso-, and iso- branched isomers. The surface activity of the B. licheniformis JF-2 surfactant was shown to depend on the presence of fermentation products and is strongly affected by the pH. Under conditions of optimal salinity and pH the interfacial tension against decane was 6 [times] 10[sup 3] mN/m which is one of the lowest values ever obtained with a microbial surfactant. Microbial compounds which exhibit particularly high surface activity are classified as biosurfactants. Microbial biosurfactants include a wide variety of surface and interfacially active compounds, such as glycolipids, lipopeptides polysaccharideprotein complexes, phospholipids, fatty acids and neutral lipids. Biosurfactants are easily biodegradable and thus are particularly suited for environmental applications such as bioremediation and the dispersion of oil spills. Bacillus licheniformis strain JF-2 has been shown to be able to grow and produce a very effective biosurfactant under both aerobic and anaerobic conditions and in the presence of high salt concentrations. The production of biosurfactants in anaerobic, high salt environments is potentially important for a variety of in situ applications such as microbial enhanced oil recovery. As a first step towards evaluating the commercial utility of the B. licheniformis JF-2 surfactant, we isolated t-he active. compound from the culture supernatant, characterized its chemical structure and investigated its phase behavior. We found that the surface activity of the surfactant is strongly dependent on the pH of the aqueous. phase. This may be important for the biological function of the surfactant and is of interest for several applications in surfactancy.

  13. Method Analysis of Microbial Resistant Gypsum Products

    EPA Science Inventory

    Abstract: Several commercially available gypsum products are marketed as microbial-resistant. During previous test method research on a microbial resistant gypsum wallboard study, a common theme from both stakeholders and product vendors was the need for a unified and accepted m...

  14. Microbial diversity and dynamics of a groundwater and a still bottled natural mineral water.

    PubMed

    França, Luís; Lopéz-Lopéz, Arantxa; Rosselló-Móra, Ramon; da Costa, Milton S

    2015-03-01

    The microbial abundance and diversity at source, after bottling and through 6 months of storage of a commercial still natural mineral water were assessed by culture-dependent and culture-independent methods. The results revealed clear shifts of the dominant communities present in the three different stages. The borehole waters displayed low cell densities that increased 1.5-fold upon bottling and storage, reaching a maximum (6.2 × 10(8)  cells l(-1) ) within 15 days after bottling, but experienced a significant decrease in diversity. In all cases, communities were largely dominated by Bacteria. The culturable heterotrophic community was characterized by recovering 3626 isolates, which were primarily affiliated with the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. This study indicates that bottling and storage induce quantitative and qualitative changes in the microbial assemblages that seem to be similar as revealed by the two sample batches collected on 2 consecutive years. To our knowledge, this is the first study combining culture-independent with culture-dependent methods, and repeated tests to reveal the microbial dynamics occurring from source to stored bottled water.

  15. Microbial origin of desert varnish.

    PubMed

    Dorn, R I; Oberlander, T M

    1981-09-11

    Scanning electron microscopy and energy dispersive x-ray analyses of desert varnish reveal that microorganisms concentrate ambient manganese that becomes greatly enhanced in brown to black varnish. Specific characteristics of desert varnish and of varnish bacteria support a microbial origin for manganese-rich films. Varnish microbes can be cultured and produce laboratory manganese films. Accordingly, natural desert varnish and also manganese-rich rock varnishes in nondesert environments appear to be a product of microbial activity. PMID:17744757

  16. Microbial origin of desert varnish.

    PubMed

    Dorn, R I; Oberlander, T M

    1981-09-11

    Scanning electron microscopy and energy dispersive x-ray analyses of desert varnish reveal that microorganisms concentrate ambient manganese that becomes greatly enhanced in brown to black varnish. Specific characteristics of desert varnish and of varnish bacteria support a microbial origin for manganese-rich films. Varnish microbes can be cultured and produce laboratory manganese films. Accordingly, natural desert varnish and also manganese-rich rock varnishes in nondesert environments appear to be a product of microbial activity.

  17. Microbial production of epoxides

    SciTech Connect

    Clark, Thomas R.; Roberto, Francisco F.

    2003-06-10

    A method for microbial production of epoxides and other oxygenated products is disclosed. The method uses a biocatalyst of methanotrophic bacteria cultured in a biphasic medium containing a major amount of a non-aqueous polar solvent. Regeneration of reducing equivalents is carried out by using endogenous hydrogenase activity together with supplied hydrogen gas. This method is especially effective with gaseous substrates and cofactors that result in liquid products.

  18. Automated Microbial Metabolism Laboratory

    NASA Technical Reports Server (NTRS)

    1973-01-01

    Development of the automated microbial metabolism laboratory (AMML) concept is reported. The focus of effort of AMML was on the advanced labeled release experiment. Labeled substrates, inhibitors, and temperatures were investigated to establish a comparative biochemical profile. Profiles at three time intervals on soil and pure cultures of bacteria isolated from soil were prepared to establish a complete library. The development of a strategy for the return of a soil sample from Mars is also reported.

  19. Hydrogen production from microbial strains

    DOEpatents

    Harwood, Caroline S; Rey, Federico E

    2012-09-18

    The present invention is directed to a method of screening microbe strains capable of generating hydrogen. This method involves inoculating one or more microbes in a sample containing cell culture medium to form an inoculated culture medium. The inoculated culture medium is then incubated under hydrogen producing conditions. Once incubating causes the inoculated culture medium to produce hydrogen, microbes in the culture medium are identified as candidate microbe strains capable of generating hydrogen. Methods of producing hydrogen using one or more of the microbial strains identified as well as the hydrogen producing strains themselves are also disclosed.

  20. [Microbial sensors: achievements, problems, prospects].

    PubMed

    Korpan, Ia I; El'skaia, A V

    1995-12-01

    The review summarizes the literature data on the design of laboratory and commercial types of biosensors based on living cells of microorganisms. The following aspects are discussed: microbiological, biochemical and physical fundamentals of microbial sensors; operation modes and fields of application of cell-based biosensors; immobilization technique for biological recognition systems; benefits and problems in this field of biotechnology.

  1. Environmental biodegradability of [¹⁴C] single-walled carbon nanotubes by Trametes versicolor and natural microbial cultures found in New Bedford Harbor sediment and aerated wastewater treatment plant sludge.

    PubMed

    Parks, Ashley N; Chandler, G Thomas; Ho, Kay T; Burgess, Robert M; Ferguson, P Lee

    2015-02-01

    Little is known about environmental biodegradability or biotransformations of single-walled carbon nanotubes (SWNT). Because of their strong association with aquatic organic matter, detailed knowledge of the ultimate fate and persistence of SWNT requires investigation of possible biotransformations (i.e., biodegradation) in environmental media. In the present study, [(14)C]SWNT were utilized to track biodegradation over 6 mo by pure liquid culture of the fungus Trametes versicolor and mixed bacterial isolates from field-collected sediment or aerated wastewater treatment plant sludge. The mixed cultures were chosen as more environmentally relevant media where SWNT will likely be deposited under both aerobic and anaerobic conditions. Activity of [(14)C] was assessed in solid, aqueous, and (14)CO2 gaseous phases to determine amounts of intact SWNT, partially soluble SWNT degradation products, and mineralized SWNT, respectively, during the 6 mo of the experiment. Mass balances based on radiocarbon activity were approximately 100% over 6 mo, and no significant degradation of SWNT was observed. Approximately 99% of the [(14)C] activity remained in the solid phase, 0.8% in the aqueous phase, and less than 0.1% was mineralized to (14)CO2, regardless of culture type. These results suggest that SWNT are not readily biodegraded by pure fungal cultures or environmental microbial communities, and are likely persistent in environmental media.

  2. Commercial Crew

    NASA Video Gallery

    Phil McAlister delivers a presentation by the Commercial Crew (CC) study team on May 25, 2010, at the NASA Exploration Enterprise Workshop held in Galveston, TX. The purpose of this workshop was to...

  3. Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

    NASA Astrophysics Data System (ADS)

    Davis, R.; Tebo, B. M.

    2013-12-01

    Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn

  4. Space Commercialization

    NASA Technical Reports Server (NTRS)

    Martin, Gary L.

    2011-01-01

    A robust and competitive commercial space sector is vital to continued progress in space. The United States is committed to encouraging and facilitating the growth of a U.S. commercial space sector that supports U.S. needs, is globally competitive, and advances U.S. leadership in the generation of new markets and innovation-driven entrepreneurship. Energize competitive domestic industries to participate in global markets and advance the development of: satellite manufacturing; satellite-based services; space launch; terrestrial applications; and increased entrepreneurship. Purchase and use commercial space capabilities and services to the maximum practical extent Actively explore the use of inventive, nontraditional arrangements for acquiring commercial space goods and services to meet United States Government requirements, including measures such as public-private partnerships, . Refrain from conducting United States Government space activities that preclude, discourage, or compete with U.S. commercial space activities. Pursue potential opportunities for transferring routine, operational space functions to the commercial space sector where beneficial and cost-effective.

  5. Genetic diversity in the lactose operons of Lactobacillus helveticus strains and its relationship to the role of these strains as commercial starter cultures.

    PubMed

    Callanan, M J; Beresford, T P; Ross, R P

    2005-03-01

    Two novel insertion sequence elements, ISLhe1 and ISLhe15, were located upstream of the genes encoding the beta-galactosidase enzyme in Lactobacillus helveticus commercial starter strains. Strains with the IS982 family element, ISLhe1, demonstrated reduced beta-galactosidase activity compared to the L. helveticus type strain, whereas strains with the ISLhe15 element expressed beta-galactosidase in the absence of lactose. PMID:15746373

  6. Examining the genetic variation of reference microbial cultures used within food and environmental laboratories using fluorescent amplified fragment length polymorphism analysis.

    PubMed

    Cross, Lisa Jane; Russell, Julie Elizabeth; Desai, Meeta

    2011-08-01

    Fluorescent amplified fragment length polymorphism (FAFLP) analysis was applied to genetically fingerprint 'working culture control strains' used by accredited food microbiology laboratories. A working culture control strain is defined as a subculture from a strain initially obtained from an authenticated source [such as the National Collection of Type Cultures (NCTC)] that is maintained for use with routine testing within the laboratory. Working culture control strains from eight food examination laboratories, representing four bacterial species, were analysed by FAFLP; these were Salmonella Nottingham, Staphylococcus aureus, Listeria monocytogenes and Bacillus cereus. The resultant FAFLP profiles of the eight working culture control strains for each of these species were compared against the appropriate freeze-dried ampoules obtained directly from NCTC. FAFLP results demonstrated that within 50% of working cultures analysed, several laboratories were routinely using working cultures that were genetically different from the original reference NCTC strains. This study highlights the need for laboratories to review the protocols used to process and maintain control strains and working cultures, with a potential view to utilize single-use quality control materials.

  7. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity. PMID:18757573

  8. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity.

  9. Microbial populations in contaminant plumes

    USGS Publications Warehouse

    Haack, S.K.; Bekins, B.A.

    2000-01-01

    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.

  10. Commercial Fishing.

    ERIC Educational Resources Information Center

    Florida State Dept. of Education, Tallahassee. Div. of Vocational Education.

    This document is a curriculum framework for a program in commercial fishing to be taught in Florida secondary and postsecondary institutions. This outline covers the major concepts/content of the program, which is designed to prepare students for employment in occupations with titles such as net fishers, pot fishers, line fishers, shrimp boat…

  11. Commercial applications

    NASA Technical Reports Server (NTRS)

    Togai, Masaki

    1990-01-01

    Viewgraphs on commercial applications of fuzzy logic in Japan are presented. Topics covered include: suitable application area of fuzzy theory; characteristics of fuzzy control; fuzzy closed-loop controller; Mitsubishi heavy air conditioner; predictive fuzzy control; the Sendai subway system; automatic transmission; fuzzy logic-based command system for antilock braking system; fuzzy feed-forward controller; and fuzzy auto-tuning system.

