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Sample records for fatty acid-degrading microbes

  1. Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation.

    Science.gov (United States)

    Demeter, Marc A; Lemire, Joseph A; Yue, Gordon; Ceri, Howard; Turner, Raymond J

    2015-01-01

    Oil sands surface mining for bitumen results in the formation of oil sands process water (OSPW), containing acutely toxic naphthenic acids (NAs). Potential exists for OSPW toxicity to be mitigated by aerobic degradation of the NAs by microorganisms indigenous to the oil sands tailings ponds, the success of which is dependent on the methods used to exploit the metabolisms of the environmental microbial community. Having hypothesized that the xenobiotic tolerant biofilm mode-of-life may represent a feasible way to harness environmental microbes for ex situ treatment of OSPW NAs, we aerobically grew OSPW microbes as single and mixed species biofilm and planktonic cultures under various conditions for the purpose of assaying their ability to tolerate and degrade NAs. The NAs evaluated were a diverse mixture of eight commercially available model compounds. Confocal microscopy confirmed the ability of mixed and single species OSPW cultures to grow as biofilms in the presence of the NAs evaluated. qPCR enumeration demonstrated that the addition of supplemental nutrients at concentrations of 1 g L(-1) resulted in a more numerous population than 0.001 g L(-1) supplementation by approximately 1 order of magnitude. GC-FID analysis revealed that mixed species cultures (regardless of the mode of growth) are the most effective at degrading the NAs tested. All constituent NAs evaluated were degraded below detectable limits with the exception of 1-adamantane carboxylic acid (ACA); subsequent experimentation with ACA as the sole NA also failed to exhibit degradation of this compound. Single species cultures degraded select few NA compounds. The degradation trends highlighted many structure-persistence relationships among the eight NAs tested, demonstrating the effect of side chain configuration and alkyl branching on compound recalcitrance. Of all the isolates, the Rhodococcus spp. degraded the greatest number of NA compounds, although still less than the mixed species cultures

  2. Free fatty acids degradation in grease trap purification using ozone bubbling and sonication

    Science.gov (United States)

    Piotr Kwiatkowski, Michal; Satoh, Saburoh; Fukuda, Shogo; Yamabe, Chobei; Ihara, Satoshi; Nieda, Masanori

    2013-02-01

    The oil and fat were treated at first by only ozone bubbling and it was confirmed that the collection efficiency of them became 98.4% when the aeration was used. It showed that the aeration method in a grease trap cleared the standard value of 90% and there was no worry on the oil and fat outflow from a grease trap. The characteristics of sonication process were studied for free fatty acids degradation. The free saturated fatty acids are the most hard-degradable compounds of the fats, oils and greases (FOGs) in the grease trap. The influence of various parameters such as immersion level of an ultrasound probe in the liquid and bubbling of various gases (Ar, O2, air, O3) on the sonochemical and energy efficiency of the sonication process was investigated. The most effective degradation treatment method for saturated free fatty acids was the combination of sonication and low flow rate argon bubbling. Contribution to the Topical Issue "13th International Symposium on High Pressure Low Temperature Plasma Chemistry (Hakone XIII)", Edited by Nicolas Gherardi, Henryca Danuta Stryczewska and Yvan Ségui.

  3. Energetics and kinetics of anaerobic aromatic and fatty acid degradation. Progress report, March 1992--June 1995

    Energy Technology Data Exchange (ETDEWEB)

    McInerney M.J.

    1995-06-23

    Factors affecting the rate and extent of benzoate degradation by anaerobic syntrophic consortia were studied. Cocultures of a syntrophic benzoate degrader, strain SB, with a hydrogen/formate-using sulfate reducer degraded benzoate to a threshold that depended on the amount of substrate and acetate present. The benzoate threshold was not a function of the inhibition of benzoate degradation capacity by acetate or the toxicity of the undissociated form of acetate. Rather, a critical or minimal Gibb`s free energy value may exist where thermodynamic constraints preclude further benzoate degradation. A sensitive assay to detect low formate concentrations was developed to measure the formate levels when the benzoate threshold was reached. We showed that increased acetate concentrations, even when hydrogen and formate levels are low, affects the extent of benzoate degradation, implicating the importance of interspecies acetate transfer. In addition to benzoate, various saturated and unsaturated fatty acids, 2-methylbutyrate, and methyl esters of fatty acids supported growth in coculture with a hydrogen-using partner. SB is the only syntrophic bacterium known to use both benzoate and fatty acids. Phylogenetic analysis showed that SB clustered with sulfate reducers in the delta subclass of the Proteobacteria. SB grew well in coculture with Desulfoarculus baarsii, a sulfate reducer that uses formate but not hydrogen. This unequivocally shows that SB can grow by interspecies formate transfer.

  4. Molecular Cloning and Characterization of Three Novel Genes Related to Fatty Acid Degradation and Their Responses to Abiotic Stresses in Gossypium hirsutum L.

    Institute of Scientific and Technical Information of China (English)

    DONG Jia; WEI Li-bin; HU Yan; GUO Wang-zhen

    2013-01-01

    Fatty acid metabolism is responsible not only for oilseed metabolism but also for plant responses to abiotic stresses. In this study, three novel genes related to fatty acid degradation designated GhACX, Gh4CL, and GhMFP, respectively, were isolated from Gossypium hirsutum acc. TM-1. The phylogenetic analysis revealed that amino acid sequences of GhACX and GhMFP have the highest homology with those from Vitis vinifera, and Gh4CL has a closer genetic relationship with that from Camellia sinensis. Tissue-and organ-specific analysis showed that the three genes expressed widely in all the tested tissues, including ovules and fiber at different developing stages, with expressed preferentially in some organs. Among them, GhACX showed the most abundant transcripts in seeds at 25 d post anthesis (DPA), however, GhMFP and Gh4CL have the strongest expression level in ovules on the day of anthesis. Based on real-time quantitative RT-PCR, the three genes were differentially regulated when induced under wounding, methyl jasmonate (MeJA), cold, and abscisic acid (ABA) treatments. The characterization and expression pattern of three novel fatty acid degradation related genes will aid both to understand the roles of fatty acid degradation related genes as precursor in stress stimuli and to elucidate the physiological function in cotton oilseed metabolism.

  5. Development of an LC-MS/MS analytical method for the simultaneous measurement of aldehydes from polyunsaturated fatty acids degradation in animal feed.

    Science.gov (United States)

    Douny, Caroline; Bayram, Pinar; Brose, François; Degand, Guy; Scippo, Marie-Louise

    2016-05-01

    Knowing that polyunsaturated fatty acids can lead to the formation of potentially toxic aldehydes as secondary oxidation products, an analytical method using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) detection was developed to measure the concentration of eight aldehydes in animal feed: malondialdehyde (MDA), 4-hydroxy-2-nonenal (4-HNE), 4-hydroxy-2-hexenal (4-HHE), crotonaldehyde (CRT), benzaldehyde (BNZ), hexanal (HXL), 2,4-nonadienal, and 2,4-decadienal. The developed method was validated according to the criteria and procedure described in international standards. The evaluated parameters were specificity/selectivity, recovery, precision, accuracy, uncertainty, limits of detection and quantification, using the concept of accuracy profiles. These parameters were determined during experiments conducted over three different days with ground Kellogg's® Corn Flakes® cereals as model matrix for animal feed and spiked at different levels of concentration. Malondialdehyde, 4-HHE, 4-HNE, crotonaldehyde, benzaldehyde, and hexanal can be analyzed in the same run in animal feed with a very good accuracy, with recovery rates ranging from 86 to 109% for a working range going from 0.16 to 12.50 mg/kg. The analysis of 2,4-nonadienal and 2,4-decadienal can also be performed but in a limited range of concentration and with a limited degree of accuracy. Their recovery rates ranged between 54 and 114% and coefficient of variation for the intermediate precision between 11 and 25% for these two compounds. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Importance of sulfide interaction with iron as regulator of the microbial community in biogas reactors and its effect on methanogenesis, volatile fatty acids turnover, and syntrophic long-chain fatty acids degradation.

    Science.gov (United States)

    Shakeri Yekta, Sepehr; Ziels, Ryan M; Björn, Annika; Skyllberg, Ulf; Ejlertsson, Jörgen; Karlsson, Anna; Svedlund, Matilda; Willén, Magnus; Svensson, Bo H

    2017-05-01

    The inhibitory effects of sulfide on microbial processes during anaerobic digestion have been widely addressed. However, other effects of sulfide are less explored, given that sulfide is a potential sulfur source for microorganisms and its high reactivity triggers a suit of abiotic reactions. We demonstrated that sulfide interaction with Fe regulates the dynamics and activities of microbial community during anaerobic digestion. This was manifested by the S:Fe molar ratio, whose increase adversely influenced the acetoclastic methanogens, Methanosaeta, and turnover of acetate. Dynamics of hydrogenotrophic methanogens, Methanoculleus and Methanobrevibacter, were presumably influenced by sulfide-induced changes in the partial pressure of hydrogen. Interestingly, conversion of the long-chain fatty acid (LCFA), oleate, to methane was enhanced together with the abundance of LCFA-degrading, β-oxidizing Syntrophomonas at an elevated S:Fe molar ratio. The results suggested that sulfur chemical speciation is a controlling factor for microbial community functions in anaerobic digestion processes. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  7. Biofuels: from microbes to molecules

    National Research Council Canada - National Science Library

    Lu, Xuefeng

    2014-01-01

    .... The production of different biofuel molecules including hydrogen, methane, ethanol, butanol, higher chain alcohols, isoprenoids and fatty acid derivatives, from genetically engineered microbes...

  8. Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: implications for lipid-based stable isotope probing methods.

    Science.gov (United States)

    Lerch, Thomas Z; Dignac, Marie-France; Barriuso, Enrique; Mariotti, André

    2011-10-01

    Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [(13)C]2,4-D, [(13)C]glucose, or mixtures of both substrates alternatively labeled with (13)C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the (13)C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.

  9. Effect of Glucose on the Fatty Acid Composition of Cupriavidus necator JMP134 during 2,4-Dichlorophenoxyacetic Acid Degradation: Implications for Lipid-Based Stable Isotope Probing Methods▿†

    Science.gov (United States)

    Lerch, Thomas Z.; Dignac, Marie-France; Barriuso, Enrique; Mariotti, André

    2011-01-01

    Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [13C]2,4-D, [13C]glucose, or mixtures of both substrates alternatively labeled with 13C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the 13C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments. PMID:21856833

  10. Energetics and kinetics of anaerobic aromatic and fatty acid degradation

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, M.J.

    1992-11-16

    The kinetics of benzoate degradation by the anaerobic syntrophic bacterium, Syntrophus buswellii, was studied in coculture with Desulfovibrio strain G11. The threshold value for benzoate degradation was dependent on the acetate concentration with benzoate threshold values ranging from 2.4 [mu]M at 20 mM acetate to 30.0 [mu]M at 65 mM acetate. Increasing acetate concentrations also inhibited the rate of benzoate degradation with a apparent K[sub i] for acetate inhibition of 7.0 mM. Lower threshold values were obtained when nitrate rather than sulfate was the terminal electron acceptor. These data are consistent with a thermodynamic explanation for the threshold, and suggest that there is a minimum Gibbs free energy value required for the degradation of benzoate. An acetoacetyl-CoA thiolase has been isolated from Syntrophomonas wolfei; it is apparently a key enzyme controlling the synthesis of poly-B-hydroxyalkanoate from acetyl-CoA in this organism. Kinetic characterization of the acetoacetyl-CoA thiolase from S. wolfei showed that it is similar in its structural, kinetic, and apparent regulatory properties to other biosynthetic acetoacetyl-CoA thiolases from phylogenetically distinct bacteria that synthesize PHA. Intracellular concentrations of CoA and acetyl-CoA are believed to be critical factors regulating the activity of the acetoacetyl-CoA thiolase in S. wolfei. We have also isolated and characterized several new halophilic anaerobic fermentative anaerobes. Phylogenetic analysis indicates that one of these bacteria is a new species in the genus, Haloanaerobium. Two other species appear to be members of the genus, Halobacteroides. Several halophilic acetoclastic methanogenic bacteria have also been isolated and their physiological properties are currently under investigation. We have also isolated an acetate-using dissimilatory iron-reducing bacterium.

  11. Evaluation of feeding glycerol on free-fatty acid production and fermentation kinetics of mixed ruminal microbes in vitro

    Science.gov (United States)

    Strategies to enrich ruminant-derived foods with unsaturated fatty acids are desired as these are considered beneficial for good human health. Ruminant-derived foods contain high proportions of saturated fats, a result of ruminal biohydrogenation, which rapidly saturates and thus limits the availab...

  12. Conjugated fatty acids and methane production by rumen microbes when incubated with linseed oil alone or mixed with fish oil and/or malate.

    Science.gov (United States)

    Li, Xiang Z; Gao, Qing S; Yan, Chang G; Choi, Seong H; Shin, Jong S; Song, Man K

    2015-08-01

    We hypothesized that manipulating metabolism with fish oil and malate as a hydrogen acceptor would affect the biohydrogenation process of α-linolenic acid by rumen microbes. This study was to examine the effect of fish oil and/or malate on the production of conjugated fatty acids and methane (CH4 ) by rumen microbes when incubated with linseed oil. Linseed oil (LO), LO with fish oil (LO-FO), LO with malate (LO-MA), or LO with fish oil and malate (LO-FO-MA) was added to diluted rumen fluid, respectively. The LO-MA and LO-FO-MA increased pH and propionate concentration compared to the other treatments. LO-MA and LO-FO-MA reduced CH4 production compared to LO. LO-MA and LO-FO-MA increased the contents of c9,t11-conjugated linoleic acid (CLA) and c9,t11,c15-conjugated linolenic acid (CLnA) compared to LO. The content of malate was rapidly reduced while that of lactate was reduced in LO-MA and LO-FO-MA from 3 h incubation time. The fold change of the quantity of methanogen related to total bacteria was decreased at both 3 h and 6 h incubation times in all treatments compared to the control. Overall data indicate that supplementation of combined malate and/or fish oil when incubated with linseed oil, could depress methane generation and increase production of propionate, CLA and CLnA under the conditions of the current in vitro study. © 2015 Japanese Society of Animal Science.

  13. Harnessing biodiesel-producing microbes: from genetic engineering of lipase to metabolic engineering of fatty acid biosynthetic pathway.

    Science.gov (United States)

    Yan, Jinyong; Yan, Yunjun; Madzak, Catherine; Han, Bingnan

    2017-02-01

    Microbial production routes, notably whole-cell lipase-mediated biotransformation and fatty-acids-derived biosynthesis, offer new opportunities for synthesizing biodiesel. They compare favorably to immobilized lipase and chemically catalyzed processes. Genetically modified whole-cell lipase-mediated in vitro route, together with in vivo and ex vivo microbial biosynthesis routes, constitutes emerging and rapidly developing research areas for effective production of biodiesel. This review presents recent advances in customizing microorganisms for producing biodiesel, via genetic engineering of lipases and metabolic engineering (including system regulation) of fatty-acids-derived pathways. Microbial hosts used include Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Aspergillus oryzae. These microbial cells can be genetically modified to produce lipases under different forms: intracellularly expressed, secreted or surface-displayed. They can be metabolically redesigned and systematically regulated to obtain balanced biodiesel-producing cells, as highlighted in this study. Such genetically or metabolically modified microbial cells can support not only in vitro biotransformation of various common oil feedstocks to biodiesel, but also de novo biosynthesis of biodiesel from glucose, glycerol or even cellulosic biomass. We believe that the genetically tractable oleaginous yeast Yarrowia lipolytica could be developed to an effective biodiesel-producing microbial cell factory. For this purpose, we propose several engineered pathways, based on lipase and wax ester synthase, in this promising oleaginous host.

  14. Balanço de nitrogênio, degradabilidade de aminoácidos e concentração de ácidos graxos voláteis no rúmen de ovinos alimentados com feno de Stylosanthes guianensis Nitrogen balance, amino acid degradability and volatile fatty acid concentration in the rumen of sheep fed Stylosanthes guianensis hay

    Directory of Open Access Journals (Sweden)

    Márcio Machado Ladeira

    2002-11-01

    Full Text Available Foram utilizados sete ovinos alimentados com feno de S. guianensis para avaliar a degradabilidade ruminal dos aminoácidos, o balanço nitrogenado e as concentrações de ácidos graxos voláteis (AGVs no rúmen. A técnica de sacos de náilon foi empregada para determinação da degradabilidade in situ dos aminoácidos do feno de Stylosanthes guianensis. A retirada dos sacos do rúmen foi feita às 6, 24 e 48 horas após sua introdução. Amostras de duodeno e fezes foram utilizadas para determinar a quantidade de N total, amônia e nitrogênio não amoniacal. Amostras de urina foram coletadas para determinação do N total. Para determinação da concentração de AGVs no líquido ruminal, amostras de 80 mL foram coletadas manualmente, imediatamente antes da alimentação e 2, 4, 6 e 8 horas após. O balanço de nitrogênio foi de 6,0 g/dia. O feno de S. guianensis apresentou 10,4 e 6,3 g de metionina e lisina, respectivamente, por 100 g de aminoácidos totais. Os aminoácidos não essenciais apresentaram taxa de degradação duas vezes maior que os essenciais. Houve alteração no perfil aminoacídico da proteína não degradada no rúmen em relação ao alimento original. A relação acetato:propionato foi de 4,31. O elevado teor de metionina encontrado e sua baixa degradabilidade podem fazer do S. guianensis um alimento importante, quando este aminoácido estiver limitando a produção.Seven sheep fed S. guianensis hay were used to evaluate ruminal amino acid degradability, nitrogen balance and rumen volatile fatty acid (VFA concentrations. Nylon bags technique was used for determination of the in situ degradabilities of amino acids. Bags were collected at 6, 24 and 48 hours after insertion. Duodenum and feces samples were used to determine amoniacal-N and non-amoniacal-N. To determine ruminal VFA concentrations, samples of 80 mL were collected immediately before feeding and 2, 4, 6 and 8 hours after. Nitrogen balance was 6.0 g/day. S

  15. Polarography of an acidic degradation product from cephalexin.

    Science.gov (United States)

    Nuñez-Vergara, L J; Squella, J A; Silva, M M

    1982-02-01

    2-Hydroxy-3-phenyl-6-methylpyrazine is identified as the product obtained by acidic degradation of cephalexin in the presence of formaldehyde. In 5M hydrochloric acid this product gives a well-defined reduction wave with a half-wave potential of -0.45 V vs. SCE. The wave is irreversible and diffusion-controlled. The diffusion current shows a linear relation with the cephalexin concentration and can be used for determination of cephalexin in plasma.

  16. Treatment of flaxseed to reduce biohydrogenation of a-linolenic acid by ruminal microbes in sheep and cattle and increase n-3 fatty acid concentrations in red meat

    Science.gov (United States)

    Our study determined if flaxseed treated with a formaldehyde-free process increased n-3 fatty acid (FA) levels in ruminant muscle. Twenty-four lambs (initial BW 43.8 ± 4.4 kg) were randomly divided into 4 groups for a 90-d trial. One treatment group (FLX) was fed 136 g/d of non-treated ground flaxse...

  17. Tannic acid degradation by Klebsiella strains isolated from goat feces

    Directory of Open Access Journals (Sweden)

    Arezoo Tahmourespour

    2016-03-01

    Full Text Available Background and Objectives: Tannins are toxic polyphenols that either bind and precipitate or condense proteins. The high tannin content of some plants is the preliminary limitation of using them as a ruminant feed. So, the aim of this study was the isolation and characterization of tannic acid degrading bacterial strains from goat feces before and after feeding on Pis- tachio-Soft Hulls as tannin rich diet (TRD.Materials and Methods: Bacterial strains capable of utilizing tannic acid as sole carbon and energy source were isolated and characterized from goat feces before and after feeding on TRD. Tannase activity, maximum tolerable concentration and biodegradation potential were assessed.Results: Four tannase positive isolates were identified as Klebsiella pneumoniae. Isolated strains showed the maximum tolerable concentration of 64g/L of tannin. The tannic acid degradation percentage at a concentration of 15.0 g/L reached a maximum of 68% after 24 h incubation, and more than 98% after 72 h incubation. The pH of the medium also decreased along with tannic acid utilization.Conclusions: It is obvious that TRD induced adaptive responses. Thus, while the bacteria were able to degrade and detoxify the tannic acids, they had to adapt in the presence of high concentrations of tannic acid. So, these isolates have an amazing potential for application in bioremediation, waste water treatment, also reduction of tannins antinutritional effects in animal feeds.Keywords: Biodegradation; Goat feces; Klebsiella strains; Tannic acid

  18. Effect of Polylactic Acid-Degradable Film Mulch on Soil Temperature and Cotton Yield

    Directory of Open Access Journals (Sweden)

    ZHANG Ni

    2016-03-01

    Full Text Available Concern on biodegradable plastic film is increasing because of pollution problems caused by the plastic films currently used. The objective of this field experiment is to evaluate the effect of two thicknesses of polyactic acid-degradable film on soil temperature and cotton yield. The results showed that small holes appeared in the polyactic acid-degradable film at 17~22 d after it was installed. Burst period appeared about 60 d after installation. Splits were observed in the polyactic acid-degradable film at 130 d after installation. Soil temperatures rose slowly under polyactic acid-degradable film during the cotton seedling stage. Daytime soil temperatures were 0.8℃ and 6.2℃ lower under 18μm and 15μm thick polyactic acid-degradable film than non-degradable plastic film(CK, respectively. Nighttime soil temperatures under the polyactic acid-degradable film were about 1℃ warmer than CK. There was no significant difference in cotton yields between the 18μm polyactic acid degradable film treatment and CK. In contrast, yields in the 15μm degradable plastic film treatment were 8.9% less than that in CK. This study indicated that 18μm polyactic acid degradable plastic film had good degradability and no negative effect on cotton growth. The 18μm polyactic acid degradable plastic film can replace ordinary plastic film in agricultural production.

  19. Energetics and kinetics of anaerobic aromatic and fatty acid degradation. Progress report, November 1992--November 1993

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, M.J.

    1993-11-12

    The kinetics of benzoate degradation by the anaerobic syntrophic bacterium, Syntrophus buswellii, in coculture with different sulfate reducers was studied with sulfate or nitrate as the electron acceptor. A threshold value for benzoate degradation dependent on the acetate concentration was observed with sulfate, but not nitrate, as the electron acceptor. No threshold was observed in tricultures containing an acetate-using sulfate reducer. The addition of the acetate-using sulfate reducer to cocultures that had degraded benzoate to its threshold value resulted in further degradation of benzoate to levels below the analytical detection limit (ca. 200 nM). These data are consistent with a thermodynamic explanation for the threshold, and exclude the possibility that the threshold was the result of the inhibitory action of the undissociated form of acetate.