  12. Commercial Art.

    ERIC Educational Resources Information Center

    Vassallo, Thomas

    This curriculum guide provides materials for a competency-based course in commercial art at the secondary level. The curriculum design uses the curriculum infused model for the teaching of basic skills as part of vocational education and demonstrates the relationship of vocationally related skills to communication, mathematics, and science…

  13. NMR bioreactor development for live in-situ microbial functional analysis

    NASA Astrophysics Data System (ADS)

    Majors, Paul D.; McLean, Jeffrey S.; Scholten, Johannes C. M.

    2008-05-01

    A live, in-situ metabolomics capability was developed for prokaryotic cultures under controlled growth conditions. Toward this goal, a radiofrequency-transparent bioreactor was developed and integrated with a commercial wide-bore nuclear magnetic resonance (NMR) imaging spectrometer and a commercial bioreactor controller. Water suppressed 1H NMR spectroscopy was used to monitor glucose and fructose utilization and byproduct excretion by Eubacterium aggregans (an anaerobic bacterial species relevant for biofuel production) under controlled batch and continuous culture conditions. The resulting metabolite profiles (short chain organic acids and ethanol) and trends are consistent with existing knowledge of its metabolism. However, our study also showed that E. aggregans produces lactate end product in significant concentrations—a result not previously reported. The advantages of live in-situ microbial metabolomics analysis and its complementariness with functional genomics/systems biology methods are discussed.

  14. NMR bioreactor development for live in-situ microbial functional analysis

    SciTech Connect

    Majors, Paul D.; Mclean, Jeffrey S.; Scholten, Johannes C.

    2008-05-01

    A live in-situ metabolomics capability was developed for prokaryotic cultures under controlled-growth conditions. Toward this goal, a radiofrequency-transparent bioreactor was developed and integrated with a commercial wide-bore nuclear magnetic resonance (NMR) imaging spectrometer and a commercial bioreactor controller. Water suppressed 1H NMR spectroscopy was used to monitor glucose and fructose utilization and byproduct excretion by Eubacterium aggregans (an anaerobic bacterial species relevant for biofuels production) under controlled batch and continuous culture conditions. The resulting metabolite profiles (short chain organic acids and ethanol) and trends are consistent with existing knowledge of its metabolism. However, our study showed the Eubacterium aggregans produces lactate end product in significant concentrations – a result not previously reported. The advantages of live in-situ microbial metabolomics analysis and its complementariness with functional genomics / systems biology methods are discussed.

  15. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms.

    PubMed

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare; Settanni, Luca

    2015-11-06

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese.

  16. Functional Stability Of A Mixed Microbial Consortia Producing PHA From Waste Carbon Sources

    SciTech Connect

    David N. Thompson; Erik R. Coats; William A. Smith; Frank J. Loge; Michael P. Wolcott

    2006-04-01

    Polyhydroxyalkanoates (PHAs), naturally-occurring biological polyesters that are microbially synthesized from a myriad of carbon sources, can be utilized as biodegradable substitutes for petroleum-derived thermoplastics. However, current PHA commercialization schemes are limited by high feedstock costs, the requirement for aseptic reactors, and high separation and purification costs. Bacteria indigenous to municipal waste streams can accumulate large quantities of PHA under environmentally controlled conditions; hence, a potentially more environmentally-effective method of production would utilize these consortia to produce PHAs from inexpensive waste carbon sources. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing mixed microbial consortia from municipal activated sludge as inoculum, in cultures grown on real wastewaters. PHA production averaged 85%, 53%, and 10% of the cell dry weight from methanol-enriched pulp-and-paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. The PHA-producing microbial consortia were examined to explore the microbial community changes that occurred during reactor operations, employing denaturing gradient gel electrophoresis (DGGE) of 16S-rDNA from PCR-amplified DNA extracts. Distinctly different communities were observed both between and within wastewaters following enrichment. More importantly, stable functions were maintained despite the differing and contrasting microbial populations.

  17. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

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

  18. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

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

  19. Microbial degradation of polyfluoroalkyl chemicals in the environment: a review.

    PubMed

    Liu, Jinxia; Mejia Avendaño, Sandra

    2013-11-01

    Polyfluoroalkyl chemicals containing perfluoroalkyl moieties have been widely used in numerous industrial and commercial applications. Many polyfluoroalkyl chemicals are potential perfluoroalkyl acid (PFAA) precursors. When they are released to the environment, abiotic and microbial degradation of non-fluorinated functionalities, polyfluoroalkyl and perfluoroalkyl moieties can result in perfluoroalkyl carboxylic (PFCAs) and sulfonic acids (PFSAs), such as perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS). These highly persistent and ubiquitously detected PFAAs are the subjects of many regulations and actions due to their toxic profiles. In order to confidently evaluate the environmental fate and effects of these precursors and their links to PFSAs and PFCAs, we present the review into the environmental biodegradability studies carried out with microbial culture, activated sludge, soil and sediment in the past decade. First, we propose that the knowledge gap caused by the lack of direct detection of precursor chemicals in environmental samples can be bridged by laboratory investigations of important precursors such as fluorotelomer-based compounds and perfluoroalkane sulfonamido derivatives. Then we evaluate the experimental setups and methodologies, sampling and sample preparation methods, and analytical techniques that have been successfully applied. Third, we provide the most updated knowledge on quantitative and qualitative relationships between precursors and PFSAs or PFCAs, microbial degradation pathways, half-lives of precursors, defluorination potential, and novel degradation intermediates and products. In the end, we identify knowledge gaps and suggest research directions with regard to future biodegradation studies, environmental monitoring and ecotoxicological assessment of perfluoroalkyl and polyfluoroalkyl chemicals.

  20. Microbial antibiotic production aboard the International Space Station.

    PubMed

    Benoit, M R; Li, W; Stodieck, L S; Lam, K S; Winther, C L; Roane, T M; Klaus, D M

    2006-04-01

    Previous studies examining metabolic characteristics of bacterial cultures have mostly suggested that reduced gravity is advantageous for microbial growth. As a consequence, the question of whether space flight would similarly enhance secondary metabolite production was raised. Results from three prior space shuttle experiments indicated that antibiotic production was stimulated in space for two different microbial systems, albeit under suboptimal growth conditions. The goal of this latest experiment was to determine whether the enhanced productivity would also occur with better growth conditions and over longer durations of weightlessness. Microbial antibiotic production was examined onboard the International Space Station during the 72-day 8A increment. Findings of increased productivity of actinomycin D by Streptomyces plicatus in space corroborated with previous findings for the early sample points (days 8 and 12); however, the flight production levels were lower than the matched ground control samples for the remainder of the mission. The overall goal of this research program is to elucidate the specific mechanisms responsible for the initial stimulation of productivity in space and translate this knowledge into methods for improving efficiency of commercial production facilities on Earth.

  1. Microbial contamination and disinfection methods of pacifiers

    PubMed Central

    NELSON, Paulo; LOUVAIN, Márcia Costa; MACARI, Soraia; LUCISANO, Marília Pacífico; da SILVA, Raquel Assed Bezerra; de QUEIROZ, Alexandra Mussolino; GATON-HERNÁNDEZ, Patrícia; da SILVA, Léa Assed Bezerra

    2015-01-01

    Objectives To evaluate the microbial contamination of pacifiers by Mutans Streptococci (MS) and the efficacy of different methods for their disinfection. Methods Twenty-eight children were assigned to a 4-stage changeover system with a 1-week interval. In each stage, children received a new pacifier and the parents were instructed to maintain their normal habits for 1 week. After this time, the pacifiers were subjected to the following 4 disinfection methods: spraying with 0.12% chlorhexidine solution, Brushtox® or sterile tap water, and immersion in boiling tap water for 15 minutes. Microbiological culture for MS and Scanning Electron Microscopy (SEM) were performed. The results were analyzed statistically by Friedman’s non-parametric test (a=0.05). Results The 0.12% chlorhexidine spray was statistically similar to the boiling water (p>0.05) and more effective than the Brushtox® spray and control (p<0.05). The analysis of SEM showed the formation of a cariogenic biofilm in all groups with positive culture. Conclusions Pacifiers become contaminated by MS after their use by children and should be disinfected routinely. Spraying with a 0.12% chlorhexidine solution and immersion in boiling water promoted better disinfection of the pacifiers compared with a commercial antiseptic toothbrush cleanser (Brushtox®). PMID:26537723

  2. Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms.

    PubMed

    Uria, A R; Zilda, D S

    2016-01-01

    Marine microorganisms are a rich reservoir of highly diverse and unique biocatalysts that offer potential applications in food, pharmaceutical, fuel, and cosmetic industries. The fact that only less than 1% of microbes in any marine habitats can be cultured under standard laboratory conditions has hampered access to their extraordinary biocatalytic potential. Metagenomics has recently emerged as a powerful and well-established tool to investigate the vast majority of hidden uncultured microbial diversity for the discovery of novel industrially relevant enzymes from different types of environmental samples, such as seawater, marine sediment, and symbiotic microbial consortia. We discuss here in this review about approaches and methods in metagenomics that have been used and can potentially be used to mine commercially useful biocatalysts from uncultured marine microbes. PMID:27452163

  3. Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms.

    PubMed

    Uria, A R; Zilda, D S

    2016-01-01

    Marine microorganisms are a rich reservoir of highly diverse and unique biocatalysts that offer potential applications in food, pharmaceutical, fuel, and cosmetic industries. The fact that only less than 1% of microbes in any marine habitats can be cultured under standard laboratory conditions has hampered access to their extraordinary biocatalytic potential. Metagenomics has recently emerged as a powerful and well-established tool to investigate the vast majority of hidden uncultured microbial diversity for the discovery of novel industrially relevant enzymes from different types of environmental samples, such as seawater, marine sediment, and symbiotic microbial consortia. We discuss here in this review about approaches and methods in metagenomics that have been used and can potentially be used to mine commercially useful biocatalysts from uncultured marine microbes.

  4. The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate.

    PubMed

    Batista, Nádia Nara; Ramos, Cíntia Lacerda; Dias, Disney Ribeiro; Pinheiro, Ana Carla Marques; Schwan, Rosane Freitas

    2016-02-01

    Theobroma cacao seeds are the main raw material for chocolate production. During their fermentation, a succession of microorganisms are responsible for the physicochemical changes occurring in the pulp and inside the beans. The aim of this study was to investigate the effects of yeast inoculation (Saccharomyces cerevisiae UFLA CA11, Pichia kluivery CCMA0237, and Hanseniaspora uvarum CCMA0236) on the profile of the volatile compounds and microbial communities in cocoa fermentation. The resulting chocolate was also evaluated by temporal dominance of sensations (TDS) analyses. The dominant microorganisms during spontaneous fermentation were S. cerevisiae, H. uvarum, H. guilliermondii, Lactobacillus fermentum, Pediococcus sp., and Acetobacter pasteurianus. Similarly, S. cerevisiae, P. kluyveri, Candida sp., Pediococcus sp., and A. pasteurianus were the predominant microorganisms assessed by Denaturing Gradient Gel Electrophoresis (DGGE) in inoculated fermentation. Sixty-seven volatile compounds were detected and quantified by gas chromatography/mass spectrometry (GC/MS) at the end of fermentation and chocolates. The main group of volatile compound found after the inoculated and spontaneous fermentations was esters (41 and 39 %, respectively). In the chocolates, the main group was acids (73 and 44 % from the inoculated and spontaneous fermentations, respectively). The TDS analyses showed a dominance of bitter and cocoa attributes in both chocolates. However, in the inoculated chocolate, lingering fruity notes were more intense, while the chocolate produced by spontaneous fermentation was more astringent. Thus, the inoculation of yeast influenced the microbial profile, which likely affected the volatile compounds that affect sensory characteristics, resulting in chocolate with dominant bitter, cocoa, and fruity attributes. PMID:27162390

  5. Synthetic microbial ecosystems for biotechnology.

    PubMed

    Pandhal, Jagroop; Noirel, Josselin

    2014-06-01

    Most highly controlled and specific applications of microorganisms in biotechnology involve pure cultures. Maintaining single strain cultures is important for industry as contaminants can reduce productivity and lead to longer "down-times" during sterilisation. However, microbes working together provide distinct advantages over pure cultures. They can undertake more metabolically complex tasks, improve efficiency and even expand applications to open systems. By combining rapidly advancing technologies with ecological theory, the use of microbial ecosystems in biotechnology will inevitably increase. This review provides insight into the use of synthetic microbial communities in biotechnology by applying the engineering paradigm of measure, model, manipulate and manufacture, and illustrate the emerging wider potential of the synthetic ecology field. Systems to improve biofuel production using microalgae are also discussed.