  20. Mathematical modelling of methanogenic reactor start-up: Importance of volatile fatty acids degrading population.

    Science.gov (United States)

    Jabłoński, Sławomir J; Łukaszewicz, Marcin

    2014-12-01

    Development of balanced community of microorganisms is one of the obligatory for stable anaerobic digestion. Application of mathematical models might be helpful in development of reliable procedures during the process start-up period. Yet, the accuracy of forecast depends on the quality of input and parameters. In this study, the specific anaerobic activity (SAA) tests were applied in order to estimate microbial community structure. Obtained data was applied as input conditions for mathematical model of anaerobic digestion. The initial values of variables describing the amount of acetate and propionate utilizing microorganisms could be calculated on the basis of SAA results. The modelling based on those optimized variables could successfully reproduce the behavior of a real system during the continuous fermentation.

  1. Energetics and kinetics of anaerobic aromatic and fatty acid degradation. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Michael J. McInerney

    1996-06-24

    The factors that affect the rate and extent of a model aromatic compound, benzoate, in methanogenic environments was studied. Benzoate is degraded to a threshold concentration below which no further substrate degradation occurs. The threshold concentration depended on the substrate concentration and the amount of acetate present. The threshold value was not a function of the kinetic ability of the organism or toxicity of the end products. Rather a minimal Gibb's free energy value may exist where thermodynamic constraints preclude further benzoate degradation. In addition, new bacterial species were isolated and described, that degrade benzoate or reduce iron, cobalt and other metals.

  2. Energetics and kinetics of anaerobic aromatic and fatty acid degradation. Progress report, November 1993--November 1994

    Energy Technology Data Exchange (ETDEWEB)

    McInerney, M.J.

    1994-12-06

    Factors influencing the rate and extent of benzoate degradation by the anaerobic syntrophic consortia were studied. Nonlinear regression analysis showed that the cause of the benzoate threshold was not a diminished benzoate degradation capacity. Analysis of cocultures with hydrogen users that differed in their hydrogen utilization capacities showed that the threshold did not depend on the kinetic properties of the syntrophic partner. These data support a thermodynamic explanation for the threshold, and exclude the possibility that a change in the affinity of the enzyme system due to acetate inhibition caused the threshold. Modeling studies showed that the threshold value could be predicted from the concentrations of the end products, assuming a critical Gibb`s free energy value. This work shows that interspecies acetate transfer is important in controlling the extent of metabolism by syntrophic organisms.

  3. Microbes: mini iron factories.

    Science.gov (United States)

    Joshi, Kumar Batuk

    2014-12-01

    Microbes have flourished in extreme habitats since beginning of the Earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. Biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. Iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via controlled or induced mineralization processes. Microbes have also been considered to play an important role in the history of evolution of sedimentary rocks on Earth from the formation of banded iron formations during the Archean to modern biotic bog iron and ochre deposits. Here, we discuss the role that microbes have been playing in precipitation of iron and the role and importance of interdisciplinary studies in the field of geology and biology in solving some of the major geological mysteries.

  4. Microbes: Mini Iron Factories

    OpenAIRE

    Joshi, Kumar Batuk

    2014-01-01

    Microbes have flourished in extreme habitats since beginning of the Earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. Biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. Iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via con...

  5. Isolation and characterization of resin acid degrading bacteria found in effluent from a bleached kraft pulp mill.

    Science.gov (United States)

    Morgan, C A; Wyndham, R C

    1996-05-01

    Thirteen resin acid degrading bacteria enriched on abietic or dehydroabietic acids were isolated from waste water from the aerated stabilization basin of a bleached kraft pulp mill. Standard biochemical tests were used to characterize each isolate. Each isolate was tested for its ability to degrade six abietane- and pimarane-type resin acids. Resin acid concentrations were determined by high pressure liquid chromatography and UV absorbance. Cluster analysis based on phenotypic characteristics identified two distinct clusters of degraders that differed in their ability to utilize carbohydrates as carbon sources. Fatty acid methyl ester analysis of representative isolates from each cluster identified A19-6a and D11-13 as Comamonas and Alcaligenes species, respectively. To determine genotypic relatedness, enterobacterial repetitive intergenic consensus sequences were used to amplify genomic DNA fragments from 10 isolates. These results supported the phenotypic analysis for all isolates tested except A19-5 and A19-6b. These two organisms were clustered closely together based on phenotype but had distinctly different banding patterns, suggesting that they are not related genotypically. All isolates degraded a subset of the six resin acid congeners. Isolates A19-3, A19-6a, A19-6b, and D11-37 were the most effective at degrading all six congeners.

  6. Microorganisms (Microbes), Role of

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2013-01-01

    Microorganisms (microbes) are those life forms too small to be seen by the naked eye; that is, those that require a microscope or other form of magnification in order to be observed. The term microorganism is thus a functional description rather than a taxonomic one, and the grouping includes...

  7. Microorganisms (Microbes), Role of

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2013-01-01

    Microorganisms (microbes) are those life forms too small to be seen by the naked eye; that is, those that require a microscope or other form of magnification in order to be observed. The term microorganism is thus a functional description rather than a taxonomic one, and the grouping includes a w...

  8. Extremophilic microbes: Diversity and perspectives

    Digital Repository Service at National Institute of Oceanography (India)

    Satyanarayana, T.; Raghukumar, C.; Shivaji, S.

    and grow in extreme en-vironments. The enzymes of these microbes, which function in extreme environments (extremozymes), have several biotechnological applications. Antibiotics, compatible solutes and other compounds obtainable from these microbes are also...

  9. Main chain acid-degradable polymers for the delivery of bioactive materials

    Science.gov (United States)

    Frechet, Jean M. J. [Oakland, CA; Standley, Stephany M [Evanston, IL; Jain, Rachna [Milpitas, CA; Lee, Cameron C [Cambridge, MA

    2012-03-20

    Novel main chain acid degradable polymer backbones and drug delivery systems comprised of materials capable of delivering bioactive materials to cells for use as vaccines or other therapeutic agents are described. The polymers are synthesized using monomers that contain acid-degradable linkages cleavable under mild acidic conditions. The main chain of the resulting polymers readily degrade into many small molecules at low pH, but remain relatively stable and intact at physiological pH. The new materials have the common characteristic of being able to degrade by acid hydrolysis under conditions commonly found within the endosomal or lysosomal compartments of cells thereby releasing their payload within the cell. The materials can also be used for the delivery of therapeutics to the acidic regions of tumors and other sites of inflammation.

  10. Molecular ecology of aquatic microbes

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1994-12-31

    Abstracts of reports are presented from a meeting on Molecular Ecology of Aquatic Microbes. Topics included: opportunities offered to aquatic ecology by molecular biology; the role of aquatic microbes in biogeochemical cycles; characterization of the microbial community; the effect of the environment on aquatic microbes; and the targeting of specific biological processes.

  11. Mechanism of Calcium Lactate Facilitating Phytic Acid Degradation in Soybean during Germination.

    Science.gov (United States)

    Hui, Qianru; Yang, Runqiang; Shen, Chang; Zhou, Yulin; Gu, Zhenxin

    2016-07-13

    Calcium lactate facilitates the growth and phytic acid degradation of soybean sprouts, but the mechanism is unclear. In this study, calcium lactate (Ca) and calcium lactate with lanthanum chloride (Ca+La) were used to treat soybean sprouts to reveal the relevant mechanism. Results showed that the phytic acid content decreased and the availability of phosphorus increased under Ca treatment. This must be due to the enhancement of enzyme activity related to phytic acid degradation. In addition, the energy metabolism was accelerated by Ca treatment. The energy status and energy metabolism-associated enzyme activity also increased. However, the transmembrane transport of calcium was inhibited by La(3+) and concentrated in intercellular space or between the cell wall and cell membrane; thus, Ca+La treatment showed reverse results compared with those of Ca treatment. Interestingly, gene expression did not vary in accordance with their enzyme activity. These results demonstrated that calcium lactate increased the rate of phytic acid degradation by enhancing growth, phosphorus metabolism, and energy metabolism.

  12. Microbe-microbe interactions in mixed culture food fermentations

    NARCIS (Netherlands)

    Smid, E.J.; Lacroix, C.

    2013-01-01

    Most known natural and industrial food fermentation processes are driven by either simple or complex communities of microorganisms. Obviously, these fermenting microbes will not only interact with the fermentable substrate but also with each other. These microbe–microbe interactions are complex but

  13. Radiation induced pesticidal microbes

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ki Yup; Lee, Y. K.; Kim, J. S.; Kim, J. K.; Lee, S. J.; Lim, D. S

    2001-01-01

    To isolate pesticidal microbes against plant pathogenic fungi, 4 strains of bacteria(K1. K3, K4, YS1) were isolated from mushroom compost and hot spring. K4, K1, K3, YS1 strain showed wide antifungal spectrum and high antifungal activities against 12 kinds of fungi. Specific proteins and the specific transcribed genes were found from the YS1 and its radiation-induced mutants. And knock-out mutants of antifungal activity were derived by transposon mutagenesis. From these knock-out mutants, the antifungal activity related genes and its modification by gamma-ray radiation are going to be studied. These results suggested that radiation could be an useful tool for the induction of functional mutants.

  14. Microbe Phobia and Kitchen Microbiology.

    Science.gov (United States)

    Williams, Robert P.; Gillen, Alan L.

    1991-01-01

    The authors present an exercise designed to help students overcome the misconception that most microbes make people sick. The activity helps students of all ages understand the important benefits of microbes such as in making bread, soy sauce, cheese, and wine. The role of microorganisms in processing cocoa and coffee and growing plants is also…

  15. Microbes central to human reproduction.

    Science.gov (United States)

    Reid, Gregor; Brigidi, Patrizia; Burton, Jeremy P; Contractor, Nikhat; Duncan, Sylvia; Fargier, Emilie; Hill, Colin; Lebeer, Sarah; Martín, Rocio; McBain, Andrew J; Mor, Gil; O'Neill, Catherine; Rodríguez, Juan Miguel; Swann, Jonathan; van Hemert, Saskia; Ansell, Juliett

    2015-01-01

    As studies uncover the breadth of microbes associated with human life, opportunities will emerge to manipulate and augment their functions in ways that improve health and longevity. From involvement in the complexities of reproduction and fetal/infant development, to delaying the onset of disease, and indeed countering many maladies, microbes offer hope for human well-being. Evidence is emerging to suggest that microbes may play a beneficial role in body sites traditionally viewed as being sterile. Although further evidence is required, we propose that much of medical dogma is about to change significantly through recognition and understanding of these hitherto unrecognized microbe-host interactions. A meeting of the International Scientific Association for Probiotics and Prebiotics held in Aberdeen, Scotland (June 2014), presented new views and challenged established concepts on the role of microbes in reproduction and health of the mother and infant. This article summarizes some of the main aspects of these discussions.

  16. Applications of Carboxylic Acid Reductases in Oleaginous Microbes

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Linger, Jeffrey; McGeehan, John; Tyo, Keith; Beckham, Gregg

    2016-04-24

    Carboxylic acid reductases (CARs) are recently emerging reductive enzymes for the direct production of aldehydes from biologically-produced carboxylic acids. Recent work has demonstrated that these powerful enzymes are able to reduce a very broad range of volatile- to long-chain fatty acids as well as aromatic acids. Here, we express four CAR enzymes from different fungal origins to test their activity against fatty acids commonly produced in oleaginous microbes. These in vitro results will inform metabolic engineering strategies to conduct mild biological reduction of carboxylic acids in situ, which is conventionally done via hydrotreating catalysis at high temperatures and hydrogen pressures.

  17. Biofuels from microbes.

    Science.gov (United States)

    Antoni, Dominik; Zverlov, Vladimir V; Schwarz, Wolfgang H

    2007-11-01

    Today, biomass covers about 10% of the world's primary energy demand. Against a backdrop of rising crude oil prices, depletion of resources, political instability in producing countries and environmental challenges, besides efficiency and intelligent use, only biomass has the potential to replace the supply of an energy hungry civilisation. Plant biomass is an abundant and renewable source of energy-rich carbohydrates which can be efficiently converted by microbes into biofuels, of which, only bioethanol is produced on an industrial scale today. Biomethane is produced on a large scale, but is not yet utilised for transportation. Biobutanol is on the agenda of several companies and may be used in the near future as a supplement for gasoline, diesel and kerosene, as well as contributing to the partially biological production of butyl-t-butylether, BTBE as does bioethanol today with ETBE. Biohydrogen, biomethanol and microbially made biodiesel still require further development. This paper reviews microbially made biofuels which have potential to replace our present day fuels, either alone, by blending, or by chemical conversion. It also summarises the history of biofuels and provides insight into the actual production in various countries, reviewing their policies and adaptivity to the energy challenges of foreseeable future.

  18. Enterococci: yin - yang microbes

    Directory of Open Access Journals (Sweden)

    Andreja Čanžek Majhenič

    2006-03-01

    Full Text Available This review deals with the duality of enterococci, which can be illustrated by their yin - yang behaviour. The rough nature of this specific group of lactic acid bacteria promotes their dissemination in various environments where they significantly influence the outcome of a certain process. In the technological meaning, enterococci are leading microbes in fermentation processes of traditional foods, where their detrimental spoilage activities are equally significant. As therapeutics, enterococci manifest the probiotic properties through their positive effects on maintaining of the normal intestinal microflora, on stimulation of the immune system, on improved nutritional value of food and with the production of antimicrobial compounds (bacteriocins. At the same time, enterococci present an emerging pool of opportunistic pathogens for humans as they cause disease, possess agents for antibiotic resistance and their transfer mechanisms, and are frequently armed with potential virulence factors. Despite the yin - yang characteristics of enterococci, the long history of safe use of certain strains of enterococci in food/feed, and reliable identification and classification of enterococci with phenotypic methods supported with modern genetic tools, enables selection of promising enterococci, which could be safely used as starter cultures or food/feed additives.

  19. Volatile fatty acid degradation kinetics in anaerobic process; Cinetica de la degradacion de acidos grasos volatiles en procesos anaerobios

    Energy Technology Data Exchange (ETDEWEB)

    Riscado, S.; Osuna, B.; Iza, J.; Ruiz, E. [Universidad del Pais Vasco. Bilbao (Spain)

    1998-10-01

    While searching for the optimal substrate load for anaerobic toxicity assays, the inhibition caused by the propionic acid has been addressed. Lab scale experiments have been carried out to assess the effects of different loads and acid ratios. Results bad been subjected to kinetic analysis and show the degradation follows a first order kinetic, and acetic is easier to degrade than propionic acid. The optimal load for a 100 ml vial assay is composed of 158 mg COD of the 3:1:1 HAc:HPr:HBu mixture. (Author) 9 refs.

  20. Microbes as forensic indicators.

    Science.gov (United States)

    Alan, G; Sarah, J P

    2012-09-01

    The forensic potential of microorganisms is becoming increasingly apparent as a consequence of advances in molecular sciences and genomics. This review discusses instances in which microbes, and in particular bacteria, can impact upon forensic investigations. There is increasing evidence that humans have an extremely diverse 'microbiome' that may prove useful in determining ethnicity, country of origin, and even personal identity. The human microbiome differs between regions of the body and may prove useful for determining the nature of stains such as those caused by saliva and vaginal fluid: it may even be possible to link the stains to the person responsible for them. Similarly, the composition of the microbiome present in a soil sample may prove a useful indicator of geographic origin or as a means of linking people, animals, or objects together or to a specific location. Microorganisms are important in the decay process and also influence the presence and concentration of alcohol, drugs, and other chemicals of forensic relevance. There is also a possibility that the entry of microorganisms into the body during the agonal period may prove useful for the diagnosis of drowning. The transmission of infectious diseases, and in particular sexually-transmitted diseases, can provide evidence linking a victim and a suspect. Microorganisms that cause fatal infections are not always identified at the time of death and may lead to the death being considered 'suspicious'. If a fatal infection can be linked to a hospital or medical procedure it can lead to prosecutions and therefore it is important to determine when and where an infection was acquired. Similarly, naturally acquired infections need to be distinguished from those that result from malicious transmission. Microorganisms can therefore provide evidence in many different forensic scenarios but most of the work is still at the experimental stage and there are therefore many opportunities for further research.

  1. Chemiluminescence and bioluminescence microbe detection

    Science.gov (United States)

    Taylor, R. E.; Chappelle, E.; Picciolo, G. L.; Jeffers, E. L.; Thomas, R. R.

    1978-01-01

    Automated biosensors for online use with NASA Water Monitoring System employs bioluminescence and chemiluminescence techniques to rapidly measure microbe contamination of water samples. System eliminates standard laboratory procedures requiring time duration of 24 hours or longer.

  2. Isolation of a novel uric-acid-degrading microbe Comamonas sp. BT UA and rapid biosensing of uric acid from extracted uricase enzyme

    Indian Academy of Sciences (India)

    Tanushree Ghosh; Priyabrata Sarkar

    2014-12-01

    Uric-acid-utilizing soil bacteria were isolated, and 16s rRNA sequence was studied for strain identification. The most prominent uricase-producing bacterium was identified as Comamonas sp BT UA. Crude enzyme was extracted, freeze-dried and its Km and Vmax were determined as 40 M and 0.047 M min−1ml−1 using Line-weaver Burke plot. An activity of 80 U/mg of total protein was observed when cultured at 37°C for 84 h at pH 7. The purified enzyme was used to measure uric acid by spectrophotometric method and electrochemical biosensor. In the biosensing system the enzyme was immobilized on the platinum electrode with a biodegradable glutaraldehyde-crosslinked gelatin film having a swelling percentage of 109±3.08, and response was observed by amperometry applying fixed potential. The electrochemical process as obtained by the anodic peak current and scan rate relationship was further configured by electrochemical impedance spectroscopy (EIS). The polymer matrix on the working electrode gave capacitive response for the electrode–electrolyte interaction. The sensitivity of the biosensor was measured as 6.93 AM−1 with a sensor affinity [m(app)] of 50 M and 95% reproducibility after 50 measurements. The spectrophotometric method could be used in the range of 6–1000 M, whereas the biosensor generated linear response in the 1.5–1000 M range with a response time of 24 s and limit of detection of 0.56 M. Uric acid was estimated in human blood samples by the biosensor and satisfactory results were obtained.

  3. Separation and recovery of nucleic acids with improved biological activity by acid-degradable polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Kim, Yoon Kyung; Kwon, Young Jik

    2010-05-01

    One of the fundamental challenges in studying biomacromolecules (e.g. nucleic acids and proteins) and their complexes in a biological system is isolating them in their structurally and functionally intact forms. Electrophoresis offers convenient and efficient separation and analysis of biomacromolecules but recovery of separated biomacromolecules is a significant challenge. In this study, DNAs of various sizes were separated by electrophoresis in an acid-degradable polyacrylamide gel. Almost 100% of the nucleic acids were recovered after the identified gel bands were hydrolyzed under a mildly acidic condition and purified using anion exchange resin. Further concentration by centrifugal filtration and a second purification using ion exchange column chromatography yielded 44-84% of DNA. The second conventional (non-degradable) gel electrophoresis confirmed that the nucleic acids recovered from acid-degradable gel bands preserved their electrophoretic properties through acidic gel hydrolysis, purification, and concentration processes. The plasmid DNA recovered from acid-degradable gel transfected cells significantly more efficiently than the starting plasmid DNA (i.e. improved biological activity via acid-degradable PAGE). Separation of other types of nucleic acids such as small interfering RNA using this convenient and efficient technique was also demonstrated.

  4. Isolation and characterization of a diverse group of phenylacetic acid degrading microorganisms from pristine soil.

    Science.gov (United States)

    O'Connor, Kevin E; O'Leary, Niall P; Marchesi, Julian R; Dobson, Alan D W; Duetz, Wouter

    2005-11-01

    A diverse range of microorganisms capable of growth on phenylacetic acid as the sole source of carbon and energy were isolated from soil. Sixty six different isolates were identified and grouped according to 16S rRNA gene RFLP analysis. Subsequent sequencing of 16S rDNA from selected strains allowed further characterization of the phenylacetic acid degrading population isolated from soil. Nearly half (30) of the isolates are Bacillus species while the rest of the isolates are strains from a variety of genera namely, Arthrobacter, Pseudomonas, Rhodococcus, Acinetobacter, Enterobacter, Flavobacterium, and Paenibacillus. Sixty-one of the sixty-six strains reproducibly grew in defined minimal liquid culture medium (E2). All strains isolated grew when at least one hydroxylated derivative of phenylacetic acid was supplied as the carbon source, while 59 out of the 61 strains tested, accumulated ortho-hydroxyphenylacetic acid in the assay buffer; when pulsed with phenylacetic acid. Oxygen consumption experiments failed to indicate a clear link between phenylacetic acid and hydroxy-substituted phenylacetic acid in isolates from a broad range of genera.

  5. Enhanced propionic acid degradation (EPAD) system: proof of principle and feasibility.

    Science.gov (United States)

    Ma, Jingxing; Carballa, Marta; Van De Caveye, Pieter; Verstraete, Willy

    2009-07-01

    Full-scale anaerobic single-phase digesters can be confronted with process instabilities, which often result in the accumulation of propionic acid (HPr). As a solution, an enhanced propionic acid degradation (EPAD) system has been conceptually designed and experimentally tested at lab-scale. The system consisted of two components: a liquid/solid separator containing a microfiltration membrane and an up-flow anaerobic sludge bed (UASB) reactor specialized in HPr degradation. Two lab-scale continuous stirred tank reactors (CSTR) were used, i.e. the CSTR(control) and the CSTR(treatment). Firstly, the CSTRs were stressed by organic overloading to obtain high HPr levels. During the recovery period, besides stop feeding, no actions were taken to decrease the residual HPr concentration in the CSTR(control), while the CSTR(treatment) was connected to EPAD system in order to accelerate its recovery. By the end of the experiment, the CSTR(treatment) completely recovered from HPr accumulation, while no significant decrease of the HPr level in the CSTR(control) was observed. Based on the experimental results, the up-scaling of EPAD system was evaluated and it would only account for about 2% of the volume of the full-scale digester, thus suggesting that the implementation of a mobile EPAD system in full-scale practice should be feasible.

  6. Transcription of the Escherichia coli fatty acid synthesis operon fabHDG is directly activated by FadR and inhibited by ppGpp.