  6. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

    PubMed Central

    Ceuppens, Siele; Delbeke, Stefanie; De Coninck, Dieter; Boussemaere, Jolien; Boon, Nico; Uyttendaele, Mieke

    2015-01-01

    Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth. PMID:26308033

  7. Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques.

    PubMed

    Ceuppens, Siele; Delbeke, Stefanie; De Coninck, Dieter; Boussemaere, Jolien; Boon, Nico; Uyttendaele, Mieke

    2015-08-01

    Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth. PMID:26308033

  8. Lactococcus lactis and Lactobacillus sakei as bio-protective culture to eliminate Leuconostoc mesenteroides spoilage and improve the shelf life and sensorial characteristics of commercial cooked bacon.

    PubMed

    Comi, Giuseppe; Andyanto, Debbie; Manzano, Marisa; Iacumin, Lucilla

    2016-09-01

    Cooked bacon is a typical Italian meat product. After production, cooked bacon is stored at 4 ± 2 °C. During storage, the microorganisms that survived pasteurisation can grow and produce spoilage. For the first time, we studied the cause of the deterioration in spoiled cooked bacon compared to unspoiled samples. Moreover, the use of bio-protective cultures to improve the quality of the product and eliminate the risk of spoilage was tested. The results show that Leuconostoc mesenteroides is responsible for spoilage and produces a greening colour of the meat, slime and various compounds that result from the fermentation of sugars and the degradation of nitrogen compounds. Finally, Lactococcus lactis spp. lactis and Lactobacillus sakei were able to reduce the risk of Leuconostoc mesenteroides spoilage.

  9. Lactococcus lactis and Lactobacillus sakei as bio-protective culture to eliminate Leuconostoc mesenteroides spoilage and improve the shelf life and sensorial characteristics of commercial cooked bacon.

    PubMed

    Comi, Giuseppe; Andyanto, Debbie; Manzano, Marisa; Iacumin, Lucilla

    2016-09-01

    Cooked bacon is a typical Italian meat product. After production, cooked bacon is stored at 4 ± 2 °C. During storage, the microorganisms that survived pasteurisation can grow and produce spoilage. For the first time, we studied the cause of the deterioration in spoiled cooked bacon compared to unspoiled samples. Moreover, the use of bio-protective cultures to improve the quality of the product and eliminate the risk of spoilage was tested. The results show that Leuconostoc mesenteroides is responsible for spoilage and produces a greening colour of the meat, slime and various compounds that result from the fermentation of sugars and the degradation of nitrogen compounds. Finally, Lactococcus lactis spp. lactis and Lactobacillus sakei were able to reduce the risk of Leuconostoc mesenteroides spoilage. PMID:27217354

  10. Towards a Microbial Thermoelectric Cell

    PubMed Central

    Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

    2013-01-01

    Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250–600 mV was achieved with 1.7 L baker’s yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices. PMID:23468862

  11. Towards a microbial thermoelectric cell.

    PubMed

    Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

    2013-01-01

    Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250-600 mV was achieved with 1.7 L baker's yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices.

  12. Commercial Capaciflector

    NASA Technical Reports Server (NTRS)

    Vranish, John M.

    1991-01-01

    A capacitive proximity/tactile sensor with unique performance capabilities ('capaciflector' or capacitive reflector) is being developed by NASA/Goddard Space Flight Center (GSFC) for use on robots and payloads in space in the interests of safety, efficiency, and ease of operation. Specifically, this sensor will permit robots and their attached payloads to avoid collisions in space with humans and other objects and to dock these payloads in a cluttered environment. The sensor is simple, robust, and inexpensive to manufacture with obvious and recognized commercial possibilities. Accordingly, NASA/GSFC, in conjunction with industry, is embarking on an effort to 'spin' this technology off into the private sector. This effort includes prototypes aimed at commercial applications. The principles of operation of these prototypes are described along with hardware, software, modelling, and test results. The hardware description includes both the physical sensor in terms of a flexible printed circuit board and the electronic circuitry. The software description will include filtering and detection techniques. The modelling will involve finite element electric field analysis and will underline techniques used for design optimization.

  13. Anti-Adhesive Activity of Cranberry Phenolic Compounds and Their Microbial-Derived Metabolites against Uropathogenic Escherichia coli in Bladder Epithelial Cell Cultures.

    PubMed

    de Llano, Dolores González; Esteban-Fernández, Adelaida; Sánchez-Patán, Fernando; Martínlvarez, Pedro J; Moreno-Arribas, Maria Victoria; Bartolomé, Begoña

    2015-01-01

    Cranberry consumption has shown prophylactic effects against urinary tract infections (UTI), although the mechanisms involved are not completely understood. In this paper, cranberry phenolic compounds and their potential microbial-derived metabolites (such as simple phenols and benzoic, phenylacetic and phenylpropionic acids) were tested for their capacity to inhibit the adherence of uropathogenic Escherichia coli (UPEC) ATCC®53503™ to T24 epithelial bladder cells. Catechol, benzoic acid, vanillic acid, phenylacetic acid and 3,4-dihydroxyphenylacetic acid showed anti-adhesive activity against UPEC in a concentration-dependent manner from 100-500 µM, whereas procyanidin A2, widely reported as an inhibitor of UPEC adherence on uroepithelium, was only statistically significant (p < 0.05) at 500 µM (51.3% inhibition). The results proved for the first time the anti-adhesive activity of some cranberry-derived phenolic metabolites against UPEC in vitro, suggesting that their presence in the urine could reduce bacterial colonization and progression of UTI. PMID:26023719

  14. Bioaugmentation of half-matured granular sludge with special microbial culture promoted establishment of 2,4-dichlorophenoxyacetic acid degrading aerobic granules.

    PubMed

    Quan, Xiangchun; Ma, Jingyun; Xiong, Weicong; Wang, Xinrui

    2015-06-01

    Aerobic granular sludge degrading recalcitrant compounds are generally hard to be cultivated. This study investigated the feasibility of cultivating 2,4-dichlorophenoxyacetic acid (2,4-D) degrading aerobic granules using half-matured sludge granules pre-grown on glucose as the seeds and bioaugmentation with a 2,4-D degrading strain Achromobacter sp. QXH. Results showed that bioaugmentation promoted the steady transformation of glucose-grown granules to 2,4-D degrading sludge granules and fast establishment of 2,4-D degradation ability. The 2,4-D degradation rate of the bioaugmented granules was enhanced by 36-62 % compared to the control at 2,4-D concentrations of 144-565 mg/L on Day 18. The inoculated strain was incorporated into the half-matured granules successfully and survived till the end of operation (220 days). Sludge granules at a mean size of 420 µm and capable of utilizing 500 mg/L 2,4-D as the sole carbon source were finally obtained. Sludge microbial community shifted slightly during the whole operation and the dominant bacteria species belonged to Proteobacteria.

  15. Comparison of four β-glucuronidase and β-galactosidase-based commercial culture methods used to detect Escherichia coli and total coliforms in water.

    PubMed

    Maheux, Andrée F; Dion-Dupont, Vanessa; Bouchard, Sébastien; Bisson, Marc-Antoine; Bergeron, Michel G; Rodriguez, Manuel J

    2015-06-01

    The MI agar, Colilert(®), Chromocult coliform(®) agar, and DC with BCIG agar chromogenic culture-based methods used to assess microbiological quality of drinking water were compared in terms of their ubiquity, sensitivity, ease of use, growth of atypical colonies and affordability. For ubiquity, 129 total coliform (representing 76 species) and 19 Escherichia coli strains were tested. Then, 635 1-L well water samples were divided into 100 mL subsamples for testing by all four methods. Test results showed that 70.5, 52.7, 36.4, and 23.3% of the non-E. coli total coliform strains and 94.7, 94.7, 89.5, and 89.5% of the 19 E. coli strains yielded a positive signal with the four methods, respectively. They also yielded a total coliform positive signal for 66.5, 51.7, 64.9, and 55.0% and an E. coli positive signal for 16.1, 14.8, 17.3, and 13.4% of the 635 well water samples tested, respectively. Results showed that Colilert(®) is the most expensive method tested in terms of reactants, yet it is the easiest to use. Large numbers of atypical colonies were also often observed on Chromocult coliform(®) and DC with BCIG, thereby challenging the target microorganism count. Thus, the MI agar method seems to be the best option for the assessment of drinking water quality.

  16. Microbial monitoring of spacecraft and associated environments

    NASA Technical Reports Server (NTRS)

    La Duc, M. T.; Kern, R.; Venkateswaran, K.

    2004-01-01

    Rapid microbial monitoring technologies are invaluable in assessing contamination of spacecraft and associated environments. Universal and widespread elements of microbial structure and chemistry are logical targets for assessing microbial burden. Several biomarkers such as ATP, LPS, and DNA (ribosomal or spore-specific), were targeted to quantify either total bioburden or specific types of microbial contamination. The findings of these assays were compared with conventional, culture-dependent methods. This review evaluates the applicability and efficacy of some of these methods in monitoring the microbial burden of spacecraft and associated environments. Samples were collected from the surfaces of spacecraft, from surfaces of assembly facilities, and from drinking water reservoirs aboard the International Space Station (ISS). Culture-dependent techniques found species of Bacillus to be dominant on these surfaces. In contrast, rapid, culture-independent techniques revealed the presence of many Gram-positive and Gram-negative microorganisms, as well as actinomycetes and fungi. These included both cultivable and noncultivable microbes, findings further confirmed by DNA-based microbial detection techniques. Although the ISS drinking water was devoid of cultivable microbes, molecular-based techniques retrieved DNA sequences of numerous opportunistic pathogens. Each of the methods tested in this study has its advantages, and by coupling two or more of these techniques even more reliable information as to microbial burden is rapidly obtained. Copyright 2004 Springer-Verlag.

  17. Optimized Use of the MALDI BioTyper System and the FilmArray BCID Panel for Direct Identification of Microbial Pathogens from Positive Blood Cultures

    PubMed Central

    Fiori, B.; D'Inzeo, T.; Giaquinto, A.; Menchinelli, G.; Liotti, F. M.; de Maio, F.; De Angelis, G.; Quaranta, G.; Nagel, D.; Tumbarello, M.; Sanguinetti, M.

    2015-01-01

    Despite the current reliance on blood cultures (BCs), the diagnosis of bloodstream infections (BSIs) can be sped up using new technologies performed directly on positive BC bottles. Two methods (the MALDI BioTyper system and FilmArray blood culture identification [BCID] panel) are potentially applicable. In this study, we performed a large-scale clinical evaluation (1,585 microorganisms from 1,394 BSI episodes) on the combined use of the MALDI BioTyper and FilmArray BCID panel compared to a reference (culture-based) method. As a result, the causative organisms of 97.7% (1,362/1,394) of the BSIs were correctly identified by our MALDI BioTyper and FilmArray BCID-based algorithm. Specifically, 65 (5.3%) out of 1,223 monomicrobial BCs that provided incorrect or invalid identifications with the MALDI BioTyper were accurately detected by the FilmArray BCID panel; additionally, 153 (89.5%) out of 171 polymicrobial BCs achieved complete identification with the FilmArray BCID panel. Conversely, full use of the MALDI BioTyper would have resulted in the identification of only 1 causative organism in 97/171 (56.7%) of the polymicrobial cultures. By applying our diagnostic algorithm, the median time to identification was shortened (19.5 h versus 41.7 h with the reference method; P < 0.001), and the minimized use of the FilmArray BCID panel led to a significant cost savings. Twenty-six out of 31 microorganisms that could not be identified were species/genera not designed to be detected with the FilmArray BCID panel, indicating that subculture was not dispensable for a few of our BSI episodes. In summary, the fast and effective testing of BC bottles is realistically adoptable in the clinical microbiology laboratory workflow, although the usefulness of this testing for the management of BSIs remains to be established. PMID:26677254

  18. Culture-Independent Characterization of a Gene Responsible for Nitrogen Fixation in the Symbiotic Microbial Community in the Gut of the Termite Neotermes koshunensis

    PubMed Central

    Noda, Satoko; Ohkuma, Moriya; Usami, Ron; Horikoshi, Koki; Kudo, Toshiaki

    1999-01-01

    Expression of the nitrogen fixation gene, nifH, in the gut of the termite Neotermes koshunensis was characterized without cultivation. nifH cDNA was directly amplified from mRNA of the mixed microbial population in the gut by reverse transcription (RT)-PCR. Analyses of the RT-PCR products revealed that, among the diverse nifH sequences, only a few corresponding to an alternative nitrogenase (encoded by the anf gene) were preferentially transcribed in the termite gut. Expression of the anf gene was further investigated quantitatively under several termite feeding conditions by competitive PCR. The levels of expression of the anf gene were largely congruent with the nitrogen fixation activity displayed by the termite. The amounts of the genomic anf gene in the population showed no significant change, indicating that the level of expression was critical for nitrogen fixation activity. Interestingly, no significant decrease in the expression level was observed when the diet contained molybdenum (Mo), which represses ordinary anf genes. A 3.6-kb DNA region downstream of the anf gene was isolated and found to contain reading frames homologous to anfH, anfD, and anfG of the Bacteria domain which encode subunits of an alternative nitrogenase having no Mo as a cofactor. This DNA region also contained reading frames encoding glnB-like proteins, which is a common feature of the nitrogenase genes of the Archaea domain. These results indicate that the anf group of nitrogenase genes is the most important group of genes responsible for nitrogen fixation in N. koshunensis and that the anf gene possesses novel features with respect to the regulation of its expression and its gene organization. PMID:10543806

  19. Culture-independent characterization of a gene responsible for nitrogen fixation in the symbiotic microbial community in the gut of the termite Neotermes koshunensis.

    PubMed

    Noda, S; Ohkuma, M; Usami, R; Horikoshi, K; Kudo, T

    1999-11-01

    Expression of the nitrogen fixation gene, nifH, in the gut of the termite Neotermes koshunensis was characterized without cultivation. nifH cDNA was directly amplified from mRNA of the mixed microbial population in the gut by reverse transcription (RT)-PCR. Analyses of the RT-PCR products revealed that, among the diverse nifH sequences, only a few corresponding to an alternative nitrogenase (encoded by the anf gene) were preferentially transcribed in the termite gut. Expression of the anf gene was further investigated quantitatively under several termite feeding conditions by competitive PCR. The levels of expression of the anf gene were largely congruent with the nitrogen fixation activity displayed by the termite. The amounts of the genomic anf gene in the population showed no significant change, indicating that the level of expression was critical for nitrogen fixation activity. Interestingly, no significant decrease in the expression level was observed when the diet contained molybdenum (Mo), which represses ordinary anf genes. A 3.6-kb DNA region downstream of the anf gene was isolated and found to contain reading frames homologous to anfH, anfD, and anfG of the Bacteria domain which encode subunits of an alternative nitrogenase having no Mo as a cofactor. This DNA region also contained reading frames encoding glnB-like proteins, which is a common feature of the nitrogenase genes of the Archaea domain. These results indicate that the anf group of nitrogenase genes is the most important group of genes responsible for nitrogen fixation in N. koshunensis and that the anf gene possesses novel features with respect to the regulation of its expression and its gene organization. PMID:10543806

  20. Pyrite oxidation by microbial consortia

    NASA Astrophysics Data System (ADS)

    Bostick, B. C.; Revill, K. L.; Doyle, C.; Kendelewicz, T.; Brown, G. E.; Spormann, A. M.; Fendorf, S.

    2003-12-01

    Acid mine drainage (AMD) is formed through pyrite oxidation, which produces acidity and releases toxic metals associated with pyrite and other sulfide minerals. Microbes accelerate pyrite oxidation markedly, thereby playing a major role in the production of AMD. Here, we probe pyrite oxidation by consortia of Thiobacillus ferrooxidans and thiooxidans using surface-sensitive photoelectron spectroscopy and X-ray absorption spectroscopy and compare them with surfaces oxidized through chemical and single species cultures. Microbial oxidation resulted in the formation of distinct oxidized surface species distributed non-uniformly over the pyrite surface; consortia produced a surface both more heterogeneous and more oxidized. In contrast, chemical oxidation proceeds without the build-up of passivating oxidation products. Surface morphology was not correlated with sites of nucleation or oxidation in any obvious manner. These results demonstrate that microbial oxidation occurs through a similar mechanism to chemical oxidation, but that the presence of complex microbial communities may impact the manner by which pyrite oxidation proceeds.

  1. Microbial Metabolomics

    PubMed Central

    Tang, Jane

    2011-01-01

    Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “omics” platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology. PMID:22379393

  2. In-vitro microbial production of conjugated linoleic acid by probiotic L. plantarum strains: Utilization as a functional starter culture in sucuk fermentation.

    PubMed

    Özer, Cem O; Kılıç, Birol; Kılıç, Gülden Başyiğit

    2016-04-01

    Twenty-three probiotic Lactobacillus plantarum strains were screened in-vitro to determine their ability to produce conjugated linoleic acid (CLA). L. plantarum AA1-2 and L. plantarum AB20-961 were identified as potential strains for CLA production. Optimum conditions for these strains to produce high levels of CLA were determined by evaluating the amount of added hydrolyzed sunflower oil (HSO) and initial pH levels in a nutrient medium. The highest CLA production was obtained in medium with pH6.0 and 2% HSO (P<0.05). Those strains were then used as starter culture in sucuk fermentation. Five sucuk treatments included a control (no starter culture), two sucuk groups with L. plantarum AA1-2 at the initial pH of 5.8 or 6.0 and two sucuk groups with L. plantarum AB20-961 at the initial pH of 5.8 or 6.0. Results indicate that L. plantarum AB20-961 produced higher amount of CLA in sucuk at initial pH of 5.8 and 6.0 levels during first 24h of fermentation compared with other groups. CLA isomer concentration decreased in all sucuk groups during the rest of the fermentation period (P<0.05) and remained quite stable during the storage. This study demonstrated that probiotic L. plantarum AB20-961 can be used in sucuk manufacturing without posing any quality problems.

  3. Microbial metropolis.

    PubMed

    Wimpenny, Julian

    2009-01-01

    Microorganisms can form tightly knit communities such as biofilms. Many others include marine snow, anaerobic digester granules, the ginger beer plant and bacterial colonies. This chapter is devoted to a survey of the main properties of these communities, with an emphasis on biofilms. We start with attachment to surfaces and the nature of adhesion. The growing community then forms within a matrix, generally of organic macromolecules. Inevitably the environment within such a matrix is different from that outside. Organisms respond by forming crowd-detection and response units; these quorum sensing systems act as switches between planktonic life and the dramatically altered conditions found inside microbial aggregates. The community then matures and changes and may even fail and disappear. Antimicrobial resistance is discussed as an example of multicellular behavior. The multicellular lifestyle has been modeled mathematically and responded to powerful molecular biological techniques. Latterly, microbial systems have been used as models for fundamental evolutionary processes, mostly because of their high rates of reproduction and the ease of genetic manipulation. The life of most microbes is a duality between the yin of the community and the yang of planktonic existence. Sadly far less research has been devoted to adaptation to free-living forms than in the opposite direction. PMID:20943124

  4. Commercial applications

    NASA Astrophysics Data System (ADS)

    The near term (one to five year) needs of domestic and foreign commercial suppliers of radiochemicals and radiopharmaceuticals for electromagnetically separated stable isotopes are assessed. Only isotopes purchased to make products for sale and profit are considered. Radiopharmaceuticals produced from enriched stable isotopes supplied by the Calutron facility at ORNL are used in about 600,000 medical procedures each year in the United States. A temporary or permanent disruption of the supply of stable isotopes to the domestic radiopharmaceutical industry could curtail, if not eliminate, the use of such diagnostic procedures as the thallium heart scan, the gallium cancer scan, the gallium abscess scan, and the low radiation dose thyroid scan. An alternative source of enriched stable isotopes exist in the USSR. Alternative starting materials could, in theory, eventually be developed for both the thallium and gallium scans. The development of a new technology for these purposes, however, would take at least five years and would be expensive. Hence, any disruption of the supply of enriched isotopes from ORNL and the resulting unavailability of critical nuclear medicine procedures would have a dramatic negative effect on the level of health care in the United States.

  5. In-vitro microbial production of conjugated linoleic acid by probiotic L. plantarum strains: Utilization as a functional starter culture in sucuk fermentation.

    PubMed

    Özer, Cem O; Kılıç, Birol; Kılıç, Gülden Başyiğit

    2016-04-01

    Twenty-three probiotic Lactobacillus plantarum strains were screened in-vitro to determine their ability to produce conjugated linoleic acid (CLA). L. plantarum AA1-2 and L. plantarum AB20-961 were identified as potential strains for CLA production. Optimum conditions for these strains to produce high levels of CLA were determined by evaluating the amount of added hydrolyzed sunflower oil (HSO) and initial pH levels in a nutrient medium. The highest CLA production was obtained in medium with pH6.0 and 2% HSO (P<0.05). Those strains were then used as starter culture in sucuk fermentation. Five sucuk treatments included a control (no starter culture), two sucuk groups with L. plantarum AA1-2 at the initial pH of 5.8 or 6.0 and two sucuk groups with L. plantarum AB20-961 at the initial pH of 5.8 or 6.0. Results indicate that L. plantarum AB20-961 produced higher amount of CLA in sucuk at initial pH of 5.8 and 6.0 levels during first 24h of fermentation compared with other groups. CLA isomer concentration decreased in all sucuk groups during the rest of the fermentation period (P<0.05) and remained quite stable during the storage. This study demonstrated that probiotic L. plantarum AB20-961 can be used in sucuk manufacturing without posing any quality problems. PMID:26720888

  6. Microbial bio-based plastics from olive-mill wastewater: Generation and properties of polyhydroxyalkanoates from mixed cultures in a two-stage pilot scale system.