    Science.gov (United States)

    My, Laetitia; Rekoske, Brian; Lemke, Justin J; Viala, Julie P; Gourse, Richard L; Bouveret, Emmanuelle

    2013-08-01

    In Escherichia coli, FadR and FabR are transcriptional regulators that control the expression of fatty acid degradation and unsaturated fatty acid synthesis genes, depending on the availability of fatty acids. In this report, we focus on the dual transcriptional regulator FadR. In the absence of fatty acids, FadR represses the transcription of fad genes required for fatty acid degradation. However, FadR is also an activator, stimulating transcription of the products of the fabA and fabB genes responsible for unsaturated fatty acid synthesis. In this study, we show that FadR directly activates another fatty acid synthesis promoter, PfabH, which transcribes the fabHDG operon, indicating that FadR is a global regulator of both fatty acid degradation and fatty acid synthesis. We also demonstrate that ppGpp and its cofactor DksA, known primarily for their role in regulation of the synthesis of the translational machinery, directly inhibit transcription from the fabH promoter. ppGpp also inhibits the fadR promoter, thereby reducing transcription activation of fabH by FadR indirectly. Our study shows that both ppGpp and FadR have direct roles in the control of fatty acid promoters, linking expression in response to both translation activity and fatty acid availability.

  7. Principles of Plant-Microbe Interactions - Microbes for Sustainable Agriculture

    Science.gov (United States)

    Crops lack resistance to many soilborne pathogens and rely on antagonistic microbes recruited from the soil microbiome to protect their roots. Disease-suppressive soils, the best examples of microbial-based defense, are soils in which a pathogen does not establish or persist, establishes but causes ...

  8. Microbes encapsulated within crosslinkable polymers

    Energy Technology Data Exchange (ETDEWEB)

    Chidambaram, Devicharan; Liu, Ying; Rafailovich, Miriam H

    2013-02-05

    The invention relates to porous films comprising crosslinked electrospun hydrogel fibers. Viable microbes are encapsulated within the crosslinked electrospun hydrogel fibers. The crosslinked electrospun hydrogel fibers are water insoluble and permeable. The invention also relates to methods of making and using such porous films.

  9. Characterization of the Complete Uric Acid Degradation Pathway in the Fungal Pathogen Cryptococcus neoformans

    Science.gov (United States)

    Lee, I. Russel; Yang, Liting; Sebetso, Gaseene; Allen, Rebecca; Doan, Thi H. N.; Blundell, Ross; Lui, Edmund Y. L.; Morrow, Carl A.; Fraser, James A.

    2013-01-01

    Degradation of purines to uric acid is generally conserved among organisms, however, the end product of uric acid degradation varies from species to species depending on the presence of active catabolic enzymes. In humans, most higher primates and birds, the urate oxidase gene is non-functional and hence uric acid is not further broken down. Uric acid in human blood plasma serves as an antioxidant and an immune enhancer; conversely, excessive amounts cause the common affliction gout. In contrast, uric acid is completely degraded to ammonia in most fungi. Currently, relatively little is known about uric acid catabolism in the fungal pathogen Cryptococcus neoformans even though this yeast is commonly isolated from uric acid-rich pigeon guano. In addition, uric acid utilization enhances the production of the cryptococcal virulence factors capsule and urease, and may potentially modulate the host immune response during infection. Based on these important observations, we employed both Agrobacterium-mediated insertional mutagenesis and bioinformatics to predict all the uric acid catabolic enzyme-encoding genes in the H99 genome. The candidate C. neoformans uric acid catabolic genes identified were named: URO1 (urate oxidase), URO2 (HIU hydrolase), URO3 (OHCU decarboxylase), DAL1 (allantoinase), DAL2,3,3 (allantoicase-ureidoglycolate hydrolase fusion protein), and URE1 (urease). All six ORFs were then deleted via homologous recombination; assaying of the deletion mutants' ability to assimilate uric acid and its pathway intermediates as the sole nitrogen source validated their enzymatic functions. While Uro1, Uro2, Uro3, Dal1 and Dal2,3,3 were demonstrated to be dispensable for virulence, the significance of using a modified animal model system of cryptococcosis for improved mimicking of human pathogenicity is discussed. PMID:23667704

  10. Safety of novel microbes for human consumption

    NARCIS (Netherlands)

    Brodmann, Theodor; Endo, Akihito; Gueimonde, Miguel; Vinderola, Gabriel; Kneifel, Wolfgang; Vos, de Willem M.; Salminen, Seppo; Gómez-Gallego, Carlos

    2017-01-01

    Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to

  11. Can chatter between microbes prevent cholera?

    Science.gov (United States)

    Thompson, Jessica A; Oliveira, Rita Almeida; Xavier, Karina B

    2014-12-01

    Tackling the global rise in antibiotic resistance requires new therapies against infectious microbes. A recent microbiome study identified commensal gut bacteria that reduce colonisation by the cholera pathogen, Vibrio cholerae. This antagonistic interaction might be mediated by quorum sensing, suggesting that these natural microbe-microbe interactions can help prevent infectious disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Fatty acid synthesis is inhibited by inefficient utilization of unusual fatty acids for glycerolipid assembly.

    Science.gov (United States)

    Bates, Philip D; Johnson, Sean R; Cao, Xia; Li, Jia; Nam, Jeong-Won; Jaworski, Jan G; Ohlrogge, John B; Browse, John

    2014-01-21

    Degradation of unusual fatty acids through β-oxidation within transgenic plants has long been hypothesized as a major factor limiting the production of industrially useful unusual fatty acids in seed oils. Arabidopsis seeds expressing the castor fatty acid hydroxylase accumulate hydroxylated fatty acids up to 17% of total fatty acids in seed triacylglycerols; however, total seed oil is also reduced up to 50%. Investigations into the cause of the reduced oil phenotype through in vivo [(14)C]acetate and [(3)H]2O metabolic labeling of developing seeds surprisingly revealed that the rate of de novo fatty acid synthesis within the transgenic seeds was approximately half that of control seeds. RNAseq analysis indicated no changes in expression of fatty acid synthesis genes in hydroxylase-expressing plants. However, differential [(14)C]acetate and [(14)C]malonate metabolic labeling of hydroxylase-expressing seeds indicated the in vivo acetyl-CoA carboxylase activity was reduced to approximately half that of control seeds. Therefore, the reduction of oil content in the transgenic seeds is consistent with reduced de novo fatty acid synthesis in the plastid rather than fatty acid degradation. Intriguingly, the coexpression of triacylglycerol synthesis isozymes from castor along with the fatty acid hydroxylase alleviated the reduced acetyl-CoA carboxylase activity, restored the rate of fatty acid synthesis, and the accumulation of seed oil was substantially recovered. Together these results suggest a previously unidentified mechanism that detects inefficient utilization of unusual fatty acids within the endoplasmic reticulum and activates an endogenous pathway for posttranslational reduction of fatty acid synthesis within the plastid.

  13. Neutrophils, from marrow to microbes

    DEFF Research Database (Denmark)

    Borregaard, Niels

    2010-01-01

    . Neutrophils circulate in the blood as dormant cells. At sites of infection, endothelial cells capture bypassing neutrophils and guide them through the endothelial cell lining whereby the neutrophils are activated and tuned for the subsequent interaction with microbes. Once in tissues, neutrophils kill...... microorganisms by microbicidal agents liberated from granules or generated by metabolic activation. As a final act, neutrophils can extrude stands of DNA with bactericidal proteins attached that act as extracellular traps for microorganisms....

  14. Soil microbes and plant fertilization.

    Science.gov (United States)

    Miransari, Mohammad

    2011-12-01

    With respect to the adverse effects of chemical fertilization on the environment and their related expenses, especially when overused, alternative methods of fertilization have been suggested and tested. For example, the combined use of chemical fertilization with organic fertilization and/or biological fertilization is among such methods. It has been indicated that the use of organic fertilization with chemical fertilization is a suitable method of providing crop plants with adequate amount of nutrients, while environmentally and economically appropriate. In this article, the importance of soil microbes to the ecosystem is reviewed, with particular emphasis on the role of plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and endophytic bacteria in providing necessary nutrients for plant growth and yield production. Such microbes are beneficial to plant growth through colonizing plant roots and inducing mechanisms by which plant growth increases. Although there has been extensive research work regarding the use of microbes as a method of fertilizing plants, it is yet a question how the efficiency of such microbial fertilization to the plant can be determined and increased. In other words, how the right combination of chemical and biological fertilization can be determined. In this article, the most recent advances regarding the effects of microbial fertilization on plant growth and yield production in their combined use with chemical fertilization are reviewed. There are also some details related to the molecular mechanisms affecting the microbial performance and how the use of biological techniques may affect the efficiency of biological fertilization.

  15. Fatty acids in an estuarine mangrove ecosystem.

    Science.gov (United States)

    Alikunhi, Nabeel M; Narayanasamy, Rajendran; Kandasamy, Kathiresan

    2010-06-01

    Fatty acids have been successfully used to trace the transfer of organic matter in coastal and estuarine food webs. To delineate these web connections, fatty acid profiles were analyzed in species of microbes (Azotobacter vinelandii, and Lactobacillus xylosus), prawns (Metapenaeus monoceros and Macrobrachium rosenbergii) and finfish (Mugil cephalus), that are associated with decomposing leaves of two mangrove species, Rhizophora apiculata and Avicennia marina. The fatty acids, except long chain fatty acids, exhibit changes during decomposition of mangrove leaves with a reduction of saturated fatty acids and an increase of monounsaturated fatty acids. The branched fatty acids are absent in undecomposed mangrove leaves, but present significantly in the decomposed leaves and in prawns and finfish, representing an important source for them. This revealed that the microbes are dominant producers that contribute significantly to the fishes and prawns in the mangrove ecosystem. This work has proved the fatty acid biomarkers as an effective tool for identifying the trophic interactions among dominant producers and consumers in this mangrove.

  16. Stability-indicating methods for the determination of erdosteine in the presence of its acid degradation products.

    Science.gov (United States)

    Moustafa, Nadia M; Badawey, Amr M; Lamie, Nesrine T; El-Aleem, Abd El-Aziz B Abd

    2014-01-01

    Four accurate, sensitive, and reproducible stability-indicating methods for the determination of erdosteine in the presence of its acid degradation products are presented. The first method involves processing the spectra by using a first-derivative method at 229 nm in a concentration range of 10-70 microg/mL. The mean percentage recovery was 100.43 +/- 0.977. The second method is based on ratio-spectra first derivative spectrophotometry at 227.4 and 255 nm over a concentration range of 10-70 microg/mL. The mean percentage recovery was 99.65 +/- 1.122% and 100.02 +/- 1.306% at 227.4 and 255 nm, respectively. The third method utilizes quantitative densitometric evaluation of the TLC of erdosteine in the presence of its acid degradation products, and uses methanol-chloroform-ammonia (7 + 3 +/- 0.01, v/v/v) as the mobile phase. TLC chromatograms were scanned at 235 nm. This method analyzes erdosteine in a concentration range of 2.4-5.6 microg/spot, with a mean percentage recovery of 100.03 +/- 1.015%. The fourth method is HPLC for the simultaneous determination of erdosteine in the presence of its acid degradation products. The mobile phase consists of water-methanol (65 + 35, v/v). The standard curve of erdosteine showed good linearity over a concentration range of 10-80 microg/mL, with a mean percentage recovery of 99.90 +/- 1.207%. These methods were successfully applied to the determination of erdosteine in bulk powder, laboratory-prepared mixtures containing different percentages of the degradation products, and pharmaceutical dosage forms. The validity of results was assessed by applying the standard addition technique. The results obtained agreed statistically with those obtained by a reported method, showing no significant differences with respect to accuracy and precision.

  17. Hidden Worlds of Marine Microbes

    Science.gov (United States)

    Armbrust, E. V.

    2016-12-01

    Every drop of seawater contains fantastically diverse groups of microbes that control key biogeochemical processes in the ocean and determine the habitability of our planet. The challenge is to scale from this world of individual cells to ecosystem function and ultimately to ocean basin processes. Our work begins with microscopic marine diatoms because they are responsible for about twenty percent of the photosynthesis that occurs on Earth each year, they form the base of highly productive marine food webs, and they help regulate past and current fluxes of CO2 into the ocean. Diatoms evolved in a dilute environment where they are never free from the influences of other microbes. We explore the specifics of these interactions via model diatom/bacteria systems that can be manipulated in the laboratory - one includes an antagonistic bacterium that inhibits the growth of diatoms and a second includes a synergistic bacterium that enhances the growth of diatoms. We scale up from the cellular level to population-level interactions through use of our continuous flow cytometer, SeaFlow, which taps into a ship's seawater intake system to provide a continuous read-out of abundance, size and type of the smallest phytoplankton. We use this data to estimate division rates and mortality rates of these phytoplankton across thousands of kilometers of ocean basins. We tie these scales together with genomic approaches in both laboratory experiments and in open ocean field studies to document how interactions with the environment and between microbes drive specific adaptations. Our ultimate goal is to understand how microbial communities will respond to and will help shape future ocean conditions.

  18. Microbes in biological processes for municipal landfill leachate treatment: Community, function and interaction

    DEFF Research Database (Denmark)

    Zhang, Duoying; Vahala, Riku; Wang, Yu

    2016-01-01

    Landfill leachate (LFL) contains high strength of ammonium and complex organic substances including biodegradable volatile fatty acids (VFAs), refractory aquatic humic substances (AHS) and micro-scale xenobiotic organic chemicals (XOCs), which promotes the diverse microbial community in LFL...... treatment bioreactors. These microbes cooperate to remove nitrogen, biodegrade organic matters, eliminate the toxicity of XOCs and produce energy. In these diverse microbes, some show dominant in the bioreactor and are prevalent in many kinds of LFL treatment bio-processes, such as Brocadia from the phylum....... High ammonium loading, low DO (bacteria (AnAOB). In anaerobic LFL treatment bioreactors, Methanosaeta...

  19. Microorganisms in environmental management: microbes and environment

    National Research Council Canada - National Science Library

    Satyanarayana, T; Johri, B. N; Prakash, Anil

    2012-01-01

    "This survey of recent scientific progress in usefully applying microbes to both environmental management and biotechnology is informed by acknowledgement of the polluting effects on the world around...

  20. Neutrophils, from marrow to microbes

    DEFF Research Database (Denmark)

    Borregaard, Niels

    2010-01-01

    . Neutrophils circulate in the blood as dormant cells. At sites of infection, endothelial cells capture bypassing neutrophils and guide them through the endothelial cell lining whereby the neutrophils are activated and tuned for the subsequent interaction with microbes. Once in tissues, neutrophils kill......Neutrophils are produced in the bone marrow from stem cells that proliferate and differentiate to mature neutrophils fully equipped with an armory of granules. These contain proteins that enable the neutrophil to deliver lethal hits against microorganisms, but also to cause great tissue damage...... microorganisms by microbicidal agents liberated from granules or generated by metabolic activation. As a final act, neutrophils can extrude stands of DNA with bactericidal proteins attached that act as extracellular traps for microorganisms....

  1. Fatty acids - trans fatty acids

    Science.gov (United States)

    The data supporting a negative effect of dietary trans fatty acids on cardiovascular disease risk is consistent. The primary dietary sources of trans fatty acids include partially hydrogenated fat and rudiment fat. The adverse effect of trans fatty acids on plasma lipoprotein profiles is consisten...

  2. Commonalities in Symbiotic Plant-Microbe Signalling

    NARCIS (Netherlands)

    Holmer, R.; Rutten, L.J.J.; Kohlen, W.; Velzen, van R.; Geurts, R.

    2017-01-01

    Plants face the problem that they have to discriminate symbionts from a diverse pool of soil microbes, including pathogens. Studies on different symbiotic systems revealed commonalities in plant-microbe signalling. In this chapter we focus on four intimate symbiotic interactions: two mycorrhizal

  3. Modulation of host immunity by beneficial microbes

    NARCIS (Netherlands)

    Zamioudis, C; Pieterse, C.M.J.

    2012-01-01

    In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and

  4. Modulation of host immunity by beneficial microbes

    NARCIS (Netherlands)

    Zamioudis, C; Pieterse, C.M.J.

    2012-01-01

    In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and

  5. Genome Sequence Analysis of the Naphthenic Acid Degrading and Metal Resistant Bacterium Cupriavidus gilardii CR3.

    Directory of Open Access Journals (Sweden)

    Xiaoyu Wang

    Full Text Available Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in size. The genome for strain CR3 encoded 4,502 putative protein-coding genes, 59 tRNA genes, and many other non-coding genes. Many genes were associated with xenobiotic biodegradation and metal resistance functions. Pathway prediction for degradation of cyclohexanecarboxylic acid, a representative naphthenic acid, suggested that naphthenic acid undergoes initial ring-cleavage, after which the ring fission products can be degraded via several plausible degradation pathways including a mechanism similar to that used for fatty acid oxidation. The final metabolic products of these pathways are unstable or volatile compounds that were not toxic to CR3. Strain CR3 was also shown to have tolerance to at least 10 heavy metals, which was mainly achieved by self-detoxification through ion efflux, metal-complexation and metal-reduction, and a powerful DNA self-repair mechanism. Our genomic analysis suggests that CR3 is well adapted to survive the harsh environment in natural asphalts containing naphthenic acids and high concentrations of heavy metals.

  6. Biochemical and structural characterization of Klebsiella pneumoniae oxamate amidohydrolase in the uric acid degradation pathway

    Energy Technology Data Exchange (ETDEWEB)

    Hicks, Katherine A.; Ealick, Steven E.

    2016-05-25

    HpxW from the ubiquitous pathogenKlebsiella pneumoniaeis involved in a novel uric acid degradation pathway downstream from the formation of oxalurate. Specifically, HpxW is an oxamate amidohydrolase which catalyzes the conversion of oxamate to oxalate and is a member of the Ntn-hydrolase superfamily. HpxW is autoprocessed from an inactive precursor to form a heterodimer, resulting in a 35.5 kDa α subunit and a 20 kDa β subunit. Here, the structure of HpxW is presented and the substrate complex is modeled. In addition, the steady-state kinetics of this enzyme and two active-site variants were characterized. These structural and biochemical studies provide further insight into this class of enzymes and allow a mechanism for catalysis consistent with other members of the Ntn-hydrolase superfamily to be proposed.

  7. Advanced stability indicating chemometric methods for quantitation of amlodipine and atorvastatin in their quinary mixture with acidic degradation products

    Science.gov (United States)

    Darwish, Hany W.; Hassan, Said A.; Salem, Maissa Y.; El-Zeany, Badr A.

    2016-02-01

    Two advanced, accurate and precise chemometric methods are developed for the simultaneous determination of amlodipine besylate (AML) and atorvastatin calcium (ATV) in the presence of their acidic degradation products in tablet dosage forms. The first method was Partial Least Squares (PLS-1) and the second was Artificial Neural Networks (ANN). PLS was compared to ANN models with and without variable selection procedure (genetic algorithm (GA)). For proper analysis, a 5-factor 5-level experimental design was established resulting in 25 mixtures containing different ratios of the interfering species. Fifteen mixtures were used as calibration set and the other ten mixtures were used as validation set to validate the prediction ability of the suggested models. The proposed methods were successfully applied to the analysis of pharmaceutical tablets containing AML and ATV. The methods indicated the ability of the mentioned models to solve the highly overlapped spectra of the quinary mixture, yet using inexpensive and easy to handle instruments like the UV-VIS spectrophotometer.

  8. Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model.

    Science.gov (United States)

    Yang, Yuqing; Chen, Ning; Chen, Ting

    2017-01-25

    The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors. We empirically show the effectiveness of the mLDM model using synthetic data, data from the TARA Oceans project, and a colorectal cancer dataset. Finally, we apply mLDM to 16S sequencing data from the western English Channel and report several associations. Our model can be used on both natural environmental and human metagenomic datasets, promoting the understanding of associations in the microbial community.

  9. A method for measuring fatty acid oxidation in C. elegans

    DEFF Research Database (Denmark)

    Elle, Ida Coordt; Rødkær, Steven Vestergaard; Fredens, Julius;

    2012-01-01

    The nematode C. elegans has during the past decade proven to be a valuable model organism to identify and examine molecular mechanisms regulating lipid storage and metabolism. While the primary approach has been to identify genes and pathways conferring alterations in lipid accumulation, only a few...... recent studies have recognized the central role of fatty acid degradation in cellular lipid homeostasis. In the present study, we show how complete oxidation of fatty acids can be determined in live C. elegans by examining oxidation of tritium-labeled fatty acids to tritiated H2O that can be measured......, the present methodology can be used to delineate the role of specific genes and pathways in the regulation of β-oxidation in C. elegans....

  10. A global census of marine microbes

    Digital Repository Service at National Institute of Oceanography (India)

    Amaral-Zettler, L.; Artigas, L.F.; Baross, J.; LokaBharathi, P.A; Boetius, A; Chandramohan, D.; Herndl, G.; Kogure, K.; Neal, P.; Pedros-Alio, C.; Ramette, A; Schouten, S.; Stal, L.; Thessen, A; De Leeuw, J.; Sogin, M.

    In this chapter we provide a brief history of what is known about marine microbial diversity, summarize our achievements in performing a global census of marine microbes, and reflect on the questions and priorities for the future of the marine...

  11. Zhongyuan Offers Drilling Service for Microbes

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhiyu

    2001-01-01

    @@ No. 1 Drilling Company of Zhongyuan Petroleum Exploration Bureau and US-based Microbes Inc.signed a drilling engineering contract for six wells in Jilin Oil Field worth more than 11 million yuan in mid-October 2001.

  12. Structural characterization of the acid-degraded secondary cell wall polymer of Geobacillus stearothermophilus PV72/p2.

    Science.gov (United States)

    Petersen, Bent O; Sára, Margit; Mader, Christoph; Mayer, Harald F; Sleytr, Uwe B; Pabst, Martin; Puchberger, Michael; Krause, Eberhard; Hofinger, Andreas; Duus, Jens Ø; Kosma, Paul

    2008-06-09

    The secondary cell wall polymer (SCWP) from Geobacillus stearothermophilus PV72/p2, which is involved in the anchoring of the surface-layer protein to the bacterial cell wall layer, is composed of 2-amino-2-deoxy- and 2-acetamido-2-deoxy-D-glucose, 2-acetamido-2-deoxy-D-mannose, and 2-acetamido-2-deoxy-D-mannuronic acid. The primary structure of the acid-degraded polysaccharide--liberated by HF-treatment from the cell wall--was determined by high-field NMR spectroscopy and mass spectrometry using N-acetylated and hydrolyzed polysaccharide derivatives as well as Smith-degradation. The polysaccharide was shown to consist of a tetrasaccharide repeating unit containing a pyruvic acid acetal at a side-chain 2-acetamido-2-deoxy-alpha-D-mannopyranosyl residue. Substoichiometric substitutions of the repeating unit were observed concerning the degree of N-acetylation of glucosamine residues and the presence of side-chain linked 2-acetamido-2-deoxy-beta-D-glucopyranosyl units: [Formula: see text].