    PubMed

    Ntaikou, I; Valencia Peroni, C; Kourmentza, C; Ilieva, V I; Morelli, A; Chiellini, E; Lyberatos, G

    2014-10-20

    The operational efficiency of a two stage pilot scale system for polyhydroxyalkanoates (PHAs) production from three phase olive oil mill wastewater (OMW) was investigated in this study. A mixed anaerobic, acidogenic culture derived from a municipal wastewater treatment plant, was used in the first stage, aiming to the acidification of OMW. The effluent of the first bioreactor that was operated in continuous mode, was collected in a sedimentation tank in which partial removal of the suspended solids was taking place, and was then forwarded to an aerobic reactor, operated in sequential batch mode under nutrient limitation. In the second stage an enriched culture of Pseudomonas sp. was used as initial inoculum for the production of PHAs from the acidified waste. Clarification of the acidified waste, using aluminium sulphate which causes flocculation and precipitation of solids, was also performed, and its effect on the composition of the acidified waste as well as on the yields and properties of PHAs was investigated. It was shown that clarification had no significant qualitative or quantitative effect on the primary carbon sources, i.e. short chain fatty acids and residual sugars, but only on the values of total suspended solids and total chemical oxygen demand of the acidified waste. The type and thermal characteristics of the produced PHAs were also similar for both types of feed. However the clarification of the waste seemed to have a positive impact on final PHAs yield, measured as gPHAs/100g of VSS, which reached up to 25%. Analysis of the final products via nuclear magnetic resonance spectroscopy revealed the existence of 3-hydroxybutyrate (3HB) and 3-hydroxyoctanoate (HO) units, leading to the conclusion that the polymer could be either a blend of P3HB and P3HO homopolymers or/and the 3HB-co-3HO co-polymer, an unusual polymer occurring in nature with advanced properties.

  7. Use of Silicate Minerals for pH Control during Reductive Dechlorination of Chloroethenes in Batch Cultures of Different Microbial Consortia

    PubMed Central

    Lacroix, Elsa; Brovelli, Alessandro; Barry, D. A.

    2014-01-01

    In chloroethene-contaminated sites undergoing in situ bioremediation, groundwater acidification is a frequent problem in the source zone, and buffering strategies have to be implemented to maintain the pH in the neutral range. An alternative to conventional soluble buffers is silicate mineral particles as a long-term source of alkalinity. In previous studies, the buffering potentials of these minerals have been evaluated based on abiotic dissolution tests and geochemical modeling. In the present study, the buffering potentials of four silicate minerals (andradite, diopside, fayalite, and forsterite) were tested in batch cultures amended with tetrachloroethene (PCE) and inoculated with different organohalide-respiring consortia. Another objective of this study was to determine the influence of pH on the different steps of PCE dechlorination. The consortia showed significant differences in sensitivities toward acidic pH for the different dechlorination steps. Molecular analysis indicated that Dehalococcoides spp. that were present in all consortia were the most pH-sensitive organohalide-respiring guild members compared to Sulfurospirillum spp. and Dehalobacter spp. In batch cultures with silicate mineral particles as pH-buffering agents, all four minerals tested were able to maintain the pH in the appropriate range for reductive dechlorination of chloroethenes. However, complete dechlorination to ethene was observed only with forsterite, diopside, and fayalite. Dissolution of andradite increased the redox potential and did not allow dechlorination. With forsterite, diopside, and fayalite, dechlorination to ethene was observed but at much lower rates for the last two dechlorination steps than with the positive control. This indicated an inhibition effect of silicate minerals and/or their dissolution products on reductive dechlorination of cis-dichloroethene and vinyl chloride. Hence, despite the proven pH-buffering potential of silicate minerals, compatibility with

  8. Bio-Augmentation of Cupriavidus sp. CY-1 into 2,4-D Contaminated Soil: Microbial Community Analysis by Culture Dependent and Independent Techniques

    PubMed Central

    Chang, Young-Cheol; Reddy, M. Venkateswar; Umemoto, Honoka; Sato, Yuki; Kang, Mi-Hye; Yajima, Yuka; Kikuchi, Shintaro

    2015-01-01

    In the present study, a 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterial strain CY-1 was isolated from the forest soil. Based on physiological, biochemical and 16S rRNA gene sequence analysis it was identified as Cupriavidus sp. CY-1. Further 2,4-D degradation experiments at different concentrations (200 to 800 mg l-1) were carried out using CY-1. Effect of NaCl and KNO3 on 2,4-D degradation was also evaluated. Degradation of 2,4-D and the metabolites produced during degradation process were analyzed using high pressure liquid chromatography (HPLC) and GC-MS respectively. The amount of chloride ions produced during the 2,4-D degradation were analyzed by Ion chromatography (IC) and it is stoichiometric with 2,4-D dechlorination. Furthermore two different types of soils collected from two different sources were used for 2,4-D degradation studies. The isolated strain CY-1 was bio-augmented into 2,4-D contaminated soils to analyze its degradation ability. Culture independent methods like denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), and culture dependent methods like colony forming units (CFU) and most probable number (MPN) were used to analyze the survivability of strain CY-1 in contaminated soil. Results of T-RFLP were coincident with the DGGE analysis. From the DGGE, T-RFLP, MPN and HPLC results it was concluded that strain CY-1 effectively degraded 2,4-D without disturbing the ecosystem of soil indigenous microorganisms. PMID:26710231

  9. Bio-Augmentation of Cupriavidus sp. CY-1 into 2,4-D Contaminated Soil: Microbial Community Analysis by Culture Dependent and Independent Techniques.

    PubMed

    Chang, Young-Cheol; Reddy, M Venkateswar; Umemoto, Honoka; Sato, Yuki; Kang, Mi-Hye; Yajima, Yuka; Kikuchi, Shintaro

    2015-01-01

    In the present study, a 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterial strain CY-1 was isolated from the forest soil. Based on physiological, biochemical and 16S rRNA gene sequence analysis it was identified as Cupriavidus sp. CY-1. Further 2,4-D degradation experiments at different concentrations (200 to 800 mg l(-1)) were carried out using CY-1. Effect of NaCl and KNO3 on 2,4-D degradation was also evaluated. Degradation of 2,4-D and the metabolites produced during degradation process were analyzed using high pressure liquid chromatography (HPLC) and GC-MS respectively. The amount of chloride ions produced during the 2,4-D degradation were analyzed by Ion chromatography (IC) and it is stoichiometric with 2,4-D dechlorination. Furthermore two different types of soils collected from two different sources were used for 2,4-D degradation studies. The isolated strain CY-1 was bio-augmented into 2,4-D contaminated soils to analyze its degradation ability. Culture independent methods like denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), and culture dependent methods like colony forming units (CFU) and most probable number (MPN) were used to analyze the survivability of strain CY-1 in contaminated soil. Results of T-RFLP were coincident with the DGGE analysis. From the DGGE, T-RFLP, MPN and HPLC results it was concluded that strain CY-1 effectively degraded 2,4-D without disturbing the ecosystem of soil indigenous microorganisms. PMID:26710231

  10. Comparing the temporal colonization and microbial diversity of showerhead biofilms in Hawai'i and Colorado.

    PubMed

    Abe, Jonathan; Alop-Mabuti, Aleena; Burger, Peyton; Button, Jackson; Ellsberry, Madeline; Hitzeman, Jaycinth; Morgenstern, David; Nunies, Kasey; Strother, Mara; Darling-Munson, Jared; Chan, Yvonne L; Cassady, Robert; Vasconcellos, Sarah Maile K; Iseman, Michael D; Chan, Edward D; Honda, Jennifer R

    2016-02-01

    The household is a potential source of opportunistic pathogens to humans, a particularly critical issue for immunodeficient individuals. An important human-microbe interface is the biofilm that develops on showerhead surfaces. Once microbe-laden biofilms become aerosolized, they can potentially be inhaled into the lungs. Understanding how quickly a new showerhead becomes colonized would provide useful information to minimize exposure to potentially pathogenic environmental microbes. High school scientists sampled the inner surfaces of pre-existing and newly fitted showerheads monthly over a nine-month period and applied standard microbiologic culture techniques to qualitatively assess microbial growth. Water chemistry was also monitored using commercial test strips. Sampling was performed in households on Oahu, Hawai'i and Denver, Colorado, representing warm/humid and cold/arid environments, respectively. Pre-existing showerheads in Hawai'i showed more diverse microbial growth and significantly greater microbial numbers than a comparable showerhead from Colorado. New, chrome-plated or plastic showerheads in Hawai'i showed diverse and abundant growth one month after installment compared to new showerheads from Colorado. The pH, total chlorine and water hardness levels varied significantly between the Hawai'i and Colorado samples. Enthusiastic student and teacher participation allowed us to answer long-standing questions regarding the temporal colonization of microbial biofilms on pre-existing and new showerhead surfaces. PMID:26764424

  11. Comparing the temporal colonization and microbial diversity of showerhead biofilms in Hawai'i and Colorado.

    PubMed

    Abe, Jonathan; Alop-Mabuti, Aleena; Burger, Peyton; Button, Jackson; Ellsberry, Madeline; Hitzeman, Jaycinth; Morgenstern, David; Nunies, Kasey; Strother, Mara; Darling-Munson, Jared; Chan, Yvonne L; Cassady, Robert; Vasconcellos, Sarah Maile K; Iseman, Michael D; Chan, Edward D; Honda, Jennifer R

    2016-02-01

    The household is a potential source of opportunistic pathogens to humans, a particularly critical issue for immunodeficient individuals. An important human-microbe interface is the biofilm that develops on showerhead surfaces. Once microbe-laden biofilms become aerosolized, they can potentially be inhaled into the lungs. Understanding how quickly a new showerhead becomes colonized would provide useful information to minimize exposure to potentially pathogenic environmental microbes. High school scientists sampled the inner surfaces of pre-existing and newly fitted showerheads monthly over a nine-month period and applied standard microbiologic culture techniques to qualitatively assess microbial growth. Water chemistry was also monitored using commercial test strips. Sampling was performed in households on Oahu, Hawai'i and Denver, Colorado, representing warm/humid and cold/arid environments, respectively. Pre-existing showerheads in Hawai'i showed more diverse microbial growth and significantly greater microbial numbers than a comparable showerhead from Colorado. New, chrome-plated or plastic showerheads in Hawai'i showed diverse and abundant growth one month after installment compared to new showerheads from Colorado. The pH, total chlorine and water hardness levels varied significantly between the Hawai'i and Colorado samples. Enthusiastic student and teacher participation allowed us to answer long-standing questions regarding the temporal colonization of microbial biofilms on pre-existing and new showerhead surfaces.

  12. The effect of microbial starter composition on cassava chips fermentation for the production of fermented cassava flour

    NASA Astrophysics Data System (ADS)

    Kresnowati, M. T. A. P.; Listianingrum, Zaenudin, Ahmad; Trihatmoko, Kharisrama

    2015-12-01

    The processing of cassava into fermented cassava flour (fercaf) or the widely known as modified cassava flour (mocaf) presents an alternative solution to improve the competitiveness of local foods and to support national food security. However, the mass production of fercaf is being limited by several problems, among which is the availability of starter cultures. This paper presents the mapping of the effect of microbial starter compositions on the nutritional content of fercaf in order to obtain the suitable nutritional composition. Based on their enzymatic activities, the combination of Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae were tested during the study. In addition, commercial starter was also tested. During the fermentation, the dynamics in microbial population were measured as well as changes in cyanogenic glucoside content. The microbial starter composition was observed to affect the dynamics in microbial populationcynaogenic glucoside content of the produced fercaf. In general, steady state microbial population was reached within 12 hours of fermentation. Cyanogenic glucoside was observed to decrease along the fermentation.

  13. Composition analysis of fractions of extracellular polymeric substances from an activated sludge culture and identification of dominant forces affecting microbial aggregation

    PubMed Central

    Guo, Xuan; Wang, Xu; Liu, Junxin

    2016-01-01

    Extracellular polymeric substances (EPS) appear to play a critical role in the formation of bioaggregates, such as sludge flocs, in activated sludge processes. Here, we systematically investigated the composition and chemical structure of various EPS fractions excreted from an activated sludge culture using multi-analysis techniques to examine the ability of the sludge to aggregate. Chemical analysis was used with a three-dimensional excitation emission matrix and Fourier transform infrared spectroscopy, applying inter-particle forces theory. The combined findings revealed that hydrophobic groups, especially protein-related N–H, were present in a greater proportion in tightly bound EPS (TB-EPS). This result, which explained the specificity of TB-EPS in the chemical structure, was consistent with data indicating that TB-EPS contained a large amount of protein-like substances (86.7 mg/g of mixed liquor volatile suspended solids, 39.7% of the total EPS). Subsequently, a novel experimental procedure was developed to pinpoint key inter-particle forces in sludge aggregation. The result revealed that hydrogen bonds are the predominant triggers that promote sludge aggregation. This comprehensive analysis indicated that hydrophobic proteins in TB-EPS are responsible for the critical role played by hydrogen bonds in sludge formation. Our findings highlight the need to elucidate the mechanisms of TB-EPS-mediated flocculation in future efforts. PMID:27311788

  14. Composition analysis of fractions of extracellular polymeric substances from an activated sludge culture and identification of dominant forces affecting microbial aggregation

    NASA Astrophysics Data System (ADS)

    Guo, Xuan; Wang, Xu; Liu, Junxin

    2016-06-01

    Extracellular polymeric substances (EPS) appear to play a critical role in the formation of bioaggregates, such as sludge flocs, in activated sludge processes. Here, we systematically investigated the composition and chemical structure of various EPS fractions excreted from an activated sludge culture using multi-analysis techniques to examine the ability of the sludge to aggregate. Chemical analysis was used with a three-dimensional excitation emission matrix and Fourier transform infrared spectroscopy, applying inter-particle forces theory. The combined findings revealed that hydrophobic groups, especially protein-related N–H, were present in a greater proportion in tightly bound EPS (TB-EPS). This result, which explained the specificity of TB-EPS in the chemical structure, was consistent with data indicating that TB-EPS contained a large amount of protein-like substances (86.7 mg/g of mixed liquor volatile suspended solids, 39.7% of the total EPS). Subsequently, a novel experimental procedure was developed to pinpoint key inter-particle forces in sludge aggregation. The result revealed that hydrogen bonds are the predominant triggers that promote sludge aggregation. This comprehensive analysis indicated that hydrophobic proteins in TB-EPS are responsible for the critical role played by hydrogen bonds in sludge formation. Our findings highlight the need to elucidate the mechanisms of TB-EPS-mediated flocculation in future efforts.

  15. Improving the batch-to-batch reproducibility of microbial cultures during recombinant protein production by regulation of the total carbon dioxide production.

    PubMed

    Jenzsch, Marco; Gnoth, Stefan; Kleinschmidt, Martin; Simutis, Rimvydas; Lübbert, Andreas

    2007-03-10

    Batch-to-batch reproducibility of fermentation processes performed during the manufacturing processes of biologics can be increased by operating the cultures at feed rate profiles that are robust against typically arising disturbances. Remaining randomly appearing deviations from the desired path should be suppressed automatically by manipulating the feed rate. With respect to the cells' physiology it is best guiding the cultivations along an optimal profile of the specific biomass growth rate mu(t). However, there are two problems that speak for further investigations: Upon severe disturbances that may happen during the fermentation, the biomass concentration X may significantly deviate from its desired value, then a fixed mu-profile leads to a diminished batch-to-batch reproducibility. Second, the specific growth rate cannot easily be estimated online to a favourably high accuracy, hence it is difficult to determine the deviations in mu from the desired profile. The alternative discussed here solves both problems by keeping the process at the corresponding total cumulative carbon dioxide production-profile: it is robust against distortions in X and the controlled variable can accurately be measured online during cultivations of all relevant sizes. As compared to the fermentation practice currently used in industry, the experimental results, presented at the example of a recombinant protein production with Escherichia coli cells, show that CPR-based corrections lead to a considerably improved batch-to-batch reproducibility.

  16. A Comprehensive Assessment of Biologicals Contained Within Commercial Airliner Cabin Air

    NASA Technical Reports Server (NTRS)

    LaDuc, Myron T.; Osman, Shariff; Dekas, Anne; Stuecker, Tara; Newcombe, Dave; Piceno, Yvette; Fuhrman, J.; Andersen, Gary; Venkateswaran, Kasthuri; Bearman, Greg

    2006-01-01

    Both culture-based and culture-independent, biomarker-targeted microbial enumeration and identification technologies were employed to estimate total microbial and viral burden and diversity within the cabin air of commercial airliners. Samples from each of twenty flights spanning three commercial carriers were collected via air-impingement. When the total viable microbial population was estimated by assaying relative concentrations of the universal energy carrier ATP, values ranged from below detection limits (BDL) to 4.1 x 106 cells/cubic m of air. The total viable microbial population was extremely low in both of Airline A (approximately 10% samples) and C (approximately 18% samples) compared to the samples collected aboard flights on Airline A and B (approximately 70% samples). When samples were collected as a function of time over the course of flights, a gradual accumulation of microbes was observed from the time of passenger boarding through mid-flight, followed by a sharp decline in microbial abundance and viability from the initiation of descent through landing. It is concluded in this study that only 10% of the viable microbes of the cabin air were cultivable and suggested a need to employ state-of-the art molecular assay that measures both cultivable and viable-but-non-cultivable microbes. Among the cultivable bacteria, colonies of Acinetobacter sp. were by far the most profuse in Phase I, and Gram-positive bacteria of the genera Staphylococcus and Bacillus were the most abundant during Phase II. The isolation of the human pathogens Acinetobacter johnsonii, A. calcoaceticus, Janibacter melonis, Microbacterium trichotecenolyticum, Massilia timonae, Staphylococcus saprophyticus, Corynebacterium lipophiloflavum is concerning, as these bacteria can cause meningitis, septicemia, and a handful of sometimes fatal diseases and infections. Molecular microbial community analyses exhibited presence of the alpha-, beta-, gamma-, and delta- proteobacteria, as well as

  17. Microbial production of scleroglucan and downstream processing.

    PubMed

    Castillo, Natalia A; Valdez, Alejandra L; Fariña, Julia I

    2015-01-01

    Synthetic petroleum-based polymers and natural plant polymers have the disadvantage of restricted sources, in addition to the non-biodegradability of the former ones. In contrast, eco-sustainable microbial polysaccharides, of low-cost and standardized production, represent an alternative to address this situation. With a strong global market, they attracted worldwide attention because of their novel and unique physico-chemical properties as well as varied industrial applications, and many of them are promptly becoming economically competitive. Scleroglucan, a β-1,3-β-1,6-glucan secreted by Sclerotium fungi, exhibits high potential for commercialization and may show different branching frequency, side-chain length, and/or molecular weight depending on the producing strain or culture conditions. Water-solubility, viscosifying ability and wide stability over temperature, pH and salinity make scleroglucan useful for different biotechnological (enhanced oil recovery, food additives, drug delivery, cosmetic and pharmaceutical products, biocompatible materials, etc.), and biomedical (immunoceutical, antitumor, etc.) applications. It can be copiously produced at bioreactor scale under standardized conditions, where a high exopolysaccharide concentration normally governs the process optimization. Operative and nutritional conditions, as well as the incidence of scleroglucan downstream processing will be discussed in this chapter. The relevance of using standardized inocula from selected strains and experiences concerning the intricate scleroglucan scaling-up will be also herein outlined. PMID:26528259

  18. Microbial production of scleroglucan and downstream processing

    PubMed Central

    Castillo, Natalia A.; Valdez, Alejandra L.; Fariña, Julia I.

    2015-01-01

    Synthetic petroleum-based polymers and natural plant polymers have the disadvantage of restricted sources, in addition to the non-biodegradability of the former ones. In contrast, eco-sustainable microbial polysaccharides, of low-cost and standardized production, represent an alternative to address this situation. With a strong global market, they attracted worldwide attention because of their novel and unique physico-chemical properties as well as varied industrial applications, and many of them are promptly becoming economically competitive. Scleroglucan, a β-1,3-β-1,6-glucan secreted by Sclerotium fungi, exhibits high potential for commercialization and may show different branching frequency, side-chain length, and/or molecular weight depending on the producing strain or culture conditions. Water-solubility, viscosifying ability and wide stability over temperature, pH and salinity make scleroglucan useful for different biotechnological (enhanced oil recovery, food additives, drug delivery, cosmetic and pharmaceutical products, biocompatible materials, etc.), and biomedical (immunoceutical, antitumor, etc.) applications. It can be copiously produced at bioreactor scale under standardized conditions, where a high exopolysaccharide concentration normally governs the process optimization. Operative and nutritional conditions, as well as the incidence of scleroglucan downstream processing will be discussed in this chapter. The relevance of using standardized inocula from selected strains and experiences concerning the intricate scleroglucan scaling-up will be also herein outlined. PMID:26528259

  19. Comparative evaluation of antimicrobial activity of miswak, propolis, sodium hypochlorite and saline as root canal irrigants by microbial culturing and quantification in chronically exposed primary teeth.

    PubMed Central

    Shingare, Poonam; Chaugule, Vishwas

    2011-01-01

    Introduction: One of the essential factors for successful root canal therapy is elimination of bacterial contaminants using an effective root canal chemical irrigant such as sodium hypochlorite which inherently possesses certain disadvantages like irritation to periapical tissues, staining of the instruments, burning of surrounding tissues etc. The aim of the study was to explore newer irrigant agents which would probably be as effective or more and at the same time less irritating to the tissues than sodium hypochlorite. Our search included two such agents, propolis and miswak. Methods: The study was performed on 40 infected primary teeth (20 male and 20 female patients). The subjects were divided into 4 groups of 10 children. Group 1 received 3% sodium hypochlorite as irrigating solution, group 2 received 12.5% alcoholic extract of miswak, group 3 received 11% alcoholic extract of propolis and group 4, 0.9% saline. We used the antimicrobial activity of sodium hypochlorite as gold standard for comparing the activities of both propolis and miswak. We collected pre- and post-irrigation samples using sterile paper points. Samples were cultured on tryptose soya agar at a temperature of 37oC for 24-48 hours. The colonies were counted with a digital colony counter. For the statistical analysis, we used the unpaired t test at level of significance 0.05 and the ANOVA test for analysis of variance. Results: The differences in pre- and post- irrigation values were calculated for each group, the greatest difference being seen in group 1 (95.549%) followed by group 2 (89.794%), group 3 (34.735%) and group 4 (28.087%). When comparing the results between groups, there was no statistically significant difference between groups 3 and 4. Conclusions: The statistically analyzed results suggested that miswak could be a good natural substitute to sodium hypochlorite, while propolis showed results comparable to those of the negative control. PMID:24432254

  20. Microbial Life Under Extreme Energy Limitation

    NASA Technical Reports Server (NTRS)

    Hoehler, Tori M.; Jorgensen, Bo Barker

    2013-01-01

    A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

  1. Microbial life under extreme energy limitation.

    PubMed

    Hoehler, Tori M; Jørgensen, Bo Barker

    2013-02-01

    A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 10⁴- to 10⁶-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

  2. Television Commercials: Symbols, Myths and Metaphors.

    ERIC Educational Resources Information Center

    Feasley, Florence G.