  13. Growth, induction, and substrate specificity of dehydroabietic acid-degrading bacteria isolated from a kraft mill effluent enrichment.

    Science.gov (United States)

    Bicho, P A; Martin, V; Saddler, J N

    1995-09-01

    We investigated resin acid degradation in five bacteria isolated from a bleach kraft mill effluent enrichment. All of the bacteria grew on dehydroabietic acid (DHA), a resin acid routinely detected in pulping effluents, or glycerol as the sole carbon source. None of the strains grew on acetate or methanol. Glycerol-grown, high-density, resting-cell suspensions were found to undergo a lag for 2 to 4 h before DHA degradation commenced, suggesting that this activity was inducible. This was further investigated by spiking similar cultures with tetracycline, a protein synthesis inhibitor, at various times during the DHA disappearance curve. Cultures to which the antibiotic was added prior to the lag did not degrade DHA. Those that were spiked with the antibiotic after the lag phase (4 h) degraded DHA at the same rate as did controls with no added tetracycline. Therefore, de novo protein synthesis was required for DHA biodegradation, confirming that this activity is inducible. The five strains were also evaluated for their ability to degrade other resin acids. All strains behaved in a similar fashion. Unchlorinated abietane-type resin acids (abietic acid, DHA, and 7-oxo-DHA) were completely degraded within 7 days, whereas pimarane resin acids (sandaracopimaric acid, isopimaric acid, and pimaric acid) were poorly degraded (25% or less). Chlorination of DHA affected biodegradation, with both 12,14-dichloro-DHA and 14-chloro-DHA showing resistance to degradation. However, 50 to 60% of the 12-chloro-DHA was consumed within the same period.

  14. Fatty Liver

    Science.gov (United States)

    ... Abbreviations Weights & Measures ENGLISH View Professional English Deutsch Japanese Espaniol Find information on medical topics, symptoms, drugs, ... inside liver cells. Just consuming a high-fat diet does not result in fatty liver. Rarely, fat ...

  15. Ordinary Stoichiometry of Extraordinary Microbes

    Science.gov (United States)

    Neveu, M.; Poret-Peterson, A. T.; Anbar, A. D.; Elser, J. J.

    2013-12-01

    Life on Earth seems to be composed of the same chemical elements in relatively conserved stoichiometric proportions. However, this observation is largely based on observations of biota from habitats spanning a moderate range of temperature and chemical composition (e.g., temperate lakes, forests, grasslands, oceanic phytoplankton). Whether this stoichiometry is conserved in settings that differ radically from such "normal" planetary settings may provide insight into the habitability of environments with radically different stoichiometries, and into possible stoichiometries for putative life beyond Earth. Here we report the first measurements of elemental stoichiometries of microbial extremophiles from hot springs of Yellowstone National Park (YNP). These phototrophic and chemotrophic microbes were collected in locations spanning large ranges of temperature (ambient to boiling) and pH (1 to 9). Microbial biomass was carefully extracted from hot spring sediment substrata following a procedure adapted from [1], which conserves cellular elemental abundances [2]. Their C and N contents were determined by Elemental Analysis Isotope Ratio Mass Spectrometry, and their P and trace element (Mg, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, and non-biogenic Al and Ti) contents were measured by Inductively Coupled Plasma Mass Spectrometry. Residual mineral contamination was an issue in some samples with low measured C and N; we eliminated these from our results. Even in the remaining samples, contamination sometimes prevented accurate determinations of cellular Mg, Ca, Mn, and Fe abundances; however, the cellular Ni, Cu, Zn, and Mo contents were several-fold above contamination level. Although hot spring water and sediment elemental abundances varied by orders of magnitude, the data showed that the extremophiles have a major and trace element stoichiometry similar to those previously measured in "normal" microbial biomass [3-6]. For example, biomass C:N:P ratios resembled those

  16. Transcriptome and proteonome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis

    NARCIS (Netherlands)

    Dihal, A.A.; Hendriksen, P.J.M.; Charif, H.; Dekker, L.J.; IJsselstijn, L.; Boer, de V.C.J.; Alink, G.M.; Rietjens, I.M.C.M.; Woutersen, R.A.; Stierum, R.H.

    2008-01-01

    Quercetin has been shown to act as an anticarcinogen in experimental colorectal cancer (CRC). The aim of the present study was to characterize transcriptome and proteome changes occurring in the distal colon mucosa of rats supplemented with 10 g quercetin/kg diet for 11 wk. Transcriptome data analyz

  17. Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis

    NARCIS (Netherlands)

    Dihal, A.A.; Woude, H. van der; Hendriksen, P.J.M.; Charif, H.; Dekker, L.J.; IJsselstijn, L.; Boer, V.C.J. de; Alink, G.M.; Burgers, P.C.; Rietjens, I.M.C.M.; Woutersen, R.A.; Stierum, R.H.

    2008-01-01

    Quercetin has been shown to act as an anticarcinogen in experimental colorectal cancer (CRC). The aim of the present study was to characterize transcriptome and proteome changes occurring in the distal colon mucosa of rats supplemented with 10 g quercetin/kg diet for 11 wk. Transcriptome data analyz

  18. Modulation of host immunity by beneficial microbes.

    Science.gov (United States)

    Zamioudis, Christos; Pieterse, Corné M J

    2012-02-01

    In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and Rhizobium bacteria that fix atmospheric nitrogen for the plant. Several other types of beneficial soilborne microbes, such as plant-growth-promoting rhizobacteria and fungi with biological control activity, can stimulate plant growth by directly suppressing deleterious soilborne pathogens or by priming aboveground plant parts for enhanced defense against foliar pathogens or insect herbivores. The establishment of beneficial associations requires mutual recognition and substantial coordination of plant and microbial responses. A growing body of evidence suggests that beneficial microbes are initially recognized as potential invaders, after which an immune response is triggered, whereas, at later stages of the interaction, mutualists are able to short-circuit plant defense responses to enable successful colonization of host roots. Here, we review our current understanding of how symbiotic and nonsymbiotic beneficial soil microbes modulate the plant immune system and discuss the role of local and systemic defense responses in establishing the delicate balance between the two partners.

  19. Genitalia-associated microbes in insects.

    Science.gov (United States)

    Otti, Oliver

    2015-03-01

    In sexual reproduction different types of symbiotic relationships between insects and microbes have become established. For example, some bacteria have evolved almost exclusive vertical transmission and even define the compatibility of insect mating partners. Many strictly sexually transmitted diseases have also been described in insects. Apart from such rather specific relationships the role of opportunistic infections in the reproductive process has been widely neglected. Opportunistic microbes transmitted passively during mating might impose an energetic cost, as the immune system will need to be alert and will use resources to fight potential intruders. Through mating wounds and contaminated reproductive organs opportunistic microbes might be transferred to mating partners and even enter the body cavity. Females as the "receiving" sex are particularly likely to have evolved adaptations to avoid or reduce opportunistic infections. Males of several species show highly complex seminal fluids, which as well as containing components that influence a males' fertilization success, also possess antimicrobial substances. The role of antimicrobials in the reproductive process is not well understood. Some evidence hints at the protection of sperm against microbes, indicating a role for natural selection in shaping the evolution of reproductive traits. By highlighting the potential importance of microbes in sexual selection and their role in reproduction in general I will make a case for studies in sexual selection, especially the ones investigating postcopulatory processes, that should incorporate environmental, as well as genotypic variation, in reproductive traits.

  20. MicrobeWorld Radio and Communications Initiative

    Energy Technology Data Exchange (ETDEWEB)

    Barbara Hyde

    2006-11-22

    MicrobeWorld is a 90-second feature broadcast daily on more than 90 public radio stations and available from several sources as a podcast, including www.microbeworld.org. The feature has a strong focus on the use and adapatbility of microbes as alternative sources of energy, in bioremediation, their role in climate, and especially the many benefits and scientific advances that have resulting from decoding microbial genomes. These audio features are permanantly archived on an educational outreach site, microbeworld.org, where they are linked to the National Science Education Standards. They are also being used by instructors at all levels to introduce students to the multiple roles and potential of microbes, including a pilot curriculum program for middle-school students in New York.

  1. Natural transfer of viable microbes in space.

    Science.gov (United States)

    Mileikowsky, C; Cucinotta, F A; Wilson, J W; Gladman, B; Horneck, G; Lindegren, L; Melosh, J; Rickman, H; Valtonen, M; Zheng, J Q

    2000-06-01

    The possibility and probability of natural transfer of viable microbes from Mars to Earth and Earth to Mars traveling in meteoroids during the first 0.5 Ga and the following 4 Ga are investigated, including: --radiation protection against the galactic cosmic ray nuclei and the solar rays, dose rates as a function of the meteorite's radial column mass (radius x density), combined with dose rates generated by natural radioactivity within the meteorite; and survival curves for some bacterial species using NASA's HZETRN transport code --other factors affecting microbe survival: vacuum; central meteorite temperatures at launch, orbiting, and arrival; pressure and acceleration at launch; spontaneous DNA decay; metal ion migration --mean sizes and numbers of unshocked meteorites ejected and percentage falling on Earth, using current semiempirical results --viable flight times for the microbe species Bacillus subtilis and Deinococcus radiodurans R1 --the approximate fraction of microbes (with properties like the two species studied) viably arriving on Earth out of those ejected from Mars during the period 4 Ga BP to the present time, and during the 700 Ma from 4.5 to 3.8 Ga. Similarly, from Earth to Mars. The conclusion is that if microbes existed or exist on Mars, viable transfer to Earth is not only possible but also highly probable, due to microbes' impressive resistance to the dangers of space transfer and to the dense traffic of billions of martian meteorites which have fallen on Earth since the dawn of our planetary system. Earth-to-Mars transfer is also possible but at a much lower frequency.

  2. Metals, minerals and microbes: geomicrobiology and bioremediation.

    Science.gov (United States)

    Gadd, Geoffrey Michael

    2010-03-01

    Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social

  3. Electrifying microbes for the production of chemicals

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Zhang, Tian

    2015-01-01

    Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES) is one of the bioelectrochemical approaches developed in the last decade that could...... have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind...

  4. Flow injection analysis of organic peroxide explosives using acid degradation and chemiluminescent detection of released hydrogen peroxide.

    Science.gov (United States)

    Mahbub, Parvez; Zakaria, Philip; Guijt, Rosanne; Macka, Mirek; Dicinoski, Greg; Breadmore, Michael; Nesterenko, Pavel N

    2015-10-01

    The applicability of acid degradation of organic peroxides into hydrogen peroxide in a pneumatically driven flow injection system with chemiluminescence reaction with luminol and Cu(2+) as a catalyst (FIA-CL) was investigated for the fast and sensitive detection of organic peroxide explosives (OPEs). The target OPEs included hexamethylene triperoxide diamine (HMTD), triacetone triperoxide (TATP) and methylethyl ketone peroxide (MEKP). Under optimised conditions maximum degradations of 70% and 54% for TATP and HMTD, respectively were achieved at 162 µL min(-1), and 9% degradation for MEKP at 180 µL min(-1). Flow rates were precisely controlled in this single source pneumatic pressure driven multi-channel FIA system by model experiments on mixing of easily detectable component solutions. The linear range for detection of TATP, HMTD and H2O2 was 1-200 µM (r(2)=0.98-0.99) at both flow rates, while that for MEKP was 20-200 µM (r(2)=0.97) at 180 µL min(-1). The detection limits (LODs) obtained were 0.5 µM for TATP, HMTD and H2O2 and 10 µM for MEKP. The detection times varied from 1.5 to 3 min in this FIA-CL system. Whilst the LOD for H2O2 was comparable with those reported by other investigators, the LODs and analysis times for TATP and HMTD were superior, and significantly, this is the first time the detection of MEKP has been reported by FIA-CL.

  5. Microbes, Immunity, and Behavior: Psychoneuroimmunology Meets the Microbiome.

    Science.gov (United States)

    Dinan, Timothy G; Cryan, John F

    2017-01-01

    There is now a large volume of evidence to support the view that the immune system is a key communication pathway between the gut and brain, which plays an important role in stress-related psychopathologies and thus provides a potentially fruitful target for psychotropic intervention. The gut microbiota is a complex ecosystem with a diverse range of organisms and a sophisticated genomic structure. Bacteria within the gut are estimated to weigh in excess of 1 kg in the adult human and the microbes within not only produce antimicrobial peptides, short chain fatty acids, and vitamins, but also most of the common neurotransmitters found in the human brain. That the microbial content of the gut plays a key role in immune development is now beyond doubt. Early disruption of the host-microbe interplay can have lifelong consequences, not just in terms of intestinal function but in distal organs including the brain. It is clear that the immune system and nervous system are in continuous communication in order to maintain a state of homeostasis. Significant gaps in knowledge remain about the effect of the gut microbiota in coordinating the immune-nervous systems dialogue. However, studies using germ-free animals, infective models, prebiotics, probiotics, and antibiotics have increased our understanding of the interplay. Early life stress can have a lifelong impact on the microbial content of the intestine and permanently alter immune functioning. That early life stress can also impact adult psychopathology has long been appreciated in psychiatry. The challenge now is to fully decipher the molecular mechanisms that link the gut microbiota, immune, and central nervous systems in a network of communication that impacts behavior patterns and psychopathology, to eventually translate these findings to the human situation both in health and disease. Even at this juncture, there is evidence to pinpoint key sites of communication where gut microbial interventions either with drugs

  6. Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1)

    Science.gov (United States)

    Demidenko, Aleksandr; Akberdin, Ilya R.; Allemann, Marco; Allen, Eric E.; Kalyuzhnaya, Marina G.

    2017-01-01

    Methane utilization by methanotrophic bacteria is an attractive application for biotechnological conversion of natural or biogas into high-added-value products. Haloalcaliphilic methanotrophic bacteria belonging to the genus Methylomicrobium are among the most promising strains for methane-based biotechnology, providing easy and inexpensive cultivation, rapid growth, and the availability of established genetic tools. A number of methane bioconversions using these microbial cultures have been discussed, including the derivation of biodiesel, alkanes, and OMEGA-3 supplements. These compounds are derived from bacterial fatty acid pools. Here, we investigate fatty acid biosynthesis in Methylomicrobium buryatense 5G(B1). Most of the genes homologous to typical Type II fatty acid biosynthesis pathways could be annotated by bioinformatics analyses, with the exception of fatty acid transport and regulatory elements. Different approaches for improving fatty acid accumulation were investigated. These studies indicated that both fatty acid degradation and acetyl- and malonyl-CoA levels are bottlenecks for higher level fatty acid production. The best strain generated in this study synthesizes 111 ± 2 mg/gDCW of extractable fatty acids, which is ~20% more than the original strain. A candidate gene for fatty acid biosynthesis regulation, farE, was identified and studied. Its deletion resulted in drastic changes to the fatty acid profile, leading to an increased pool of C18-fatty acid methyl ester. The FarE-regulon was further investigated by RNA-seq analysis of gene expression in farE-knockout mutants and farE-overexpressing strains. These gene profiles highlighted a novel set of enzymes and regulators involved in fatty acid biosynthesis. The gene expression and fatty acid profiles of the different farE-strains support the hypothesis that metabolic fluxes upstream of fatty acid biosynthesis restrict fatty acid production in the methanotroph. PMID:28119683

  7. Gut Microbes Linked to Rheumatoid Arthritis

    Science.gov (United States)

    ... of microorganisms that live in and on the human body. These microbes outnumber the body’s cells by 10 ... this is indeed the case.” — by Carol Torgan, Ph.D. Related Links Feeling Out of ... Autoimmune Diseases Rheumatoid Arthritis References: Expansion ...

  8. Plant immune responses triggered by beneficial microbes

    NARCIS (Netherlands)

    Wees, A.C.M. van; Ent, S. van der; Pieterse, C.M.J.

    2008-01-01

    Beneficial soil-borne microorganisms, such as plant growth promoting rhizobacteria and mycorrhizal fungi,can improve plant performance by inducing systemic defense responses that confer broad-spectrum resistance to plant pathogens and even insect herbivores. Different beneficial microbe-associated m

  9. Natural products from microbes associated with insects

    DEFF Research Database (Denmark)

    Beemelmanns, Christine; Guo, Huijuan; Rischer, Maja;

    2016-01-01

    Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We...

  10. Induced systemic resistance by beneficial microbes

    NARCIS (Netherlands)

    Pieterse, Corné M J|info:eu-repo/dai/nl/113115113; Zamioudis, Christos|info:eu-repo/dai/nl/313964742; Berendsen, Roeland L.|info:eu-repo/dai/nl/304824151; Weller, David M.; van Wees, Saskia C M|info:eu-repo/dai/nl/185445373; Bakker, Peter A H M|info:eu-repo/dai/nl/074744623

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of patho

  11. Induced systemic resistance by beneficial microbes

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Zamioudis, C.; Berendsen, R.L.; Weller, D.M.; Van Wees, S.C.M.; Bakker, P.A.H.M.

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of patho

  12. Induced systemic resistance by beneficial microbes

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Zamioudis, C.; Berendsen, R.L.; Weller, D.M.; Van Wees, S.C.M.; Bakker, P.A.H.M.

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of patho

  13. Multiscale simulation of microbe structure and dynamics.

    Science.gov (United States)

    Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V; Cheluvaraja, Srinath C; Ortoleva, Peter J

    2011-10-01

    A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin.

  14. Microbe inhibition by Tribolium flour beetles varies with beetle species, strain, sex, and microbe group.

    Science.gov (United States)

    Prendeville, Holly R; Stevens, Lori

    2002-06-01

    Tribolium flour beetles produce defensive compounds, including quinones, putatively aimed at deterring predators and inhibiting microbes. Here we examine how effective the defensive secretions of Tribolium confusum and T. castaneum are at inhibiting growth of various microbes and how this varies with species, geographic strain, and sex of the beetles. We explore differences at both the kingdom and species level of common flour microbes in their susceptibility to defensive compounds. Beetle species and strains vary in their ability to inhibit microbial growth. In addition, microbes vary in their sensitivity to the beetles' defense compounds. The capability to suppress microbial growth is likely under stabilizing selection with optimum quinone production varying among populations and may be dependent on several environmental factors including temperature, humidity, and predators.

  15. Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome.

    Science.gov (United States)

    Bakker, Matthew G; Schlatter, Daniel C; Otto-Hanson, Lindsey; Kinkel, Linda L

    2014-03-01

    A conceptual model emphasizing direct host-microbe interactions has dominated work on host-associated microbiomes. To understand plant-microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant-plant and microbe-microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics. © 2013 John Wiley & Sons Ltd.

  16. The role of lipids in host microbe interactions.

    Science.gov (United States)

    Lang, Roland; Mattner, Jochen

    2017-06-01

    Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

  17. Induced systemic resistance by beneficial microbes.

    Science.gov (United States)

    Pieterse, Corné M J; Zamioudis, Christos; Berendsen, Roeland L; Weller, David M; Van Wees, Saskia C M; Bakker, Peter A H M

    2014-01-01

    Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.

  18. Electrifying microbes for the production of chemicals

    Directory of Open Access Journals (Sweden)

    Pier-Luc eTremblay

    2015-03-01

    Full Text Available Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable strategy to reduce our dependence on oil. Microbial electrosynthesis (MES is one of the bioelectrochemical approaches developed in the last decade that could have critical impact on the current methods of chemical synthesis. MES is a process in which electroautotrophic microbes use electrical current as electron source to reduce CO2 to multicarbon organics. Electricity necessary for MES can be harvested from renewable resources such as solar energy, wind turbine or wastewater treatment processes. The net outcome is that renewable energy is stored in the covalent bonds of organic compounds synthesized from greenhouse gas. This review will discuss the future of MES and the challenges that lie ahead for its development into a mature technology.

  19. Darwin, microbes and evolution by natural selection.

    Science.gov (United States)

    Moxon, E Richard

    2011-01-01

    Born 200 years ago, Darwin's revolutionary ideas were derived largely from his observations on life forms that evolved relatively recently, including various flowering plants, worms, birds and domesticated animals. Yet, life appeared on planet earth close to 4 billion years ago in the form of unicellular organisms collectively called bacteria. It was only shortly after "On the Origin of Species" was published (1859) that the "germ theory" of infectious diseases was formulated. Microbes (viruses, bacteria, fungi and microparasites) received scant mention in Darwin's writings, although pioneers of the Golden Age of Bacteriology, such as Louis Pasteur (1822-1895), were contemporaries. Today, microbes offer extraordinary testimony and powerful model systems of direct relevance to the essentials of Darwinian selection, such as understanding microbial-host interactions, the evolution of pathogens and the emergence of drug- or vaccine-related resistance.

  20. Ecological Interactions Between Metals and Microbes

    Energy Technology Data Exchange (ETDEWEB)

    Konopka, Allan E.

    2004-06-01

    Analyses of chromium resistant microbes. Culturable xylene-degrading and chromate-resistant microbes were obtained from chronically cocontaminated soil using a microcosm enrichment technique, and shown to correlate to dominant soil populations using culture independent techniques. The soil microbial community proved able to mount a respiratory response to addition of xylene in the presence of chromate. The majority of isolates belonged to the ubiquitous but poorly studied high %G+C Gram positive genus Arthrobacter, and exhibited considerable genotypic and phenotypic variability. Phenotypic assays uncovered a wide variation in the levels of chromate resistance, even between very closely related strains. Primers designed against conserved motifs in the known chrA chromate efflux gene failed to detect similar sequences among the chromate resistant Arthrobacter isolates obtained through enrichment.

  1. Dietary microbes modulate transgenerational cancer risk.

    Science.gov (United States)

    Poutahidis, Theofilos; Varian, Bernard J; Levkovich, Tatiana; Lakritz, Jessica R; Mirabal, Sheyla; Kwok, Caitlin; Ibrahim, Yassin M; Kearney, Sean M; Chatzigiagkos, Antonis; Alm, Eric J; Erdman, Susan E

    2015-04-01

    Environmental factors are suspected in the increase of obesity and cancer in industrialized countries but are poorly understood. Here, we used animal models to test how future generations may be affected by Westernized diets. We discover long-term consequences of grandmothers' in utero dietary exposures, leading to high rates of obesity and frequent cancers of lung and liver in two subsequent generations of mice. Transgenerational effects were transplantable using diet-associated bacteria communities alone. Consequently, feeding of beneficial microbes was sufficient to lower transgenerational risk for cancer and obesity regardless of diet history. Targeting microbes may be a highly effective population-based approach to lower risk for cancer. ©2015 American Association for Cancer Research.