    Television commercials convey to the audience through symbols, metaphors, and myths the feelings and emotions deeply rooted in our culture. While commercials on one level are concerned with a representation of the product or service, they are on another level a symbol of a larger meaning: love, family, romance, motherhood, or hero worship. A can…

  3. Combination of an Enzymatically Hydrolyzed Yeast and Yeast Culture with a Direct-fed Microbial in the Feeds of Broiler Chickens

    PubMed Central

    Gómez, S.; Angeles, M. L.; Mojica, M. C.; Jalukar, S.

    2012-01-01

    A balance trial experiment was carried out to evaluate the potential relationship between an enzymatically hydrolyzed yeast (EHY) and yeast culture combined with a live Bacillus subtilis (Bs) on the productive parameters, ileal digestibility, retention of nutrient and energy and villus morphology in broilers. Seventy two 28 d old, Ross B308 male broilers were assigned to a factorial combination of 2 levels of EHY (0 and 1 kg/ton of feed) and 2 levels of Bs (0 and 125 g/ton of feed). The experiment lasted 2 weeks. Several treatment interactions were observed. EHY-fed broilers showed the lowest feed intake and feed conversion ratio whereas Bs-fed broilers showed the highest feed intake and intermediate feed conversion ratio (EHY and BS interaction, p<0.05). Also, EHY-fed broilers had greater ileal digestibility of dry matter (EHY and BS interaction, p<0.01) and energy (EHY and BS interaction, p<0.05) but these responses were counterbalanced by the combination of EHY and Bs. The thickness of the mucosa was similar between the control and EHY-fed broilers, but was lowest when Bs was added alone (EHY and BS interaction, p<0.01). The thickness of the villus was greater in EHY plus Bs-fed broilers, intermediate for the control and lower for Bs or EHY-fed broilers (EHY and BS interaction, p<0.05). The area of the villus was greater in the control and EHY plus Bs-fed broilers (EHY and BS interaction, p<0.05). In addition, EHY-fed broilers showed greater breast yield and nitrogen retention (p<0.01) and ashes digestibility (p<0.05). On the other hand, Bs-fed broilers had greater carcass and breast weight, nitrogen retention, energy excretion and villus height (p<0.05). In summary, EHY and Bs enhanced some growth, carcass and nutrient retention responses, but did not show any synergic relationship in these responses. Opposite to this, the results suggest that the positive effect of EHY on the feed conversion and digestibility of nutrients were counterbalanced by the addition

  4. Microbial activity at Yucca Mountain

    SciTech Connect

    Horn, J.M.; Meike, A.

    1995-09-25

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified.

  5. Microbial production of lactic acid.

    PubMed

    Eiteman, Mark A; Ramalingam, Subramanian

    2015-05-01

    Lactic acid is an important commodity chemical having a wide range of applications. Microbial production effectively competes with chemical synthesis methods because biochemical synthesis permits the generation of either one of the two enantiomers with high optical purity at high yield and titer, a result which is particularly beneficial for the production of poly(lactic acid) polymers having specific properties. The commercial viability of microbial lactic acid production relies on utilization of inexpensive carbon substrates derived from agricultural or waste resources. Therefore, optimal lactic acid formation requires an understanding and engineering of both the competing pathways involved in carbohydrate metabolism, as well as pathways leading to potential by-products which both affect product yield. Recent research leverages those biochemical pathways, while researchers also continue to seek strains with improved tolerance and ability to perform under desirable industrial conditions, for example, of pH and temperature.

  6. Microbial biofilms on facial prostheses.

    PubMed

    Ariani, Nina; Vissink, Arjan; van Oort, Robert P; Kusdhany, Lindawati; Djais, Ariadna; Rahardjo, Tri Budi W; van der Mei, Henny C; Krom, Bastiaan P

    2012-01-01

    The composition of microbial biofilms on silicone rubber facial prostheses was investigated and compared with the microbial flora on healthy and prosthesis-covered skin. Scanning electron microscopy showed the presence of mixed bacterial and yeast biofilms on and deterioration of the surface of the prostheses. Microbial culturing confirmed the presence of yeasts and bacteria. Microbial colonization was significantly increased on prosthesis-covered skin compared to healthy skin. Candida spp. were exclusively isolated from prosthesis-covered skin and from prostheses. Biofilms from prostheses showed the least diverse band-profile in denaturing gradient gel electrophoresis (DGGE) whereas prosthesis-covered skin showed the most diverse band-profile. Bacterial diversity exceeded yeast diversity in all samples. It is concluded that occlusion of the skin by prostheses creates a favorable niche for opportunistic pathogens such as Candida spp. and Staphylococcus aureus. Biofilms on healthy skin, skin underneath the prosthesis and on the prosthesis had a comparable composition, but the numbers present differed according to the microorganism.

  7. 21 CFR 173.150 - Milk-clotting enzymes, microbial.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the...

  8. 21 CFR 173.150 - Milk-clotting enzymes, microbial.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the...

  9. 21 CFR 173.150 - Milk-clotting enzymes, microbial.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture... conditions: (a) Milk-clotting enzyme is derived from one of the following organisms by a...

  10. 21 CFR 173.150 - Milk-clotting enzymes, microbial.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the...

  11. 21 CFR 173.150 - Milk-clotting enzymes, microbial.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Milk-clotting enzymes, microbial. 173.150 Section... HUMAN CONSUMPTION Enzyme Preparations and Microorganisms § 173.150 Milk-clotting enzymes, microbial. Milk-clotting enzyme produced by pure-culture fermentation process may be safely used in the...

  12. Which Microbial Communities Are Present? Sequence-Based Metagenomics

    NASA Astrophysics Data System (ADS)

    Caffrey, Sean M.

    The use of metagenomic methods that directly sequence environmental samples has revealed the extraordinary microbial diversity missed by traditional culture-based methodologies. Therefore, to develop a complete and representative model of an environment's microbial community and activities, metagenomic analysis is an essential tool.

  13. The high reutilization value potential of high-salinity anchovy fishmeal wastewater through microbial degradation.

    PubMed

    Figueroa, Juan Gerardo Santoyo; Jung, Hyun Yi; Jeong, Gwi-Taek; Kim, Joong Kyun

    2015-10-01

    To provide an option for the reutilization of high-salinity anchovy fishmeal wastewater (FMW), generated during the anchovy fishmeal manufacturing processes, its potential for biodegradation was assessed in 1-l five-neck flasks using a halotolerant and proteolytic microbial consortium. During the first 41 h of biodegradation, the pH, DO, ORP, and dry-sludge weight decreased as the total cell number of the microbial consortium increased steadily; the COD(Cr)/TN ratios remained between 4.0 and 5.5, respectively, indicating the stable metabolic degradation of organic matter. The ORP tended to increase after 41 h, and the unpleasant fishy smell disappeared once positive ORP values were achieved. The removal percentages of COD(Cr) and TN were 59.0 and 54.4%, respectively, and the dry-sludge weight decreased from 115.5 to 68.0 g, with a degradation rate of 0.59 g h(-1), during the 80 h experiment. The supernatant from the culture of the anchovy FMW at 70 h (culture supernatant) was phytotoxin-free, and the level of total amino acids was 8.04 g 100 g(-1), comparable to that of commercial fertilizers. In hydroponic cultures containing red bean and barley, the culture supernatant demonstrated a good fertilizing ability. The culture supernatant also exhibited a high degree of antioxidant activity, with a 52.3% hydroxyl radical-scavenging activity and 0.16 reducing power (at OD 700 nm). Moreover, the culture supernatant inhibited DNA damage from hydroxyl radicals, enhancing the reutilization value of anchovy FMW. This report presents the first description of high-salinity anchovy FMW possessing a high reutilization value potential both for agriculture and medicine.

  14. The high reutilization value potential of high-salinity anchovy fishmeal wastewater through microbial degradation.

    PubMed

    Figueroa, Juan Gerardo Santoyo; Jung, Hyun Yi; Jeong, Gwi-Taek; Kim, Joong Kyun

    2015-10-01

    To provide an option for the reutilization of high-salinity anchovy fishmeal wastewater (FMW), generated during the anchovy fishmeal manufacturing processes, its potential for biodegradation was assessed in 1-l five-neck flasks using a halotolerant and proteolytic microbial consortium. During the first 41 h of biodegradation, the pH, DO, ORP, and dry-sludge weight decreased as the total cell number of the microbial consortium increased steadily; the COD(Cr)/TN ratios remained between 4.0 and 5.5, respectively, indicating the stable metabolic degradation of organic matter. The ORP tended to increase after 41 h, and the unpleasant fishy smell disappeared once positive ORP values were achieved. The removal percentages of COD(Cr) and TN were 59.0 and 54.4%, respectively, and the dry-sludge weight decreased from 115.5 to 68.0 g, with a degradation rate of 0.59 g h(-1), during the 80 h experiment. The supernatant from the culture of the anchovy FMW at 70 h (culture supernatant) was phytotoxin-free, and the level of total amino acids was 8.04 g 100 g(-1), comparable to that of commercial fertilizers. In hydroponic cultures containing red bean and barley, the culture supernatant demonstrated a good fertilizing ability. The culture supernatant also exhibited a high degree of antioxidant activity, with a 52.3% hydroxyl radical-scavenging activity and 0.16 reducing power (at OD 700 nm). Moreover, the culture supernatant inhibited DNA damage from hydroxyl radicals, enhancing the reutilization value of anchovy FMW. This report presents the first description of high-salinity anchovy FMW possessing a high reutilization value potential both for agriculture and medicine. PMID:26201424

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

    SciTech Connect

    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.

  16. Use of nonpathogenic, green fluorescent protein-marked Escherichia coli Biotype I cultures to evaluate the self-cleansing capabilities of a commercial beef grinding system after a contamination event.

    PubMed

    Wages, Jennifer A; Williams, Jennifer; Adams, Jacquelyn; George, Bruce; Oxford, Eric; Zelenka, Dan

    2014-11-01

    Inoculated beef trim containing a cocktail of green fluorescent protein-marked Escherichia coli biotype I cultures as surrogates for E. coli O157:H7 was introduced into two large, commercial grinding facilities capable of producing 180,000 kg of ground product in 1 day. Three repetitions were performed over 3 days. Sampling occurred at three different points within the process: postprimary grind, postsecondary grind-blender, and postpackaging. Resulting data show that, as the inoculated meat passes through the system, the presence of the marked surrogate quickly diminishes. The depletion rates are directly related to the amount of product in kilograms (represented by time) that has passed through the system, but these rates vary with each step of the process. The primary grinder appears to rid itself of the contaminant the most quickly; in all repetitions, the contaminant was not detected within 5 min of introduction of the contaminated combo bin into the system, which in all cases, was prior to the introduction of a second combo bin and within 1,800 kg of product. After the blending step and subsequent secondary grinding, the contaminant was detected in product produced from both the parent combo and the combo bin added directly after the parent combo bin; however, for those days on which three combo bins (approximately 2,700 kg) were available for sampling, the contaminant was not detected from product representing the third combo bin. Similarly, at the packaging step, the contaminant was detected in the product produced by both the parent and second combo bins; however, on those days when a third combo bin was available for sampling (repetitions 2 and 3), the contaminant was not detected from product produced from the third combo bin.

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

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

    Because the International Space Station is a closed environment with rotations of astronauts and equipment that each introduce their own microbial flora, it is necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor- and time-intensive methods to enumerate total bacterial and fungal cells, with limited characterization, during in-flight testing. Although this culture-based method is sufficient for monitoring the International Space Station, on future long-duration missions more detailed characterization will need to be performed during flight, as sample return and ground characterization may not be available. At a workshop held in 2011 at NASA's Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these long-term exploration missions, molecular-based methodologies such as polymerase chain reaction (PCR) were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for space flight environmental monitoring. The goal was to evaluate quantitative or semi-quantitative PCR approaches for low-cost in-flight rapid identification of microorganisms that could affect crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity. This phase was followed by proof-of-concept testing of the highest qualifying candidates with a universally available challenge organism, Salmonella enterica. The analysis identified two technologies that were able to perform sample-to-answer testing with initial cell sample concentrations between 50 and 400 cells. In addition, the commercial systems were evaluated for initial flight safety and readiness.

  18. Microbial Activation of Wooden Vats Used for Traditional Cheese Production and Evolution of Neoformed Biofilms

    PubMed Central

    Gaglio, Raimondo; Cruciata, Margherita; Di Gerlando, Rosalia; Scatassa, Maria Luisa; Cardamone, Cinzia; Mancuso, Isabella; Sardina, Maria Teresa; Moschetti, Giancarlo; Portolano, Baldassare

    2015-01-01

    Three Lactococcus lactis subsp. cremoris strains were used to develop ad hoc biofilms on the surfaces of virgin wooden vats used for cheese production. Two vats (TZ) were tested under controlled conditions (pilot plant), and two vats (TA) were tested under uncontrolled conditions (industrial plant). In each plant, one vat (TA1 and TZ1) was used for the control, traditional production of PDO Vastedda della Valle del Belìce (Vastedda) cheese, and one (TA2 and TZ2) was used for experimental production performed after lactococcal biofilm activation and the daily addition of a natural whey starter culture (NWSC). Microbiological and scanning electron microscopy analyses showed differences in terms of microbial levels and composition of the neoformed biofilms. The levels of the microbial groups investigated during cheese production showed significant differences between the control trials and between the control and experimental trials, but the differences were not particularly marked between the TA2 and TZ2 productions, which showed the largest numbers of mesophilic lactic acid bacterium (LAB) cocci. LAB populations were characterized phenotypically and genotypically, and 44 dominant strains belonging to 10 species were identified. Direct comparison of the polymorphic profiles of the LAB collected during cheese making showed that the addition of the NWSC reduced their biodiversity. Sensory evaluation showed that the microbial activation of the wooden vats with the multistrain Lactococcus culture generated cheeses with sensory attributes comparable to those of commercial cheese. Thus, neoformed biofilms enable a reduction of microbial variability and stabilize the sensorial attributes of Vastedda cheese. PMID:26546430

  19. Towards a Miniaturized System for Microbial Monitoring of Life Support Applications

    NASA Astrophysics Data System (ADS)

    Abaibou, Hafid; Storrs, Michele; Broyer, Patrick; Drevet, Christophe; Guy, Michel; Mabilat, Claude; Lasseur, Christophe

    Russian astronauts and associated research organisations have demonstrated the risks associ-ated with microbial contamination for long term manned missions. These risks concern both crew health through the contamination of metabolic consumables (water, air) and also degra-dation of hardware. Over the last 10 years, ESA and bioMérieux S.A. (F, I, NL) have been developing an automated instrument for rapid microbial detection for air and surface samples based on molecular detection. Rapid molecular biology techniques are perceived as an attractive alternative to traditional culture-based methods for the detection of microbial contamination allowing fast time to results and permitting fast implementation of appropriate corrective action if needed. To date, there are no commercially-available fully automated systems allowing such tests due to the technical challenges required for test development and the need for full automation. This presentation will first explain the life support requirements for long term manned space missions and then describe the rapid molecular tools which have been developed in collaboration between ESA and bioMérieux. These tools allow the detection of nucleic acids of all bacteria and all fungi (microbial load) in a sample, that is a molecular total count of all microbes present in a sample. We will also describe a prototype instrument which can simultaneously perform nucleic acid extraction from environmental samples (air, surfaces and water) and amplification/detection of their purified nucleic acids, enabling a molecular microbial load count in less than 3 hours. It is currently being adapted to life support context with the help of an European space industry (NTE, Spain). This system was presented at Cospar 2008 from a planetary protection viewpoint. Here we update on the development concentrating on crew health aspects.

  20. Microbial Flocculant for Nature Soda

    SciTech Connect

    Qin, Peiyong; Zhang, Tong; Chen, Cuixian

    2004-03-31

    Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

  1. MICROBIAL CHARACTERIZATION OF DRINKING WATER SYSTEMS RECEIVING GROUNDWATER AND SURFACE WATER AS THE PRIMARY SOURCES OF WATER

    EPA Science Inventory

    Earlier descriptions of water distribution systems (WDS) microbial communities have relied on culturing techniques. These techniques are known to be highly selective in nature, but more importantly, they tend to grossly underestimate the microbial diversity of most environments. ...

  2. Prevalence of Yersinia Species in Traditional and Commercial Dairy Products in Isfahan Province, Iran

    PubMed Central

    Rahimi, Ebrahim; Sepehri, Sara; Safarpoor Dehkordi, Farhad; Shaygan, Shima; Momtaz, Hassan

    2014-01-01

    Background: Yersinia species, especially Yersinia enterocolitica, are considered as the most prevalent milk-borne pathogens. Several serological and molecular techniques have been developed for rapid and safe diagnosis of yersiniosis. Objectives: This study was carried out to assess the prevalence rate of Yersinia species, especially Y. enterocolitica, in milk and dairy products in Isfahan province, Iran. Materials and Methods: A total of 285 commercial and traditional dairy products as well as 267 pasteurized and raw milk samples were collected during one year. The samples were studied by culturing and the positive-culture samples were investigated using PCR techniques. Results: The results of culture showed that 52 (9.42%) and 28 (5.07%) of the total 552 milk and dairy samples were positive for presences of Yersinia species and Y. enterocolitica, respectively. Totally, 24 of 28 Y. enterocolitica isolates by culture were positive in PCR test (4.59%). Raw cow milk and traditional cheese had the highest prevalence of Yersinia species and Y. enterocolitica, respectively. There were no positive results for pasteurized cow milk, raw camel milk, commercial ice cream, commercial cheese, yoghurt, Doogh, butter and curd. Yersinia species and Y. enterocolitica had the highest prevalence in autumn (15.15% and 10.6%, respectively). Significant differences regarding P < 0.05 were observed between the presences of Yersinia species and Y. enterocolitica in various samples and seasons. Conclusions: Sanitation and pasteurization are the best ways to increase the microbial quality and particularly decrease the load of Yersinia species. The ability of Yersinia species to growth in Doogh, yoghurt, curd and butter is very low. PMID:25147698

  3. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  4. MICROBIAL SOURCE TRACKING: DIFFERENT USES AND APPROACHES

    EPA Science Inventory

    Microbial Source Tracking (MST) methods are used to determine the origin of fecal pollution impacting natural water systems. Several methods require the isolation of pure cultures in order to develop phenotypic or genotypic fingerprint libraries of both source and water bacterial...

  5. Microbial Engineering for Aldehyde Synthesis

    PubMed Central

    Kunjapur, Aditya M.

    2015-01-01

    Aldehydes are a class of chemicals with many industrial uses. Several aldehydes are responsible for flavors and fragrances present in plants, but aldehydes are not known to accumulate in most natural microorganisms. In many cases, microbial production of aldehydes presents an attractive alternative to extraction from plants or chemical synthesis. During the past 2 decades, a variety of aldehyde biosynthetic enzymes have undergone detailed characterization. Although metabolic pathways that result in alcohol synthesis via aldehyde intermediates were long known, only recent investigations in model microbes such as Escherichia coli have succeeded in minimizing the rapid endogenous conversion of aldehydes into their corresponding alcohols. Such efforts have provided a foundation for microbial aldehyde synthesis and broader utilization of aldehydes as intermediates for other synthetically challenging biochemical classes. However, aldehyde toxicity imposes a practical limit on achievable aldehyde titers and remains an issue of academic and commercial interest. In this minireview, we summarize published efforts of microbial engineering for aldehyde synthesis, with an emphasis on de novo synthesis, engineered aldehyde accumulation in E. coli, and the challenge of aldehyde toxicity. PMID:25576610

  6. Understanding the Environment of the Commercializing University Researcher: Cases for Commercial Success

    ERIC Educational Resources Information Center

    Gann, James R.

    2012-01-01

    As the U.S. continues its transition from an economy based upon manufacturing to one based upon innovation, one must look at the environment of the person at the epicenter of this change: The commercializing university researcher. This investigation provides insight into the cultural and regulatory life of the commercializing researcher, with the…

  7. Microfluidics and microbial engineering.

    PubMed

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

    2016-02-01

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

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

    NASA Technical Reports Server (NTRS)

    Birmele, Michele

    2012-01-01

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

  9. Raman Spectroscopy of Microbial Pigments

    PubMed Central

    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

  10. Commercial Buildings Characteristics, 1992

    SciTech Connect

    Not Available

    1994-04-29

    Commercial Buildings Characteristics 1992 presents statistics about the number, type, and size of commercial buildings in the United States as well as their energy-related characteristics. These data are collected in the Commercial Buildings Energy Consumption Survey (CBECS), a national survey of buildings in the commercial sector. The 1992 CBECS is the fifth in a series conducted since 1979 by the Energy Information Administration. Approximately 6,600 commercial buildings were surveyed, representing the characteristics and energy consumption of 4.8 million commercial buildings and 67.9 billion square feet of commercial floorspace nationwide. Overall, the amount of commercial floorspace in the United States increased an average of 2.4 percent annually between 1989 and 1992, while the number of commercial buildings increased an average of 2.0 percent annually.

  11. Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

    PubMed Central

    Milshteyn, Aleksandr; Schneider, Jessica S.; Brady, Sean F.

    2014-01-01

    Summary Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of re-invigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities. PMID:25237864

  12. Biomass, microorganisms for special applications, microbial products I, energy from renewable resources

    SciTech Connect

    Rehm, H.J.; Reed, G.

    1982-01-01

    The book contains the following sections: biomass from carbohydrates; biomass from higher n-alkanes; biomass from methane and methanol; phototropic microalgae; edible mushrooms; starter cultures for milk and meat processing; starter cultures for other purposes; microbial soil amelioration; bacteria for nitrogen fixation; microbial insecticides; ethanol fermentation; acetic acid; lactic acid; citric acid; gluconic acid; organic acids of minor importance; amino acids; extracellular polysaccharides; microbial emulsifiers and de-emulsifiers; and energy from renewable resources. 190 figures, 205 tabels. (CKK)

  13. Microbial Communities in Pre-Columbian Coprolites

    PubMed Central

    Santiago-Rodriguez, Tasha M.; Narganes-Storde, Yvonne M.; Chanlatte, Luis; Crespo-Torres, Edwin; Toranzos, Gary A.; Jimenez-Flores, Rafael; Hamrick, Alice; Cano, Raul J.

    2013-01-01

    The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures. PMID:23755194

  14. Cheese Microbial Risk Assessments — A Review

    PubMed Central

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

    2016-01-01

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

  15. Microbial Cellulose Utilization: Fundamentals and Biotechnology

    PubMed Central

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

    2002-01-01

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

  16. Cheese Microbial Risk Assessments - A Review.

    PubMed

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

    2016-03-01

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

  17. Microbial cellulose utilization: fundamentals and biotechnology.

    PubMed

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

    2002-09-01

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

  18. Systems Biology of Microbial Exopolysaccharides Production

    PubMed Central

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran. PMID:26734603

  19. Systems Biology of Microbial Exopolysaccharides Production.

    PubMed

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly assoc