  2. The Study of the Microbes Degraded Polystyrene

    Directory of Open Access Journals (Sweden)

    Zhi-Long Tang

    2017-01-01

    Full Text Available Under the observation that Tenebrio molitor and Zophobas morio could eat polystyrene (PS, we setup the platform to screen the gut microbes of these two worms. To take advantage of that Tenebrio molitor and Zophobas morio can eat and digest polystyrene as its diet, we analyzed these special microbes with PS plate and PS turbidity system with time courses. There were two strains TM1 and ZM1 which isolated from Tenebrio molitor and Zophobas morio, and were identified by 16S rDNA sequencing. The results showed that TM1 and ZM1 were cocci-like and short rod shape Gram-negative bacteria under microscope. The PS plate and turbidity assay showed that TM1 and ZM1 could utilize polystyrene as their carbon sources. The further study of PS degraded enzyme and cloning warrants our attention that this platform will be an excellent tools to explore and solve this problem.

  3. Working with miraculous microbes against corrosion

    Institute of Scientific and Technical Information of China (English)

    XIN Ling

    2009-01-01

    @@ Microorganisms, despite of their simple structure and tiny size, are often vital to humans and the environment. You might know about their contributions to the Earth's carbon cycle and amazing ability to decompose waste products. But have you ever heard of microbes that eat away undersea metal, or those who protect iron from corrosion? Some may even wow you with the feat to generate electricity and clean up polluted water!

  4. An Astrobiology Microbes Exhibit and Education Module

    Science.gov (United States)

    Lindstrom, Marilyn M.; Allen, Jaclyn S.; Stocco, Karen; Tobola, Kay; Olendzenski, Lorraine

    2001-01-01

    Telling the story of NASA-sponsored scientific research to the public in exhibits is best done by partnerships of scientists and museum professionals. Likewise, preparing classroom activities and training teachers to use them should be done by teams of teachers and scientists. Here we describe how we used such partnerships to develop a new astrobiology augmentation to the Microbes! traveling exhibit and a companion education module. "Additional information is contained in the original extended abstract."

  5. The MicrOBS study around Taiwan

    Science.gov (United States)

    Liang, C.; Lee, C.

    2007-12-01

    Since 2005, we have managed 16 MicrOBS, designed by the French IFREMER, to study the earthquake and crustal structute around Taiwan. The instrument itself is very light (20 kgs) and easy to operate. This OBS has a measuring period up to 2 weeks in the seafloor. We have conducted the works, aiming to get a better understanding of the ¡§marine¡¨ earthquakes, from the in situ small event to the big earthquake. For example, a study of the seismic gaps in the offshore region becomes workable as compare with the time when we only have the land seismological instruments. We have also used this instrument to obtain a detail study of the gas hydrate and free gas zone. Whenever a large seismic source is available, we then conduct the local and regional crustal studies, such as in the Philippine Sea and South China Sea. In the last 3 years, we have directed 285 deployments of MicrOBS around Taiwan. More than 80 per cent of the natural earthquakes in Taiwan (in an average of about 15,000 events of Mm greater than 2 events per year) were occurred in offshore area. Big earthquakes (i.e. Mm greater than 6) are more often happen in the offshore area than that in the onshore region. Therefore, the tools (MicrOBS and OBS) to measure these ¡§marine¡¨ earthquakes become essential to understand the character and origin of crustal dynamics, particularly in the seismogenic zone.

  6. The Role of Microbes in the Nutrition of Detritivorous Invertebrates: A Stoichiometric Analysis

    Science.gov (United States)

    Anderson, Thomas R.; Pond, David W.; Mayor, Daniel J.

    2017-01-01

    Detritus represents an important pool in the global carbon cycle, providing a food source for detritivorous invertebrates that are conspicuous components of almost all ecosystems. Our knowledge of how these organisms meet their nutritional demands on a diet that is typically comprised of refractory, carbon-rich compounds nevertheless remains incomplete. “Trophic upgrading” of detritus by the attached microbial community (enhancement of zooplankton diet by the inclusion of heterotrophic protozoans) represents a potential source of nutrition for detritivores as both bacteria and their flagellated protistan predators are capable of biosynthesizing essential micronutrients such as polyunsaturated fatty acids (PUFAs). There is however a trade-off because although microbes enhance the substrate in terms of its micronutrient content, the quantity of organic carbon is diminished though metabolic losses as energy passes through the microbial food web. Here, we develop a simple stoichiometric model to examine this trade-off in the nutrition of detritivorous copepods inhabiting the mesopelagic zone of the ocean, focusing on their requirements for carbon and an essential PUFA, docosahexaenoic acid (DHA). Results indicate that feeding on microbes may be a highly favorable strategy for these invertebrates, although the potential for carbon to become limiting when consuming a microbial diet exists because of the inefficiencies of trophic transfer within the microbial food web. Our study highlights the need for improved knowledge at the detritus-microbe-metazoan interface, including interactions between the physiology and ecology of the associated organisms. PMID:28101083

  7. Plant-driven selection of microbes in the rhizosphere and plant-microbe feedbacks

    Directory of Open Access Journals (Sweden)

    Adil ESSARIOUI

    2017-09-01

    Full Text Available Plant impacts on soil microbial communities and plant-microbe feedbacks have become the focus of much research. Recent advances in plant-microbe interactions investigations show that plants are able to shape their rhizosphere microbiome through diverse mechanisms. In this review, we gather findings from across multiple studies on the role of plants in altering the structure and functions of microbes in the rhizosphere. In addition, we discuss the roles of diverse phytochemicals in mediating these effects. Finally, we highlight that selective enrichment of specific microorganisms in the rhizosphere has either negative feedbacks, with pathogen accumulation in the rhizosphere; or, perhaps most importantly, positive feedbacks as a result of the recruitment of a beneficial microflora. Insights into the mechanisms that underpin plant selection of microbial communities with positive feedbacks will provide new opportunities to increase crop production.

  8. Protecting drinking water: Rapid detection of human fecal contamination, injured and non-culturable pathogenic microbes in water systems

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C.; Nivens, D.E.; Arrage, A.A.; Appelgate, B.M.; Reardon, S.R.; Sayler, G.S.

    1996-05-01

    The rapid, potentially-automatable extraction of filter retentates has allowed quantitative detection of the unique biomarker for human fecal contamination, coprostanol, and the signature lipid biomarkers for total cellular biomass, viable cellular biomass, lipopolysaccharide (endotoxin). This method may be integrated with DNA based gene probe analysis for specific strains and enzyme activities. Not only does the analysis provide for detection of injured and non-culturable microbes but it also provides biomarkers characteristic of microbes exposed to biocides and disinfectants that can be utilized to monitor effectiveness of water mitigation/treatment. The analysis schemes involve filtration of the water or direct extraction of biofilms in sidestream chambers, supercritical fluid and/or liquid extraction, derivatization, and analysis of ``signature`` patterns by gas chromatography/mass spectrometry. Signature lipid biomarkers of interest are diglycerides, steroids including coprostanol and its isomers, poly-{beta}- hydroxyalcanoates (PHA), phospholipid ester-linked fatty acids (PLFA), and the lipopolysaccharide lipid A hydroxy fatty acids. PLFA found in polar lipid fractions estimate total viable cellular biomass, whereas the total cellular biomass can be calculated from diglyceride/phospholipid ester-linked fatty acids ratios. Furthermore, direct evidence of mitigation/treatment effectiveness can be ascertained by detection of diglycerides, respiratory quinones, PHA, and PLFA markers indicative of metabolic stress and toxicity such as trans monoenoic PLFA as well as oxirane and dicarboxylic fatty acids derived from the PLFA.

  9. Companion animals symposium: microbes and gastrointestinal health of dogs and cats.

    Science.gov (United States)

    Suchodolski, J S

    2011-05-01

    Recent molecular studies have revealed complex bacterial, fungal, archaeal, and viral communities in the gastrointestinal tract of dogs and cats. More than 10 bacterial phyla have been identified, with Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria constituting more than 99% of all gut microbiota. Microbes act as a defending barrier against invading pathogens, aid in digestion, provide nutritional support for enterocytes, and play a crucial role in the development of the immune system. Of significance for gastrointestinal health is their ability to ferment dietary substrates into short-chain fatty acids, predominantly to acetate, propionate, and butyrate. However, microbes can have also a detrimental effect on host health. Specific pathogens (e.g., Salmonella, Campylobacter jejuni, and enterotoxigenic Clostridium perfringens) have been implicated in acute and chronic gastrointestinal disease. Compositional changes in the small intestinal microbiota, potentially leading to changes in intestinal permeability and digestive function, have been suggested in canine small intestinal dysbiosis or antibiotic-responsive diarrhea. There is mounting evidence that microbes play an important role in the pathogenesis of canine and feline inflammatory bowel disease (IBD). Current theories for the development of IBD favor a combination of environmental factors, the intestinal microbiota, and a genetic susceptibility of the host. Recent studies have revealed a genetic susceptibility for defective bacterial clearance in Boxer dogs with granulomatous colitis. Differential expression of pathogen recognition receptors (i.e., Toll-like receptors) were identified in dogs with chronic enteropathies. Similarly to humans, a microbial dysbiosis has been identified in feline and canine IBD. Commonly observed microbial changes are increased Proteobacteria (i.e., Escherichia coli) with concurrent decreases in Firmicutes, especially a reduced diversity in Clostridium

  10. Natural products from microbes associated with insects

    Directory of Open Access Journals (Sweden)

    Christine Beemelmanns

    2016-02-01

    Full Text Available Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We demonstrate that the exploration of specific microbial–host interactions, in combination with multidisciplinary dereplication processes, has emerged as a successful strategy to identify novel chemical entities and to shed light on the ecology and evolution of defensive associations.

  11. Will ocean acidification affect marine microbes?

    Science.gov (United States)

    Joint, Ian; Doney, Scott C; Karl, David M

    2011-01-01

    The pH of the surface ocean is changing as a result of increases in atmospheric carbon dioxide (CO(2)), and there are concerns about potential impacts of lower pH and associated alterations in seawater carbonate chemistry on the biogeochemical processes in the ocean. However, it is important to place these changes within the context of pH in the present-day ocean, which is not constant; it varies systematically with season, depth and along productivity gradients. Yet this natural variability in pH has rarely been considered in assessments of the effect of ocean acidification on marine microbes. Surface pH can change as a consequence of microbial utilization and production of carbon dioxide, and to a lesser extent other microbially mediated processes such as nitrification. Useful comparisons can be made with microbes in other aquatic environments that readily accommodate very large and rapid pH change. For example, in many freshwater lakes, pH changes that are orders of magnitude greater than those projected for the twenty second century oceans can occur over periods of hours. Marine and freshwater assemblages have always experienced variable pH conditions. Therefore, an appropriate null hypothesis may be, until evidence is obtained to the contrary, that major biogeochemical processes in the oceans other than calcification will not be fundamentally different under future higher CO(2)/lower pH conditions.

  12. Collective decision-making in microbes

    Science.gov (United States)

    Ross-Gillespie, Adin; Kümmerli, Rolf

    2014-01-01

    Microbes are intensely social organisms that routinely cooperate and coordinate their activities to express elaborate population level phenotypes. Such coordination requires a process of collective decision-making, in which individuals detect and collate information not only from their physical environment, but also from their social environment, in order to arrive at an appropriately calibrated response. Here, we present a conceptual overview of collective decision-making as it applies to all group-living organisms; we introduce key concepts and principles developed in the context of animal and human group decisions; and we discuss, with appropriate examples, the applicability of each of these concepts in microbial contexts. In particular, we discuss the roles of information pooling, control skew, speed vs. accuracy trade-offs, local feedbacks, quorum thresholds, conflicts of interest, and the reliability of social information. We conclude that collective decision-making in microbes shares many features with collective decision-making in higher taxa, and we call for greater integration between this fledgling field and other allied areas of research, including in the humanities and the physical sciences. PMID:24624121

  13. Diversity of microbes in amniotic fluid.

    Science.gov (United States)

    DiGiulio, Daniel B

    2012-02-01

    Recent polymerase chain reaction (PCR)-based studies estimate the prevalence of microbial invasion of the amniotic cavity (MIAC) to be ≥30-50% higher than that detected by cultivation-based methods. Some species that have been long implicated in causing MIAC remain among the common invaders (e.g. Ureaplasma spp., Mycoplasma spp., Fusobacterium spp. Streptococcus spp., Bacteroides spp. and Prevotella spp.). Yet we now know from studies based on PCR of the 16S ribosomal DNA that cultivation-resistant anaerobes belonging to the family Fusobacteriaceae (particularly Sneathia sanguinegens, and Leptotrichia spp.) are also commonly found in amniotic fluid. Other diverse microbes detected by PCR of amniotic fluid include as-yet uncultivated and uncharacterized species. The presence of some microbial taxa is associated with specific host factors (e.g. Candida spp. and an indwelling intrauterine device). It appears that MIAC is polymicrobial in 24-67% of cases, but the potential role of pathogen synergy is poorly understood. A causal relationship between diverse microbes, as detected by PCR, and preterm birth is supported by types of association (e.g. space, time and dose) proposed as alternatives to Koch's postulates for inferring causality from molecular findings. The microbial census of the amniotic cavity remains unfinished. A more complete understanding may inform future research directions leading to improved strategies for preventing, diagnosing and treating MIAC.

  14. Collective decision-making in microbes.

    Science.gov (United States)

    Ross-Gillespie, Adin; Kümmerli, Rolf

    2014-01-01

    Microbes are intensely social organisms that routinely cooperate and coordinate their activities to express elaborate population level phenotypes. Such coordination requires a process of collective decision-making, in which individuals detect and collate information not only from their physical environment, but also from their social environment, in order to arrive at an appropriately calibrated response. Here, we present a conceptual overview of collective decision-making as it applies to all group-living organisms; we introduce key concepts and principles developed in the context of animal and human group decisions; and we discuss, with appropriate examples, the applicability of each of these concepts in microbial contexts. In particular, we discuss the roles of information pooling, control skew, speed vs. accuracy trade-offs, local feedbacks, quorum thresholds, conflicts of interest, and the reliability of social information. We conclude that collective decision-making in microbes shares many features with collective decision-making in higher taxa, and we call for greater integration between this fledgling field and other allied areas of research, including in the humanities and the physical sciences.

  15. Biological Function of REE in Plants & Microbes

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Rare earth elements (REE) and their compounds are widely applied in agronomic and medical fields for many years. The bioinorganic chemical research of REE during the past few years indicates that REE play important roles in the promotion of photosynthetic rate as well as root absorption, regulation of hormone and nitrogen metabolism, and suppression of microbes, etc. The metallic or non-metallic targets of key biomolecule in various physiological processes can be chosen by REE for the chelation or replacement, which enables REE to regulate the biological functions or behaviors of those biomolecule and consequently leads to significant embodiment of biological function of REE in plants and microbes.Overdose of REE, however, shows an inhibitory effect on living organisms. Therefore, this paper proposes two suggestions that will be available in the extension of full use of REE's biological function. One is to obey the dose law of REE and control REE concentrations within a safe range. The other is to further test the bioaccumulation and long-period influence of REE on organisms.

  16. Soil plant microbe interactions in phytoremediation.

    Science.gov (United States)

    Karthikeyan, R; Kulakow, P A

    2003-01-01

    Use of vegetation in remediation of soil and groundwater contaminated with organic materials is a promising, cost-effective alternative to the more established treatment methods used at hazardous waste sites. Plants can transpire groundwater and lower the concentrations of organic contaminants in soils and groundwater. The evapotranspirational activity of vegetation acts as a natural pump-and-treatment system. Plants have shown the capacity to absorb, uptake, and convert organic contaminants to less toxic metabolites in laboratory and field studies. Vegetation also plays a significant role in bioremediation. This is because plants stimulate the degradation of organic compounds in the rhizosphere by the release of root exudates and enzymes. Success of any plant-based remediation system depends on the interaction of plants with the surrounding soil medium and the contaminant. Knowing the fate of an organic contaminant in the soil can help determine the persistence of the contaminant in the terrestrial environment and ultimately the success of any remediation method. Also, an understanding is needed of soil-plant-microbe interactions that determine the fate of organic contaminants in the soil-plant ecosystem. This paper presents an overview of the subsurface environment and fate and transport processes of organic contaminants as affected by soil-plant-microbe interactions.

  17. Lipid and fatty acid metabolism in Ralstonia eutropha: relevance for the biotechnological production of value-added products.

    Science.gov (United States)

    Riedel, Sebastian L; Lu, Jingnan; Stahl, Ulf; Brigham, Christopher J

    2014-02-01

    Lipid and fatty acid metabolism has been well studied in model microbial organisms like Escherichia coli and Bacillus subtilis. The major precursor of fatty acid biosynthesis is also the major product of fatty acid degradation (β-oxidation), acetyl-CoA, which is a key metabolite for all organisms. Controlling carbon flux to fatty acid biosynthesis and from β-oxidation allows for the biosynthesis of natural products of biotechnological importance. Ralstonia eutropha can utilize acetyl-CoA from fatty acid metabolism to produce intracellular polyhydroxyalkanoate (PHA). R. eutropha can also be engineered to utilize fatty acid metabolism intermediates to produce different PHA precursors. Metabolism of lipids and fatty acids can be rerouted to convert carbon into other value-added compounds like biofuels. This review discusses the lipid and fatty acid metabolic pathways in R. eutropha and how they can be used to construct reagents for the biosynthesis of products of industrial importance. Specifically, how the use of lipids or fatty acids as the sole carbon source in R. eutropha cultures adds value to these biotechnological products will be discussed here.

  18. Degradation of Microbes for the Crude Oil Contaminants

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    Production and storage-transportation of crude oil can not only give rise to soil pollution but also destroy ecological environment. Degradation of microbes for oily soil was studied with the instnunent, Geofina Hydrocarbon Meter (GHM), by experimental analysis qualitatively and quantitatively in the paper. Analytical result showed that the crude oil could be considerably degraded by eating-oil microbes in oily soil and the number of eating-oil microbes increased while the working hours of oil-well risi...

  19. A comparison of anaerobic 2, 4-dichlorophenoxy acetic acid degradation in single-fed and sequencing batch reactor systems

    Science.gov (United States)

    Elefsiniotis, P.; Wareham, D. G.; Fongsatitukul, P.

    2017-08-01

    This paper compares the practical limits of 2, 4-dichlorophenoxy acetic acid (2,4-D) degradation that can be obtained in two laboratory-scale anaerobic digestion systems; namely, a sequencing batch reactor (SBR) and a single-fed batch reactor (SFBR) system. The comparison involved synthesizing a decade of research conducted by the lead author and drawing summative conclusions about the ability of each system to accommodate industrial-strength concentrations of 2,4-D. In the main, 2 L liquid volume anaerobic SBRs were used with glucose as a supplemental carbon source for both acid-phase and two-phase conditions. Volatile fatty acids however were used as a supplemental carbon source for the methanogenic SBRs. The anaerobic SBRs were operated at an hydraulic retention time of 48 hours, while being subjected to increasing concentrations of 2,4-D. The SBRs were able to degrade between 130 and 180 mg/L of 2,4-D depending upon whether they were operated in the acid-phase or two-phase regime. The methanogenic-only phase did not achieve 2,4-D degradation however this was primarily attributed to difficulties with obtaining a sufficiently long SRT. For the two-phase SFBR system, 3.5 L liquid-volume digesters were used and no difficulty was experienced with degrading 100 % of the 2,4-D concentration applied (300 mg/L).

  20. FadD is required for utilization of endogenous fatty acids released from membrane lipids.

    Science.gov (United States)

    Pech-Canul, Ángel; Nogales, Joaquina; Miranda-Molina, Alfonso; Álvarez, Laura; Geiger, Otto; Soto, María José; López-Lara, Isabel M

    2011-11-01

    FadD is an acyl coenzyme A (CoA) synthetase responsible for the activation of exogenous long-chain fatty acids (LCFA) into acyl-CoAs. Mutation of fadD in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti promotes swarming motility and leads to defects in nodulation of alfalfa plants. In this study, we found that S. meliloti fadD mutants accumulated a mixture of free fatty acids during the stationary phase of growth. The composition of the free fatty acid pool and the results obtained after specific labeling of esterified fatty acids with a Δ5-desaturase (Δ5-Des) were in agreement with membrane phospholipids being the origin of the released fatty acids. Escherichia coli fadD mutants also accumulated free fatty acids released from membrane lipids in the stationary phase. This phenomenon did not occur in a mutant of E. coli with a deficient FadL fatty acid transporter, suggesting that the accumulation of fatty acids in fadD mutants occurs inside the cell. Our results indicate that, besides the activation of exogenous LCFA, in bacteria FadD plays a major role in the activation of endogenous fatty acids released from membrane lipids. Furthermore, expression analysis performed with S. meliloti revealed that a functional FadD is required for the upregulation of genes involved in fatty acid degradation and suggested that in the wild-type strain, the fatty acids released from membrane lipids are degraded by β-oxidation in the stationary phase of growth.

  1. Rhizosphere interactions: root exudates, microbes and microbial communities

    National Research Council Canada - National Science Library

    Huang, Xing-Feng; Chaparro, Jacqueline M; Reardon, Kenneth F; Zhang, Ruifu; Shen, Qirong; Vivanco, Jorge M

    2014-01-01

    .... In this review, we summarize recent progress made in unraveling the interactions between plants and rhizosphere microbes through plant root exudates, focusing on how root exudate compounds mediate...

  2. Engineered Production of Short Chain Fatty Acid in Escherichia coli Using Fatty Acid Synthesis Pathway.

    Science.gov (United States)

    Jawed, Kamran; Mattam, Anu Jose; Fatma, Zia; Wajid, Saima; Abdin, Malik Z; Yazdani, Syed Shams

    2016-01-01

    Short-chain fatty acids (SCFAs), such as butyric acid, have a broad range of applications in chemical and fuel industries. Worldwide demand of sustainable fuels and chemicals has encouraged researchers for microbial synthesis of SCFAs. In this study we compared three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron, for production of SCFAs in Escherichia coli utilizing native fatty acid synthesis (FASII) pathway and modulated the genetic and bioprocess parameters to improve its yield and productivity. E. coli strain expressing tesBT gene yielded maximum butyric acid titer at 1.46 g L-1, followed by tesBF at 0.85 g L-1 and tesAT at 0.12 g L-1. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. The modulation of genetic factors that are known to influence long chain fatty acid production, such as deletion of the fadD and fadE that initiates the fatty acid degradation cycle and overexpression of fadR that is a global transcriptional activator of fatty acid biosynthesis and repressor of degradation cycle, did not improve the butyric acid titer significantly. Use of chemical inhibitor cerulenin, which restricts the fatty acid elongation cycle, increased the butyric acid titer by 1.7-fold in case of TesBF, while it had adverse impact in case of TesBT. In vitro enzyme assay indicated that cerulenin also inhibited short chain specific thioesterase, though inhibitory concentration varied according to the type of thioesterase used. Further process optimization followed by fed-batch cultivation under phosphorous limited condition led to production of 14.3 g L-1 butyric acid and 17.5 g L-1 total free fatty acid at 28% of theoretical yield. This study expands our understanding of SCFAs production in E. coli through FASII pathway and highlights role of genetic and process optimization to enhance the desired product.

  3. Engineered Production of Short Chain Fatty Acid in Escherichia coli Using Fatty Acid Synthesis Pathway

    Science.gov (United States)

    Jawed, Kamran; Mattam, Anu Jose; Fatma, Zia; Wajid, Saima; Abdin, Malik Z.; Yazdani, Syed Shams

    2016-01-01

    Short-chain fatty acids (SCFAs), such as butyric acid, have a broad range of applications in chemical and fuel industries. Worldwide demand of sustainable fuels and chemicals has encouraged researchers for microbial synthesis of SCFAs. In this study we compared three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron, for production of SCFAs in Escherichia coli utilizing native fatty acid synthesis (FASII) pathway and modulated the genetic and bioprocess parameters to improve its yield and productivity. E. coli strain expressing tesBT gene yielded maximum butyric acid titer at 1.46 g L-1, followed by tesBF at 0.85 g L-1 and tesAT at 0.12 g L-1. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. The modulation of genetic factors that are known to influence long chain fatty acid production, such as deletion of the fadD and fadE that initiates the fatty acid degradation cycle and overexpression of fadR that is a global transcriptional activator of fatty acid biosynthesis and repressor of degradation cycle, did not improve the butyric acid titer significantly. Use of chemical inhibitor cerulenin, which restricts the fatty acid elongation cycle, increased the butyric acid titer by 1.7-fold in case of TesBF, while it had adverse impact in case of TesBT. In vitro enzyme assay indicated that cerulenin also inhibited short chain specific thioesterase, though inhibitory concentration varied according to the type of thioesterase used. Further process optimization followed by fed-batch cultivation under phosphorous limited condition led to production of 14.3 g L-1 butyric acid and 17.5 g L-1 total free fatty acid at 28% of theoretical yield. This study expands our understanding of SCFAs production in E. coli through FASII pathway and highlights role of genetic and process optimization to enhance the desired product. PMID:27466817

  4. Arsenic transport in prokaryotes and eukaryotic microbes.

    Science.gov (United States)

    Rosen, Barry P; Tamás, Markus J

    2010-01-01

    Aquaporins (AQPs) and aquaglyceroporins facilitate transport of a broad spectrum of substrates such as water, glycerol and other small uncharged solutes. More recently, AQPs ave also been shown to facilitate diffusion of metalloids such as arsenic (As) and antimony (Sb). At neutral pH, the trivalent forms of these metalloids are structurally similar to glycerol and hence they can enter cells through AQPs. As- and Sb-containing compounds are toxic to cells, yet both metalloids are used as chemotherapeutic agents for treating acute promyelocytic leukemia and diseases caused by protozoan parasites. In this chapter, we will review the role of AQPs and other proteins in metalloid transport in prokaryotes and eukaryotic microbes.

  5. Gut ecosystem: how microbes help us.

    Science.gov (United States)

    Martín, R; Miquel, S; Ulmer, J; Langella, P; Bermúdez-Humarán, L G

    2014-09-01

    The human gut houses one of the most complex and abundant ecosystems composed of up to 1013-1014 microorganisms. Although the anthropocentric concept of life has concealed the function of microorganisms inside us, the important role of gut bacterial community in human health is well recognised today. Moreover, different microorganims, which are commonly present in a large diversity of food products, transit through our gut every day adding in some cases a beneficial effect to our health (probiotics). This crosstalk is concentrated mainly in the intestinal epithelium, where microbes provide the host with essential nutrients and modulation of the immune system. Furthermore, microorganisms also display antimicrobial activities maintaining a gut ecosystem stable. This review summarises some of the recent findings on the interaction of both commensal and probiotic bacteria with each other and with the host. The aim is to highlight the cooperative status found in healthy individuals as well as the importance of this crosstalk in the maintenance of human homeostasis.

  6. Engineering microbes with synthetic biology frameworks.

    Science.gov (United States)

    Leonard, Effendi; Nielsen, David; Solomon, Kevin; Prather, Kristala Jones

    2008-12-01

    Typically, the outcome of biologically engineered unit operations cannot be controlled a priori due to the incorporation of ad hoc design into complex natural systems. To mitigate this problem, synthetic biology presents a systematic approach to standardizing biological components for the purpose of increasing their programmability and robustness when assembled with the aim to achieve novel biological functions. A complex engineered biological system using only standardized biological components is yet to exist. Nevertheless, current attempts to create and to implement modular, standardized biological components pave the way for the future creation of highly predictable artificial biological systems. Although synthetic biology frameworks can be applied to any biological engineering endeavor, this article will focus on providing a brief overview of advances in the field and its recent utilization for the engineering of microbes.

  7. Inactivation of microbes using ultrasound: a review.

    Science.gov (United States)

    Piyasena, P; Mohareb, E; McKellar, R C

    2003-11-01

    Alternative methods for pasteurization and sterilization are gaining importance, due to increased consumer demand for new methods of food processing that have a reduced impact on nutritional content and overall food quality. Ultrasound processing or sonication is one of the alternative technologies that has shown promise in the food industry. Sonication alone is not very effective in killing bacteria in food; however, the use of ultrasound coupled with pressure and/or heat is promising. Thermosonic (heat plus sonication), manosonic (pressure plus sonication), and manothermosonic (heat and pressure plus sonication) treatments are likely the best methods to inactivate microbes, as they are more energy-efficient and effective in killing microorganisms. Ultrasonic processing is still in its infancy and requires a great deal of future research in order to develop the technology on an industrial scale, and to more fully elucidate the effect of ultrasound on the properties of foods.

  8. The Plot Thickens: Diet Microbe Interactions May Modulate Thrombosis Risk.

    Science.gov (United States)

    Martínez-Del Campo, Ana; Romano, Kymberleigh A; Rey, Federico E; Balskus, Emily P

    2016-04-12

    Thrombosis plays an important role in cardiovascular disease (CVD). Platelet activation is an essential step in the genesis and propagation of atherothrombotic complications. In a recent publication, Zhu and colleagues report that gut microbe-derived TMAO enhances platelet responsiveness and thrombosis, providing a novel mechanistic connection between microbes and CVD (Zhu et al., 2016).

  9. Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

    Energy Technology Data Exchange (ETDEWEB)

    Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.; Roberto, F.F.; Tsang, M.N.; Pinhero, P.J. [INEEL (US); Brey, R.F. [ISU (US); Wright, R.N.; Windes, W.F.

    1999-09-03

    Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additional microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10{sup 3} and 6 x 10{sup 4} rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10{sup 4} rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10{sup 5} rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance.

  10. A robust GC-MS method for the quantitation of fatty acids in biological systems.

    Science.gov (United States)

    Jayasinghe, Nirupama Samanmalie; Dias, Daniel Anthony

    2013-01-01

    Fatty acids (FAs) are involved in a wide range of functions in biological systems. It is important to measure the exact amount of fatty acids in biological matrices in order to determine the level of fatty acids and understand the role they play. The ability to quantify fatty acids in various systems, especially plant species and microbes has recently paved the way to the mass production of pharmaceuticals and energy substitutes including biodiesel. This chapter describes an efficient method to quantify the total fatty acids (TFAs) in biological systems using gas chromatography-mass spectrometry (GC-MS) and a commercially available standard mix of fatty acid methyl esters (FAMEs) using a step-by-step methodology to setup a quantitation method using the Agilent Chemstation software.

  11. Sources and Bioactive Properties of Conjugated Dietary Fatty Acids.

    Science.gov (United States)

    Hennessy, Alan A; Ross, Paul R; Fitzgerald, Gerald F; Stanton, Catherine

    2016-04-01

    The group of conjugated fatty acids known as conjugated linoleic acid (CLA) isomers have been extensively studied with regard to their bioactive potential in treating some of the most prominent human health malignancies. However, CLA isomers are not the only group of potentially bioactive conjugated fatty acids currently undergoing study. In this regard, isomers of conjugated α-linolenic acid, conjugated nonadecadienoic acid and conjugated eicosapentaenoic acid, to name but a few, have undergone experimental assessment. These studies have indicated many of these conjugated fatty acid isomers commonly possess anti-carcinogenic, anti-adipogenic, anti-inflammatory and immune modulating properties, a number of which will be discussed in this review. The mechanisms through which these bioactivities are mediated have not yet been fully elucidated. However, existing evidence indicates that these fatty acids may play a role in modulating the expression of several oncogenes, cell cycle regulators, and genes associated with energy metabolism. Despite such bioactive potential, interest in these conjugated fatty acids has remained low relative to the CLA isomers. This may be partly attributed to the relatively recent emergence of these fatty acids as bioactives, but also due to a lack of awareness regarding sources from which they can be produced. In this review, we will also highlight the common sources of these conjugated fatty acids, including plants, algae, microbes and chemosynthesis.

  12. Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

    DEFF Research Database (Denmark)

    Treu, Laura; Campanaro, Stefano; Kougias, Panagiotis

    2016-01-01

    In the present study, RNA-sequencing was used to elucidate the change of anaerobic digestion metatranscriptome after long chain fatty acids (oleate) exposure. To explore the general transcriptional behavior of the microbiome, the analysis was first performed on shotgun reads without considering...... a reference metagenome. As a second step, RNA reads were aligned on the genes encoded by the microbial community, revealing the expression of more than 51 000 different transcripts. The present study is the first research which was able to dissect the transcriptional behavior at a single species level...... by considering the 106 microbial genomes previously identified. The exploration of the metabolic pathways confirmed the importance of Syntrophomonas species in fatty acids degradation, and also highlighted the presence of protective mechanisms toward the long chain fatty acid effects in bacteria belonging...

  13. Lipids in plant-microbe interactions.

    Science.gov (United States)

    Siebers, Meike; Brands, Mathias; Wewer, Vera; Duan, Yanjiao; Hölzl, Georg; Dörmann, Peter

    2016-09-01

    Bacteria and fungi can undergo symbiotic or pathogenic interactions with plants. Membrane lipids and lipid-derived molecules from the plant or the microbial organism play important roles during the infection process. For example, lipids (phospholipids, glycolipids, sphingolipids, sterol lipids) are involved in establishing the membrane interface between the two organisms. Furthermore, lipid-derived molecules are crucial for intracellular signaling in the plant cell, and lipids serve as signals during plant-microbial communication. These signal lipids include phosphatidic acid, diacylglycerol, lysophospholipids, and free fatty acids derived from phospholipase activity, apocarotenoids, and sphingolipid breakdown products such as ceramide, ceramide-phosphate, long chain base, and long chain base-phosphate. Fatty acids are the precursors for oxylipins, including jasmonic acid, and for azelaic acid, which together with glycerol-3-phosphate are crucial for the regulation of systemic acquired resistance. This article is part of a Special Issue titled "Plant Lipid Biology," guest editors Kent Chapman and Ivo Feussner. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Amphibian skin may select for rare environmental microbes.

    Science.gov (United States)

    Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Cormier, Guy; Jensen, Roderick V; Belden, Lisa K

    2014-11-01

    Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians' core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment.

  15. Belowground microbes mitigate plant-plant competition.

    Science.gov (United States)

    Fonseca, Márcia Bacelar; Dias, Teresa; Carolino, Maria Manuela; França, Marcel Giovanni Costa; Cruz, Cristina

    2017-09-01

    Dimorphandra wilsonii, a Cerrado endemic Fabaceae tree, is threatened by land-use changes. The few remaining individuals occur in areas dominated by alien grasses like Urochloa decumbens. We tested the impact of nitrogen (N) availability and symbionts' presence on mitigating the effects of competition from U. decumbens. Dimorphandra wilsonii seedlings were 50-week pot-cultivated under limiting (3mM) or non-limiting (10mM) N, with or without U. decumbens, and inoculated or not with a N-fixer (Bradyrhizobium sp.) and an arbuscular mycorrhizal fungus (AMF - Glomus etunicatum), both forming symbioses in the field. Since D. wilsonii seedlings grew more and 'lost' fewer nutrients under the symbionts' presence, symbionts mitigated plant-plant competition. Under limiting N, inoculated D. wilsonii seedlings grew more (despite no nodulation), but N fixation was only suggested when inoculated D. wilsonii seedlings competed with U. decumbens. D. wilsonii(13)C, and substrate's carbon and respiration suggest that only the microbes performing key functions received plant carbon. Under non-limiting N, inoculated D. wilsonii seedlings became enriched in (13)C, substrate accumulated carbon and microbial respiration increased, suggesting a more generalist microbial community. Data suggest inoculating D. wilsonii seeds/seedlings with AMF and N-fixers as a conservation measure. However, long-term field-studies need to confirm these conclusions. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Microbes are trophic analogs of animals.

    Science.gov (United States)

    Steffan, Shawn A; Chikaraishi, Yoshito; Currie, Cameron R; Horn, Heidi; Gaines-Day, Hannah R; Pauli, Jonathan N; Zalapa, Juan E; Ohkouchi, Naohiko

    2015-12-01

    In most ecosystems, microbes are the dominant consumers, commandeering much of the heterotrophic biomass circulating through food webs. Characterizing functional diversity within the microbiome, therefore, is critical to understanding ecosystem functioning, particularly in an era of global biodiversity loss. Using isotopic fingerprinting, we investigated the trophic positions of a broad diversity of heterotrophic organisms. Specifically, we examined the naturally occurring stable isotopes of nitrogen ((15)N:(14)N) within amino acids extracted from proteobacteria, actinomycetes, ascomycetes, and basidiomycetes, as well as from vertebrate and invertebrate macrofauna (crustaceans, fish, insects, and mammals). Here, we report that patterns of intertrophic (15)N-discrimination were remarkably similar among bacteria, fungi, and animals, which permitted unambiguous measurement of consumer trophic position, independent of phylogeny or ecosystem type. The observed similarities among bacterial, fungal, and animal consumers suggest that within a trophic hierarchy, microbiota are equivalent to, and can be interdigitated with, macrobiota. To further test the universality of this finding, we examined Neotropical fungus gardens, communities in which bacteria, fungi, and animals are entwined in an ancient, quadripartite symbiosis. We reveal that this symbiosis is a discrete four-level food chain, wherein bacteria function as the apex carnivores, animals and fungi are meso-consumers, and the sole herbivores are fungi. Together, our findings demonstrate that bacteria, fungi, and animals can be integrated within a food chain, effectively uniting the macro- and microbiome in food web ecology and facilitating greater inclusion of the microbiome in studies of functional diversity.

  17. The SAPHO syndrome--are microbes involved?

    Science.gov (United States)

    Assmann, G; Simon, P

    2011-06-01

    The syndrome of synovitis, acne, pustulosis, hyperostosis and osteitis (SAPHO) includes a rare group of chronic, relapsing, inflammatory osteoarticular disorders that is conventionally associated with manifestations in the skin. Diagnostic dilemmas can arise due to incomplete manifestations or confusion generated through mimicking of other conditions, such as osteomyelitis. The aetiology of this syndrome remains unclear, but probably involves genetic, immunological and infectious mechanisms. The possible pathogenetic role of infectious agents in genetically predisposed individuals, resulting in a 'reactive osteitis', has been suggested because microbes such as Propionibacterium acnes have been recovered from bone biopsy samples. However, this hypothesis has not been demonstrated as yet. Current knowledge with regard to treatment of this syndrome is based on results reported from small case studies and, thus, is still empiric. The use of antibiotics, instituted based on the isolation of Propionibacterium acnes, has been reported to show conflicting results. Promising results for potential future application have recently been reported for treatment of SAPHO with bisphosphonates and antagonists of tumour necrosis factor-α. This review aims to evaluate the existing knowledge on the SAPHO syndrome and to provide information on symptoms, diagnosis and treatment options for this disease.

  18. Proteome-wide systems analysis of a cellulosic biofuel-producing microbe.

    Science.gov (United States)

    Tolonen, Andrew C; Haas, Wilhelm; Chilaka, Amanda C; Aach, John; Gygi, Steven P; Church, George M

    2011-01-18

    Fermentation of plant biomass by microbes like Clostridium phytofermentans recycles carbon globally and can make biofuels from inedible feedstocks. We analyzed C. phytofermentans fermenting cellulosic substrates by integrating quantitative mass spectrometry of more than 2500 proteins with measurements of growth, enzyme activities, fermentation products, and electron microscopy. Absolute protein concentrations were estimated using Absolute Protein EXpression (APEX); relative changes between treatments were quantified with chemical stable isotope labeling by reductive dimethylation (ReDi). We identified the different combinations of carbohydratases used to degrade cellulose and hemicellulose, many of which were secreted based on quantification of supernatant proteins, as well as the repertoires of glycolytic enzymes and alcohol dehydrogenases (ADHs) enabling ethanol production at near maximal yields. Growth on cellulose also resulted in diverse changes such as increased expression of tryptophan synthesis proteins and repression of proteins for fatty acid metabolism and cell motility. This study gives a systems-level understanding of how this microbe ferments biomass and provides a rational, empirical basis to identify engineering targets for industrial cellulosic fermentation.

  19. Omega-3 Fatty Acids

    Science.gov (United States)

    Omega-3 fatty acids are used together with lifestyle changes (diet, weight-loss, exercise) to reduce the ... the blood in people with very high triglycerides. Omega-3 fatty acids are in a class of ...

  20. Omega-6 Fatty Acids

    Science.gov (United States)

    Omega-6 fatty acids are types of fats. Some types are found in vegetable oils, including corn, evening primrose seed, safflower, and soybean oils. Other types of omega-6 fatty acids are found in black currant ...

  1. Immunoglobulin and fatty acids

    DEFF Research Database (Denmark)

    2009-01-01

    The present invention relates to a composition comprising 0.1-10 w/w % immunoglobulin (Ig), 4-14 w/w % saturated fatty acids, 4-14 w/w % mono-unsaturated fatty acids and 0-5 w/w % poly-unsaturated fatty acids, wherein the weight percentages are based on the content of dry matter in the composition...

  2. The peroxisomal enzyme L-PBE is required to prevent the dietary toxicity of medium-chain fatty acids.

    Science.gov (United States)

    Ding, Jun; Loizides-Mangold, Ursula; Rando, Gianpaolo; Zoete, Vincent; Michielin, Olivier; Reddy, Janardan K; Wahli, Walter; Riezman, Howard; Thorens, Bernard

    2013-10-17

    Specific metabolic pathways are activated by different nutrients to adapt the organism to available resources. Although essential, these mechanisms are incompletely defined. Here, we report that medium-chain fatty acids contained in coconut oil, a major source of dietary fat, induce the liver ω-oxidation genes Cyp4a10 and Cyp4a14 to increase the production of dicarboxylic fatty acids. Furthermore, these activate all ω- and β-oxidation pathways through peroxisome proliferator activated receptor (PPAR) α and PPARγ, an activation loop normally kept under control by dicarboxylic fatty acid degradation by the peroxisomal enzyme L-PBE. Indeed, L-pbe(-/-) mice fed coconut oil overaccumulate dicarboxylic fatty acids, which activate all fatty acid oxidation pathways and lead to liver inflammation, fibrosis, and death. Thus, the correct homeostasis of dicarboxylic fatty acids is a means to regulate the efficient utilization of ingested medium-chain fatty acids, and its deregulation exemplifies the intricate relationship between impaired metabolism and inflammation. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  3. The Peroxisomal Enzyme L-PBE Is Required to Prevent the Dietary Toxicity of Medium-Chain Fatty Acids

    Directory of Open Access Journals (Sweden)

    Jun Ding

    2013-10-01

    Full Text Available Specific metabolic pathways are activated by different nutrients to adapt the organism to available resources. Although essential, these mechanisms are incompletely defined. Here, we report that medium-chain fatty acids contained in coconut oil, a major source of dietary fat, induce the liver ω-oxidation genes Cyp4a10 and Cyp4a14 to increase the production of dicarboxylic fatty acids. Furthermore, these activate all ω- and β-oxidation pathways through peroxisome proliferator activated receptor (PPAR α and PPARγ, an activation loop normally kept under control by dicarboxylic fatty acid degradation by the peroxisomal enzyme L-PBE. Indeed, L-pbe−/− mice fed coconut oil overaccumulate dicarboxylic fatty acids, which activate all fatty acid oxidation pathways and lead to liver inflammation, fibrosis, and death. Thus, the correct homeostasis of dicarboxylic fatty acids is a means to regulate the efficient utilization of ingested medium-chain fatty acids, and its deregulation exemplifies the intricate relationship between impaired metabolism and inflammation.

  4. Dielectrophoretic analysis of microbes in water.

    Science.gov (United States)

    Betts, W B; Brown, A P

    1998-12-01

    Traditional microbiological methods are still used extensively for analysis of micro-organisms in water. However, they are inefficient due to a high labour input requirement, a low sample capacity, and often a long time lag before results are available. Analytical stages involving incubation and growth (enrichments and colony isolation) contribute the greatest delay in reporting, although subsequent identification can also be protracted. The use of electrometric growth analysers (measuring impedance, conductance or capacitance changes) is now more common in water microbiology. Although these instruments can provide more rapid results and provide increased handling capacity, the bacterial generation times required to provide detectable changes cause delays and suitable selective media are not fully developed for all microbes of interest. Most other recent methods have equally disappointing drawbacks and thus extensive research continues in order to realise the ambition of 'real-time' analytical microbiology. Several research groups have demonstrated the potential of dielectrophoresis in providing microbial concentration, separation and identification systems which are not limited by bacterial growth and are therefore extremely rapid. Dielectrophoresis occurs when cells are placed in non-uniform electric fields. The cells move towards the electrodes (regardless of the direction of the applied field) as determined by their dielectric properties (conductivity and permittivity) rather than by their charge as occurs in electrophoresis. Also, the polarisability of the cells, and therefore the polarity and magnitude of the dielectrophoretic force, varies as a function of the electric field frequency. Because the dielectric properties of a particular cell type have characteristic frequency-dependent components, if cell collection at electrodes is observed across a frequency range, the collection spectrum produced is distinctive for the cell type under investigation. This

  5. Environmental restoration using plant-microbe bioaugmentation

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, M.T.; Metting, F.B.; Fredrickson, J.K.; Seidler, R.J.

    1993-04-01

    Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10[sup 8] or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10[sup 9]/g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PP0301/pRO101 and PP0301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation.

  6. Environmental restoration using plant-microbe bioaugmentation

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, M.T.; Fredrickson, J.K.; Metting, F.B.; Seidler, R.J.

    1993-04-01

    Land farming, for the purpose of bioremediation, refers traditionally to the spreading of contaminated soil, sediments, or other material over land; mechanically mixing it; incorporating various amendments, such as fertilizer or mulch; and sometimes inoculating with degradative microorganisms. Populations of bacteria added to soils often decline rapidly and become metabolically inactive. To efficiently degrade contaminants, microorganisms must be metabolically active. Thus, a significant obstacle to the successful use of microorganisms for environmental applications is their long-term survival and the expression of their degradative genes in situ. Rhizosphere microorganisms are known to be more metabolically active than those in bulk soil, because they obtain carbon and energy from root exudates and decaying root matter. Rhizosphere populations are also more abundant, often containing 10{sup 8} or more culturable bacteria per gram of soil, and bacterial populations on the rhizoplane can exceed 10{sup 9}/g root. Many of the critical parameters that influence the competitive ability of rhizosphere bacteria have not been identified, but microorganisms have frequently been introduced into soil (bioaugmentation) as part of routine or novel agronomic practices. However, the use of rhizosphere bacteria and their in situ stimulation by plant roots for degrading organic contaminants has received little attention. Published studies have demonstrated the feasibility of using rhizobacteria (Pseudomonas putida) for the rapid removal of chlorinated pesticides from contaminated soil, and to promote germination of radish seeds in the presence of otherwise phytotoxic levels of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), and phenoxyacetic acid (PAA). The present investigation was undertaken to determine if these strains (Pseudomonas putida PPO301/pRO101 and PPO301/pRO103) could be used to bioremediate 2,4-D-amended soil via plant-microbe bioaugmentation.

  7. Perchlorate reduction by microbes inhabiting oil reservoirs

    Science.gov (United States)

    Liebensteiner, Martin; Stams, Alfons; Lomans, Bart

    2014-05-01

    Microbial perchlorate and chlorate reduction is a unique type of anaerobic respiration as during reduction of (per)chlorate chlorite is formed, which is then split into chloride and molecular oxygen. In recent years it was demonstrated that (per)chlorate-reducing bacteria may employ oxygenase-dependent pathways for the degradation of aromatic and aliphatic hydrocarbons. These findings suggested that (per)chlorate may be used as oxygen-releasing compound in anoxic environments that contain hydrocarbons, such as polluted soil sites and oil reservoirs. We started to study perchlorate reduction by microbes possibly inhabiting oil reservoirs. One of the organisms studied was Archaeoglobus fulgidus. This extremely thermophilic archaeon is known as a major contributor to souring in hot oil reservoirs. A. fulgidus turned out to be able to use perchlorate as terminal electron acceptor for growth with lactate (Liebensteiner et al 2013). Genome based physiological experiments indicated that A. fulgidus possesses a novel perchlorate reduction pathway. Perchlorate is first reduced to chlorite, but chlorite is not split into chloride and molecular oxygen as occurs in bacteria. Rather, chlorite reacts chemically with sulfide, forming oxidized sulfur compounds, which are reduced to sulfide in the electron transport chain by the archaeon. The dependence of perchlorate reduction on sulfur compounds could be shown. The implications of our findings as novel strategy for microbiological enhanced oil recovery and for souring mitigation are discussed. Liebensteiner MG, Pinkse MWH, Schaap PJ, Stams AJM and Lomans BP (2013) Archaeal (per)chlorate reduction at high temperature, a matter of abiotic-biotic reactions. Science 340: 85-87

  8. Microbes of the avian cecum: types present and substrates utilized.

    Science.gov (United States)

    Mead, G C

    1989-01-01

    This paper discusses the types and properties of microorganisms found in avian ceca, with special reference to the chicken. Microbial activity in the cecum is primarily fermentative, but there has been little evidence of cellulose fermentation, and the predominant bacterial types are relatively inactive against other high-molecular-weight compounds of dietary origin. In all avian species examined, the consistent presence of large populations of uric acid-degrading bacteria supports the view that microbial populations in the ceca permit reabsorption of water and possibly nonprotein nitrogen from the backflow of urine. These capabilities may be of particular importance to wild birds under conditions of water and food deprivation.

  9. Collective unconscious: how gut microbes shape human behavior.

    Science.gov (United States)

    Dinan, Timothy G; Stilling, Roman M; Stanton, Catherine; Cryan, John F

    2015-04-01

    The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.

  10. The importance of engineering physiological functionality into microbes

    NARCIS (Netherlands)

    Zhang, Y.; Zhu, Y.; Zhu, Y.; Li, Y.

    2009-01-01

    Good physiological performance of industrial microbes is crucial for successful bioprocesses. Conventional metabolism-oriented engineering strategies often fail to obtain expected phenotypes owing to focusing narrowly on targeted metabolic capabilities while neglecting microbial physiological respon

  11. Host-microbe interactions in the developing zebrafish

    Science.gov (United States)

    Kanther, Michelle; Rawls, John F.

    2010-01-01

    Summary of recent advances The amenability of the zebrafish to in vivo imaging and genetic analysis has fueled expanded use of this vertebrate model to investigate the molecular and cellular foundations of host-microbe relationships. Study of microbial encounters in zebrafish hosts has concentrated on developing embryonic and larval stages, when the advantages of the zebrafish model are maximized. A comprehensive understanding of these host-microbe interactions requires appreciation of the developmental context into which a microbe is introduced, as well as the effects of that microbial challenge on host ontogeny. In this review, we discuss how in vivo imaging and genetic analysis in zebrafish has advanced our knowledge of host-microbe interactions in the context of a developing vertebrate host. We focus on recent insights into immune cell ontogeny and function, commensal microbial relationships in the intestine, and microbial pathogenesis in zebrafish hosts. PMID:20153622

  12. Study of Host–Microbe Interactions in Zebrafish

    Science.gov (United States)

    Milligan-Myhre, Kathryn; Charette, Jeremy R.; Phennicie, Ryan T.; Stephens, W. Zac; Rawls, John F.; Guillemin, Karen; Kim, Carol H.

    2015-01-01

    All animals are ecosystems, home to diverse microbial populations. Animal-associated microbes play important roles in the normal development and physiology of their hosts, but can also be agents of infectious disease. Traditionally, mice have been used to study pathogenic and beneficial associations between microbes and vertebrate animals. The zebrafish is emerging as a valuable new model system for host-microbe interaction studies, affording researchers with the opportunity to survey large populations of hosts and to visualize microbe-host associations at a cellular level in living animals. This chapter provides detailed protocols for the analysis of zebrafish-associated microbial communities, the derivation and husbandry of germ-free zebrafish, and the modeling of infectious disease in different stages of zebrafish development via different routes of inoculation. These protocols offer a starting point for researchers to address a multitude of questions about animals’ coexistence with microorganisms. PMID:21951527

  13. Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production.

    Science.gov (United States)

    Parisutham, Vinuselvi; Kim, Tae Hyun; Lee, Sung Kuk

    2014-06-01

    Lignocelluloses are rich sugar treasures, which can be converted to useful commodities such as biofuel with the help of efficient combination of enzymes and microbes. Although several bioprocessing approaches have been proposed, biofuel production from lignocelluloses is limited because of economically infeasible technologies for pretreatment, saccharification and fermentation. Use of consolidated bioprocessing (CBP) microbes is the most promising method for the cost-effective production of biofuels. However, lignocelluloses are obtained from highly diverse environment and hence are heterogeneous in nature. Therefore, it is necessary to develop and integrate tailor-designed pretreatment processes and efficient microbes that can thrive on many different kinds of biomass. In this review, the progress towards the construction of consolidated bioprocessing microbes, which can efficiently convert heterogeneous lignocellulosic biomass to bioenergy, has been discussed; in addition, the potential and constraints of current bioprocessing technologies for cellulosic biofuel production have been discussed.

  14. FadD Is Required for Utilization of Endogenous Fatty Acids Released from Membrane Lipids ▿ †

    Science.gov (United States)

    Pech-Canul, Ángel; Nogales, Joaquina; Miranda-Molina, Alfonso; Álvarez, Laura; Geiger, Otto; Soto, María José; López-Lara, Isabel M.

    2011-01-01

    FadD is an acyl coenzyme A (CoA) synthetase responsible for the activation of exogenous long-chain fatty acids (LCFA) into acyl-CoAs. Mutation of fadD in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti promotes swarming motility and leads to defects in nodulation of alfalfa plants. In this study, we found that S. meliloti fadD mutants accumulated a mixture of free fatty acids during the stationary phase of growth. The composition of the free fatty acid pool and the results obtained after specific labeling of esterified fatty acids with a Δ5-desaturase (Δ5-Des) were in agreement with membrane phospholipids being the origin of the released fatty acids. Escherichia coli fadD mutants also accumulated free fatty acids released from membrane lipids in the stationary phase. This phenomenon did not occur in a mutant of E. coli with a deficient FadL fatty acid transporter, suggesting that the accumulation of fatty acids in fadD mutants occurs inside the cell. Our results indicate that, besides the activation of exogenous LCFA, in bacteria FadD plays a major role in the activation of endogenous fatty acids released from membrane lipids. Furthermore, expression analysis performed with S. meliloti revealed that a functional FadD is required for the upregulation of genes involved in fatty acid degradation and suggested that in the wild-type strain, the fatty acids released from membrane lipids are degraded by β-oxidation in the stationary phase of growth. PMID:21926226

  15. Microbes Online: an integrated portal for comparative functional genomics

    OpenAIRE

    Arkin, Adam P.

    2014-01-01

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi, as well as 1000s of viruses and plasmids. In addition to standard comparative genomic analysis, including gene prediction, sequence homology, domain identification, gene family assignments and functional annotations from E.C. and GO, MicrobesOnline integrates data from ...

  16. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications

    OpenAIRE

    Imam, Jahangir; Singh, Puneet K.; Shukla, Pratyoosh

    2016-01-01

    Deciphering plant–microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in ...

  17. Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade).

    Science.gov (United States)

    Drüppel, Katharina; Hensler, Michael; Trautwein, Kathleen; Koßmehl, Sebastian; Wöhlbrand, Lars; Schmidt-Hohagen, Kerstin; Ulbrich, Marcus; Bergen, Nils; Meier-Kolthoff, Jan P; Göker, Markus; Klenk, Hans-Peter; Schomburg, Dietmar; Rabus, Ralf

    2014-01-01

    Combining omics and enzymatic approaches, catabolic routes of nine selected amino acids (tryptophan, phenylalanine, methionine, leucine, isoleucine, valine, histidine, lysine and threonine) were elucidated in substrate-adapted cells of Phaeobacter inhibens DSM 17395 (displaying conspicuous morphotypes). The catabolic network [excluding tricarboxylic acid (TCA) cycle] was reconstructed from 71 genes (scattered across the chromosome; one-third newly assigned), with 69 encoded proteins and 20 specific metabolites identified, and activities of 10 different enzymes determined. For example, Ph. inhibens DSM 17395 does not degrade lysine via the widespread saccharopine pathway but might rather employ two parallel pathways via 5-aminopentanoate or 2-aminoadipate. Tryptophan degradation proceeds via kynurenine and 2-aminobenzoate; the latter is metabolized as known from Azoarcus evansii. Histidine degradation is analogous to the Pseudomonas-type Hut pathway via N-formyl-l-glutamate. For threonine, only one of the three genome-predicted degradation pathways (employing threonine 3-dehydrogenase) is used. Proteins of the individual peripheral degradation sequences in Ph. inhibens DSM 17395 were apparently substrate-specifically formed contrasting the non-modulated TCA cycle enzymes. Comparison of genes for the reconstructed amino acid degradation network in Ph. inhibens DSM 17395 across 27 other complete genomes of Roseobacter clade members revealed most of them to be widespread among roseobacters.

  18. Development and validation of HPLC and CE methods for simultaneous determination of amlodipine and atorvastatin in the presence of their acidic degradation products in tablets

    Directory of Open Access Journals (Sweden)

    Hassan Said A.

    2016-12-01

    Full Text Available Two methods were developed for separation and quantitation of amlodipine (AML and atorvastatin (ATV in the presence of their acidic degradation products. The first method was a simple isocratic RP-HPLC method while the second was capillary electrophoresis (CE. Degradation products were obtained by acidic hydrolysis of the two drugs and their structures were elucidated for the first time by IR and MS spectra. Degradation products did not interfere with the determination of either drug and the assays were therefore stability-indicating. The linearity of the proposed methods was established over the ranges 1-50 μg mL-1 for AML and ATV in the HPLC method and in the range of 3-50 and 4-50 μg mL-1 for AML and ATV, respectively, in the CE method. The proposed methods were validated according to ICH guidelines. The methods were successfully applied to estimation of AML and ATV in combined tablets.

  19. Can Terrestrial Microbes Grow on Mars?

    Science.gov (United States)

    Rothschild, Lynn

    2012-01-01

    conditions. We are constructing newly engineered genetic parts for different valuable host organisms, designed to increased long-term survival and functional retention. These methods should be applied for DNA and strain storage and transportation. In parallel, we seek inspiration from natural organisms that have developed means for survival in extreme environmental conditions. We are utilizing novel techniques for analysis of lipid biomarkers in the Antarctic Dry Valleys in order to identify resident microbes in the Antarctic soil and permafrost, as well as biomarker fossils of organisms that survived in the valleys in ages past. Through the identification of these life forms, we hope to understand and draw on new biological tools and strategies for synthetic biological applications on Mars.

  20. Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity

    NARCIS (Netherlands)

    Rovenich, Hanna; Zuccaro, Alga; Thomma, Bart P.H.J.

    2016-01-01

    I. II. III. IV. V. VI. References Summary: All filamentous microbes produce and release a wide range of glycans, which are essential determinants of microbe-microbe and microbe-host interactions. Major cell wall constituents, such as chitin and β-glucans, are elicitors of host immune responses.

  1. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities.

    Science.gov (United States)

    Akhtar, M Kalim; Turner, Nicholas J; Jones, Patrik R

    2013-01-02

    Aliphatic hydrocarbons such as fatty alcohols and petroleum-derived alkanes have numerous applications in the chemical industry. In recent years, the renewable synthesis of aliphatic hydrocarbons has been made possible by engineering microbes to overaccumulate fatty acids. However, to generate end products with the desired physicochemical properties (e.g., fatty aldehydes, alkanes, and alcohols), further conversion of the fatty acid is necessary. A carboxylic acid reductase (CAR) from Mycobacterium marinum was found to convert a wide range of aliphatic fatty acids (C(6)-C(18)) into corresponding aldehydes. Together with the broad-substrate specificity of an aldehyde reductase or an aldehyde decarbonylase, the catalytic conversion of fatty acids to fatty alcohols (C(8)-C(16)) or fatty alkanes (C(7)-C(15)) was reconstituted in vitro. This concept was applied in vivo, in combination with a chain-length-specific thioesterase, to engineer Escherichia coli BL21(DE3) strains that were capable of synthesizing fatty alcohols and alkanes. A fatty alcohol titer exceeding 350 mg·L(-1) was obtained in minimal media supplemented with glucose. Moreover, by combining the CAR-dependent pathway with an exogenous fatty acid-generating lipase, natural oils (coconut oil, palm oil, and algal oil bodies) were enzymatically converted into fatty alcohols across a broad chain-length range (C(8)-C(18)). Together with complementing enzymes, the broad substrate specificity and kinetic characteristics of CAR opens the road for direct and tailored enzyme-catalyzed conversion of lipids into user-ready chemical commodities.

  2. Safety assessment of sFat-1 transgenic pigs by detecting their co-habitant microbe in intestinal tract.

    Science.gov (United States)

    Tang, Maoxue; Zheng, Xinmin; Cheng, Wenke; Jin, Erhui; Chen, Hongxing; Yang, Shulin; Cui, Wentao; Li, Kui

    2011-08-01

    Transgenic pigs containing sFat-1 (synthesized fatty acid desaturase-1) gene were produced by DNA microinjection. The meat of these pigs contain ω-3 unsaturated fatty acid which is beneficial to the health of human being. The aim of this study is to assess the effects of expression of sFat-1 in pig on the health of animal themselves and on the safety of environment from the angle of the changes in microbe population of pig intestinal tract. Four F1 male semi-sibling of sFat-1 transgenic pigs and four F1 female semi-sibling of sFat-1 transgenic pigs were used as experimental animals, together with their none transgenic siblings as control animals. For inspection of any change in populations of microbial flora in various parts of intestinal tract and feces of sFat-1 transgenic pigs total aerobe, total anaerobe, main beneficial bacteria and main harmful bacteria were cultured and analyzed. At the same time foreign gene drift was assessed by PCR amplifying foreign fragment in samples of total aerobe and total anaerobe. Results indicated that in comparison with control pig microbe population of various species in different parts of intestinal tract and feces of sFat-1 transgenic pig remained unchanged and foreign gene sequence could not be detected in DNA of total aerobe and total anaerobe. In conclusion, the data of this study suggest that microbe population in intestinal tract and feces of transgenic pig was not influenced by the expression of transferred foreign gene sFat-1 and also foreign gene drifting from animal genome to microbial genome must be a rare incident.

  3. Perspectives of plant-associated microbes in heavy metal phytoremediation.

    Science.gov (United States)

    Rajkumar, M; Sandhya, S; Prasad, M N V; Freitas, H

    2012-01-01

    "Phytoremediation" know-how to do-how is rapidly expanding and is being commercialized by harnessing the phyto-microbial diversity. This technology employs biodiversity to remove/contain pollutants from the air, soil and water. In recent years, there has been a considerable knowledge explosion in understanding plant-microbes-heavy metals interactions. Novel applications of plant-associated microbes have opened up promising areas of research in the field of phytoremediation technology. Various metabolites (e.g., 1-aminocyclopropane-1-carboxylic acid deaminase, indole-3-acetic acid, siderophores, organic acids, etc.) produced by plant-associated microbes (e.g., plant growth promoting bacteria, mycorrhizae) have been proposed to be involved in many biogeochemical processes operating in the rhizosphere. The salient functions include nutrient acquisition, cell elongation, metal detoxification and alleviation of biotic/abiotic stress in plants. Rhizosphere microbes accelerate metal mobility, or immobilization. Plants and associated microbes release inorganic and organic compounds possessing acidifying, chelating and/or reductive power. These functions are implicated to play an essential role in plant metal uptake. Overall the plant-associated beneficial microbes enhance the efficiency of phytoremediation process directly by altering the metal accumulation in plant tissues and indirectly by promoting the shoot and root biomass production. The present work aims to provide a comprehensive review of some of the promising processes mediated by plant-associated microbes and to illustrate how such processes influence heavy metal uptake through various biogeochemical processes including translocation, transformation, chelation, immobilization, solubilization, precipitation, volatilization and complexation of heavy metals ultimately facilitating phytoremediation. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Explorative analysis of microbes, colloids and gases

    Energy Technology Data Exchange (ETDEWEB)

    Hallbeck, Lotta; Pedersen, Karsten (Microbial Analytics Sweden AB, Goeteborg (Sweden))

    2008-08-15

    The overall objectives of the hydrogeochemical description for Forsmark are to establish a detailed understanding of the hydrogeochemical conditions at the site and to develop models that fulfil the needs identified by the safety assessment groups during the site investigation phase. Issues of concern to safety assessment are radionuclide transport and technical barrier behaviour, both of which are dependent on the chemistry of groundwater and pore water and their evolution with time. In this report, part of the final hydrogeochemical evaluation work of the site investigation at the Forsmark site, is presented. The work was conducted by SKB's hydrogeochemical project group, ChemNet, which consists of independent consultants and Univ. researchers with expertise in geochemistry, hydrochemistry, hydrogeochemistry, microbiology, geomicrobiology, analytical chemistry etc. The resulting site descriptive model version, mainly based on 2.2 data and complementary 2.3 data, was carried out during September 2006 to December 2007. This report focuses on microbiology, colloids and gases: - Microbes (Chapter 1): Several methods must be used to characterize active microbial communities in groundwater. Microbial parameters of interest are the total number of cells (TNC) and the presence of various metabolic groups of microorganisms. Different microbial groups influence the environment in different ways, depending on what metabolic group is dominant. Typically, the following redox couples are utilized by bacteria in granitic groundwater: H{sub 2}O/O{sub 2}, NO{sub 3}-/N{sub 2}, Mn2+/Mn(IV), Fe2+/Fe(III), S2-/SO{sub 4}2-, CH{sub 4}/CO{sub 2}, CH{sub 3}COOH/CO{sub 2}, and H{sub 2}/H+. The data will indicate the activity of specific microbial populations at particular sites and how they may affect the geochemistry. - Colloids (Chapter 2): Particles in the size range from 1 to 1x10-3 mum are regarded as colloids. Their small size prohibits them from settling, which gives them the

  5. Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas.

    Directory of Open Access Journals (Sweden)

    Tue Kjærgaard Nielsen

    Full Text Available The 2-methyl-4-chlorophenoxyacetic (MCPA acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA-degradation genotype among the sphingomonads.

  6. Novel Insight into the Genetic Context of the cadAB Genes from a 4-chloro-2-methylphenoxyacetic Acid-Degrading Sphingomonas

    Science.gov (United States)

    Nielsen, Tue Kjærgaard; Xu, Zhuofei; Gözdereliler, Erkin; Aamand, Jens; Hansen, Lars Hestbjerg; Sørensen, Sebastian R.

    2013-01-01

    The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads. PMID:24391756

  7. HPLC, TLC, and first-derivative spectrophotometry stability-indicating methods for the determination of tropisetron in the presence of its acid degradates.

    Science.gov (United States)

    Abdel-Fattah, Laila S; El-Sherif, Zeinab A; Kilani, Khadiga M; El-Haddad, Dalia A

    2010-01-01

    Three stability-indicating assay methods were developed for the determination of tropisetron in a pharmaceutical dosage form in the presence of its degradation products. The proposed techniques are HPLC, TLC, and first-derivative spectrophotometry (1D). Acid degradation was carried out, and the degradation products were separated by TLC and identified by IR, NMR, and MS techniques. The HPLC method was based on determination of tropisetron in the presence of its acid-induced degradation product on an RP Nucleosil C18 column using methanol-water-acetonitrile-trimethylamine (65 + 20 + 15 + 0.2, v/v/v/v) mobile phase and UV detection at 285 nm. The TLC method was based on the separation of tropisetron and its acid-induced degradation products, followed by densitometric measurement of the intact spot at 285 nm. The separation was carried out on silica gel 60 F254 aluminum sheets using methanol-glacial acetic acid (22 + 3, v/v) mobile phase. The 1D method was based on the measurement of first-derivative amplitudes of tropisetron in H2O at the zero-crossing point of its acid-induced degradation product at 271.9 nm. Linearity, accuracy, and precision were found to be acceptable over concentration ranges of 40-240 microg/mL, 1-10 microg/spot, and 6-36 micro/mL for the HPLC, TLC, and 1D methods, respectively. The suggested methods were successfully applied for the determination of the drug in bulk powder, laboratory-prepared mixtures, and a commercial sample.

  8. A molecular study of microbe transfer between distant environments.

    Directory of Open Access Journals (Sweden)

    Sean D Hooper

    Full Text Available BACKGROUND: Environments and their organic content are generally not static and isolated, but in a constant state of exchange and interaction with each other. Through physical or biological processes, organisms, especially microbes, may be transferred between environments whose characteristics may be quite different. The transferred microbes may not survive in their new environment, but their DNA will be deposited. In this study, we compare two environmental sequencing projects to find molecular evidence of transfer of microbes over vast geographical distances. METHODOLOGY: By studying synonymous nucleotide composition, oligomer frequency and orthology between predicted genes in metagenomics data from two environments, terrestrial and aquatic, and by correlating with phylogenetic mappings, we find that both environments are likely to contain trace amounts of microbes which have been far removed from their original habitat. We also suggest a bias in direction from soil to sea, which is consistent with the cycles of planetary wind and water. CONCLUSIONS: Our findings support the Baas-Becking hypothesis formulated in 1934, which states that due to dispersion and population sizes, microbes are likely to be found in widely disparate environments. Furthermore, the availability of genetic material from distant environments is a possible font of novel gene functions for lateral gene transfer.

  9. MAMP (Microbe-Associated Molecular Pattern triggered immunity in Plants

    Directory of Open Access Journals (Sweden)

    Mari-Anne eNewman

    2013-05-01

    Full Text Available Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs, are recognized by the plant innate immune systems pattern recognition receptors (PRRs. General elicitors like flagellin (Flg, elongation factor Tu (EF-Tu, peptidoglycan (PGN, lipopolysaccharides (LPS, Ax21 (Activator of XA21-mediated immunity in rice, fungal chitin and β-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI in plants.

  10. Microfabricated microbial fuel cell arrays reveal electrochemically active microbes.

    Directory of Open Access Journals (Sweden)

    Huijie Hou

    Full Text Available Microbial fuel cells (MFCs are remarkable "green energy" devices that exploit microbes to generate electricity from organic compounds. MFC devices currently being used and studied do not generate sufficient power to support widespread and cost-effective applications. Hence, research has focused on strategies to enhance the power output of the MFC devices, including exploring more electrochemically active microbes to expand the few already known electricigen families. However, most of the MFC devices are not compatible with high throughput screening for finding microbes with higher electricity generation capabilities. Here, we describe the development of a microfabricated MFC array, a compact and user-friendly platform for the identification and characterization of electrochemically active microbes. The MFC array consists of 24 integrated anode and cathode chambers, which function as 24 independent miniature MFCs and support direct and parallel comparisons of microbial electrochemical activities. The electricity generation profiles of spatially distinct MFC chambers on the array loaded with Shewanella oneidensis MR-1 differed by less than 8%. A screen of environmental microbes using the array identified an isolate that was related to Shewanella putrefaciens IR-1 and Shewanella sp. MR-7, and displayed 2.3-fold higher power output than the S. oneidensis MR-1 reference strain. Therefore, the utility of the MFC array was demonstrated.

  11. The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.

    Science.gov (United States)

    Lang, Jenna M; Eisen, Jonathan A; Zivkovic, Angela M

    2014-01-01

    Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10(9) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10(6) and 1.4 × 10(6) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories

  12. Microbes Should Be Central to Ecological Education and Outreach

    Directory of Open Access Journals (Sweden)

    Albert Barberán

    2015-09-01

    Full Text Available Our planet is changing rapidly, and responding to the ensuing environmental challenges will require an informed citizenry that can understand the inherent complexity of ecological systems. However, microorganisms are usually neglected in the narratives that we use to understand nature. Here, we advocate for the inclusion of microbial ecology across education levels and delineate the often neglected benefits of incorporating microbes into ecology curricula. We provide examples across education levels, from secondary school (by considering one’s self as a microbial ecosystem, to higher education (by incorporating our knowledge of the global ecological role and medical application of microbes, to the general public (by engagement through citizen-science projects. The greater inclusion of microbes in ecological education and outreach will not only help us appreciate the natural world we are part of, but will ultimately aid in building a citizenry better prepared to make informed decisions on health and environmental policies.

  13. Microbes can help explain the evolution of host altruism

    Science.gov (United States)

    Lewin-Epstein, Ohad; Aharonov, Ranit; Hadany, Lilach

    2017-01-01

    The evolution of altruistic behaviour, which is costly to the donor but beneficial for the recipient, is among the most intriguing questions in evolutionary biology. Several theories have been proposed to explain it, including kin selection, group selection and reciprocity. Here we propose that microbes that manipulate their hosts to act altruistically could be favoured by selection, and may play a role in the widespread occurrence of altruism. Using computational models, we find that microbe-induced altruism can explain the evolution of host altruistic behaviour under wider conditions than host-centred theories, including in a fully mixed host population, without repeating interactions or individual recognition. Our results suggest that factors such as antibiotics that kill microbes might negatively affect cooperation in a wide range of organisms. PMID:28079112

  14. Gut microbes of mammalian herbivores facilitate intake of plant toxins.

    Science.gov (United States)

    Kohl, Kevin D; Weiss, Robert B; Cox, James; Dale, Colin; Dearing, M Denise

    2014-10-01

    The foraging ecology of mammalian herbivores is strongly shaped by plant secondary compounds (PSCs) that defend plants against herbivory. Conventional wisdom holds that gut microbes facilitate the ingestion of toxic plants; however, this notion lacks empirical evidence. We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. Creosote toxins altered the population structure of the gut microbiome to facilitate an increase in abundance of genes that metabolise toxic compounds. In addition, woodrats were unable to consume creosote toxins after the microbiota was disrupted with antibiotics. Last, ingestion of toxins by naïve hosts was increased through microbial transplants from experienced donors. These results demonstrate that microbes can enhance the ability of hosts to consume PSCs and therefore expand the dietary niche breadth of mammalian herbivores.

  15. Emerging Sponge Models of Animal-Microbe Symbioses

    Science.gov (United States)

    Pita, Lucia; Fraune, Sebastian; Hentschel, Ute

    2016-01-01

    Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host–microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota. PMID:28066403

  16. Theory of microbe motion in a poisoned environment.

    Science.gov (United States)

    Hoell, Christian; Löwen, Hartmut

    2011-10-01

    The motility of a microorganism which tries to avoid a poisoned environment by chemotaxis is studied within a simple model which couples its velocity to the concentration field of the poison. The latter is time independent but inhomogeneous in space. The presence of the poison is assumed to irreversibly reduce the propulsion speed. The model is solved analytically for different couplings of the total poison dose experienced by the microbe to the propulsion mechanism. In a stationary poison field resulting from a constant emission of a fixed point source, we find a power law for the distance traveled by the microbe as a function of time with a nonuniversal exponent which depends on the coupling in the model. With an inverted sign in the couplings, the acceleration of microbe motion induced by a food field can also be described.

  17. Association of an ACSL1 gene variant with polyunsaturated fatty acids in bovine skeletal muscle

    Directory of Open Access Journals (Sweden)

    Widmann Philipp

    2011-11-01

    Full Text Available Abstract Background The intramuscular fat deposition and the fatty acid profiles of beef affect meat quality. High proportions of unsaturated fatty acids are related to beef flavor and are beneficial for the nutritional value of meat. Moreover, a variety of clinical and epidemiologic studies showed that particularly long-chain omega-3 fatty acids from animal sources have a positive impact on human health and disease. Results To screen for genetic factors affecting fatty acid profiles in beef, we initially performed a microsatellite-based genome scan in a F2 Charolais × German Holstein resource population and identified a quantitative trait locus (QTL for fatty acid composition in a region on bovine chromosome 27 where previously QTL affecting marbling score had been detected in beef cattle populations. The long-chain acyl-CoA synthetase 1 (ACSL1 gene was identified as the most plausible functional and positional candidate gene in the QTL interval due to its direct impact on fatty acid metabolism and its position in the QTL interval. ACSL1 is necessary for synthesis of long-chain acyl-CoA esters, fatty acid degradation and phospholipid remodeling. We validated the genomic annotation of the bovine ACSL1 gene by in silico comparative sequence analysis and experimental verification. Re-sequencing of the complete coding, exon-flanking intronic sequences, 3' untranslated region (3'UTR and partial promoter region of the ACSL1 gene revealed three synonymous mutations in exons 6, 7, and 20, six noncoding intronic gene variants, six polymorphisms in the promoter region, and four variants in the 3' UTR region. The association analysis identified the gene variant in intron 5 of the ACSL1 gene (c.481-233A>G to be significantly associated with the relative content of distinct fractions and ratios of fatty acids (e.g., n-3 fatty acids, polyunsaturated, n-3 long-chain polyunsaturated fatty acids, trans vaccenic acid in skeletal muscle. A tentative association

  18. Microbes bind complement inhibitor factor H via a common site.

    Directory of Open Access Journals (Sweden)

    T Meri

    Full Text Available To cause infections microbes need to evade host defense systems, one of these being the evolutionarily old and important arm of innate immunity, the alternative pathway of complement. It can attack all kinds of targets and is tightly controlled in plasma and on host cells by plasma complement regulator factor H (FH. FH binds simultaneously to host cell surface structures such as heparin or glycosaminoglycans via domain 20 and to the main complement opsonin C3b via domain 19. Many pathogenic microbes protect themselves from complement by recruiting host FH. We analyzed how and why different microbes bind FH via domains 19-20 (FH19-20. We used a selection of FH19-20 point mutants to reveal the binding sites of several microbial proteins and whole microbes (Haemophilus influenzae, Bordetella pertussis, Pseudomonas aeruginosa, Streptococcus pneumonia, Candida albicans, Borrelia burgdorferi, and Borrelia hermsii. We show that all studied microbes use the same binding region located on one side of domain 20. Binding of FH to the microbial proteins was inhibited with heparin showing that the common microbial binding site overlaps with the heparin site needed for efficient binding of FH to host cells. Surprisingly, the microbial proteins enhanced binding of FH19-20 to C3b and down-regulation of complement activation. We show that this is caused by formation of a tripartite complex between the microbial protein, FH, and C3b. In this study we reveal that seven microbes representing different phyla utilize a common binding site on the domain 20 of FH for complement evasion. Binding via this site not only mimics the glycosaminoglycans of the host cells, but also enhances function of FH on the microbial surfaces via the novel mechanism of tripartite complex formation. This is a unique example of convergent evolution resulting in enhanced immune evasion of important pathogens via utilization of a "superevasion site."

  19. The microbe-free plant: fact or artifact?

    Science.gov (United States)

    Partida-Martínez, Laila P; Heil, Martin

    2011-01-01

    Plant-microbe interactions are ubiquitous. Plants are threatened by pathogens, but they are even more commonly engaged in neutral or mutualistic interactions with microbes: belowground microbial plant associates are mycorrhizal fungi, Rhizobia, and plant-growth promoting rhizosphere bacteria, aboveground plant parts are colonized by internally living bacteria and fungi (endophytes) and by microbes in the phyllosphere (epiphytes). We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host-plant affects multiple vital parameters such as plant nutrition, growth rate, resistance to biotic and abiotic stressors, and plant survival and distribution. The mechanisms involved reach from direct ones such as nutrient acquisition, the production of plant hormones, or direct antibiosis, to indirect ones that are mediated by effects on host resistance genes or via interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the current environment. Thus, the outcome of the interaction for the plant host is highly context dependent. We argue that considering the microbe-free plant as the "normal" or control stage significantly impairs research into important phenomena such as (1) phenotypic and epigenetic plasticity, (2) the "normal" ecological outcome of a given interaction, and (3) the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host

  20. The microbe-free plant: fact or artefact?

    Directory of Open Access Journals (Sweden)

    Laila P. Pamela Partida-Martinez

    2011-12-01

    Full Text Available Plant-microbe interactions are ubiquitous. Plants are often colonized by pathogens but even more commonly engaged in neutral or mutualistic interactions with microbes: below-ground microbial plant associates are mycorrhizal fungi, Rhizobia and rhizosphere bacteria, above-ground plant parts are colonized by bacterial and fungal endophytes and by microbes in the phyllosphere. We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host plant affects plant nutrition, growth rate, resistance to biotic and abiotic stress, and plant survival and distribution. The mechanisms involved reach from nutrient acquisition, the production of plant hormones or direct antibiosis to effects on host resistance genes or interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the environment. Thus, the outcome of the interaction is highly context-dependent. Considering the microbe-free plant as the ‘normal’ or control stage significantly impairs research into important phenomena such as (1 phenotypic and epigenetic plasticity, (2 the ‘normal’ ecological outcome of a given interaction and (3 the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host-endophyte combinations under various environmental conditions and study at the genetic, transcriptional and physiological level the parameters that shift the interaction along the mutualism

  1. UNDERSTANDING SOCIAL INTERACTIONS OF MICROBES USING TRANSCRIPTOMICS : A CODICIL

    Directory of Open Access Journals (Sweden)

    Prem Saran Tirumalai

    2015-06-01

    Full Text Available Sociobiology of microbes is an emerging branch of science that has delivered interesting and intriguing research findings over the last few years. The revelations are such that the research perspective of microbes is gradually drifting from pure culture analysis to community analysis. We review to substantiate the need for microbial socio-bio studies and codicil the decade long research pursuit and their findings using advanced technologies of Microarrays and Next Generation Sequencing, prompting for more lunge in transcriptomic and metatranscriptomic studies.

  2. Metagenomic search strategies for interactions among plants and multiple microbes

    Directory of Open Access Journals (Sweden)

    Ulrich Karl Melcher

    2014-06-01

    Full Text Available Plants harbor multiple microbes. Metagenomics can facilitate understanding of the significance, for the plant, of the microbes and of the interactions among them. However, current approaches to metagenomic analysis of plants are computationally time-consuming. Efforts to speed the discovery process include improvement of computational speed, condensing the sequencing reads into smaller datasets before BLAST searches, simplifying the target database of BLAST searches, and flipping the roles of metagenomic and reference datasets. The latter is exemplified by the E-probe diagnostic nucleic acid analysis (EDNA approach originally devised for improving analysis during plant quarantine.

  3. Fats and fatty acids

    Science.gov (United States)

    The absolute fat requirement of the human species is the amount of essential fatty acids needed to maintain optimal fatty acid composition of all tissues and normal eicosanoid synthesis. At most, this requirement is no more than about 5% of an adequate energy intake. However, fat accounts for appro...

  4. Host responses to the pathogen Mycobacterium avium subsp. paratuberculosis and beneficial microbes exhibit host sex specificity.

    Science.gov (United States)

    Karunasena, Enusha; McMahon, K Wyatt; Chang, David; Brashears, Mindy M

    2014-08-01

    Differences between microbial pathogenesis in male and female hosts are well characterized in disease conditions connected to sexual transmission. However, limited biological insight is available on variances attributed to sex specificity in host-microbe interactions, and it is most often a minimized variable outside these transmission events. In this work, we studied two gut microbes-a pathogen, Mycobacterium avium subsp. paratuberculosis, and a probiotic, Lactobacillus animalis NP-51-and the interaction between each agent and the male and female gastrointestinal systems. This trial was conducted in BALB/c mice (n=5 per experimental group and per sex at a given time point), with analysis at four time points over 180 days. Host responses to M.avium subsp. paratuberculosis and L. animalis were sensitive to sex. Cytokines that were significantly different (P ≤ 0.05) betweenthe sexes included interleukin-1α/β (IL-1α/β), IL-17, IL-6, IL-10, IL-12, and gamma interferon (IFN-) and were dependent on experimental conditions. However, granulocyte-macrophage colony-stimulating factor (GM-CSF), vascular endothelial growth factor (VEGF), and IL-13/23 showed no sex specificity. A metabolomics study indicated a 0.5- to 2.0-fold (log2 scale) increase in short-chain fatty acids (butyrate and acetate) in males and greater increases in o-phosphocholine or histidine from female colon tissues; variances distinct to each sex were observed with age or long-term probiotic consumption. Two genera, Staphylococcus and Roseburia, were consistently overrepresented in females compared to males; other species were specific to one sex but fluctuated depending on experimental conditions. The differences observed suggest that male and female gut tissues and microbiota respond to newly introduced microorganisms differently and that gut-associated microorganisms with host immune system responses and metabolic activity are supported by biology distinct to the host sex.

  5. Halogenated fatty acids

    DEFF Research Database (Denmark)

    Mu, Huiling; Wesén, Clas; Sundin, Peter

    1997-01-01

    Chlorinated fatty acids have been found to be major contributors to organohalogen compounds in fish, bivalves, jellyfish, and lobster, and they have been indicated to contribute considerably to organohalogens in marine mammals. Brominated fatty acids have been found in marine sponges. Also......, chlorinated lipids have been found in meat exposed to hypochlorite disinfected water, and in chlorine-treated flour and in products made from such flour. Following exposure to chlorine bleached pulp mill effluents, aquatic organisms may have elevated concentrations of chlorinated fatty acids in their lipids....... However, a natural production of halogenated fatty acids is also possible. In this paper we summarize the present knowledge of the occurrence of halogenated fatty acids in lipids and suggested ways of their formation. In Part II (Trends Anal. Chem. 16 (1997) 274) we deal with methods...

  6. Physiological function and ecological aspects of fatty acid-amino acid conjugates in insects.

    Science.gov (United States)

    Yoshinaga, Naoko

    2016-07-01

    In tritrophic interactions, plants recognize herbivore-produced elicitors and release a blend of volatile compounds (VOCs), which work as chemical cues for parasitoids or predators to locate their hosts. From detection of elicitors to VOC emissions, plants utilize sophisticated systems that resemble the plant-microbe interaction system. Fatty acid-amino acid conjugates (FACs), a class of insect elicitors, resemble compounds synthesized by microbes in nature. Recent evidence suggests that the recognition of insect elicitors by an ancestral microbe-associated defense system may be the origin of tritrophic interactions mediated by FACs. Here we discuss our findings in light of how plants have customized this defense to be effective against insect herbivores, and how some insects have successfully adapted to these defenses.

  7. Terrestrial microbes in martian and chondritic meteorites

    Science.gov (United States)

    Airieau, S.; Picenco, Y.; Andersen, G.

    2007-08-01

    Bank sequences using the BLAST program. The closest matches were in the genus Microbacterium. Soil and plant isolates were close relatives by sequence comparison. Los Angeles. After 11 months of incubation in a fridge, a yellow colony grew at the center of a culture plate of Los Angeles dust grains (1:1000 R2A). There was no cell activity in the other agars. A DNA extraction yielded no usable results [7]. Sequencing was not performed because the culture plate became contaminated with outside organisms that overtook the colony of interest. Conclusions: The sequences for EET 87770 and Leoville were of a good quality and the sequence reads were long, so the data are clear that these are typical soil and/or plant-related bacteria commonly found in Earth habitats. Microbial species present in a dozen chondritic samples from isolates are not yet identified, and the contaminant in Los Angeles needs to be recovered. In addition, isotopic analyses of samples with various amounts of microbial contamination could help quantified isotopic impact of microbes on protoplanetary chemistry in these rocks. References : [1] Gounelle, M. and Zolensky M. LPS, (2001) LPS XXXII, Abstract #999. [2] Fries, M. et al. (2005) Meteoritical Society Meeting 68, Abstract # 5201. [3] Burckle, L. H. and Delaney, J. S (1999) Meteoritics & Planet. Sci., 32, 475-478. [4] Whitby, C. et al. (2000) ) LPS XXXI, Abstract #1732. [5] Airieau, S. A. et al (2005) Geochim. Cosmochim. Acta, 69, 4166-4171. [6] Unpublished data, with H. J. Cleaves, A. Aubrey, J. Bada (Scripps Institution of Oceanography), M. Thiemens (UC San Diego) and M. Fogel (Carnegie Institution of Washington). [7] Unpublished data, with A. Steele (CIW), and N. Wainwright (Marine Biological Laboratory). Acknowledgements: Lisa Welleberger for access to SNC samples at USNM; Ralph Harvey for organizing ANSMET; Denise C. Thiry and Andrew Steele for long term storage of samples, NormWainwright for LAL measurements. A small portion of this work was funded with a

  8. The high life: Transport of microbes in the atmosphere

    Science.gov (United States)

    Smith, David J.; Griffin, Dale W.; Jaffe, Daniel A.

    2011-07-01

    Microbes (bacteria, fungi, algae, and viruses) are the most successful types of life on Earth because of their ability to adapt to new environments, reproduce quickly, and disperse globally. Dispersal occurs through a number of vectors, such as migrating animals or the hydrological cycle, but transport by wind may be the most common way microbes spread. General awareness of airborne microbes predates the science of microbiology. People took advantage of wild airborne yeasts to cultivate lighter, more desirable bread as far back as ancient Egypt by simply leaving a mixture of grain and liquids near an open window. In 1862, Louis Pasteur's quest to disprove spontaneous generation resulted in the discovery that microbes were actually single-celled, living creatures, prevalent in the environment and easily killed with heat (pasteurization). His rudimentary experiments determined that any nutrient medium left open to the air would eventually teem with microbial life because of free-floating, colonizing cells. The same can happen in a kitchen: Opportunistic fungal and bacterial cells cause food items exposed to the air to eventually spoil.

  9. Phenolic Acids in Plant-Soil-Microbe System: A Review

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Phenolic acids are very common compounds in pedosphere. The objective of this review was to summarize the current knowledge of the behaviors of phenolic acids in plant-soil-microbe system. When phenolic acids originated from leaching, decomposition and exudation of living and dead plant tissues enter soils, they can react physicochemically with soil particle surfaces and/or incorporate into humic matter. Phenolic acids desorbed from soil particle surfaces and remained in solution phase can be utilized by microbe as carbon sources and absorbed by plants. The degradation products of phenolic acids by microbe include some organic and/or inorganic compounds such as new phenolic acids. In addition, phenolic acids in soils can stimulate population and activity of microbe. Phenolic acids can inhibit plants growth by affecting ion leakage, phytohormone activity, membrane permeability, hydraulic conductivity, net nutrient uptake, and enzyme activity. Behaviors of phenolic acids in soils are influenced by other organic compounds (phenolic acids, methionine, glucose, etc.) and/or inorganic ions. The role of phenolic acids as allelopathic agents should not be neglected only based on their low specific concentrations in natural soils, because numbers and interactions of phenolic acids will increase their allelopathic activities.

  10. Microbes from raw milk for fermented dairy products

    NARCIS (Netherlands)

    Wouters, J.T.M.; Ayad, E.H.E.; Hugenholtz, J.; Smit, G.

    2002-01-01

    Milk has a high nutritive value, not only For the new-born mammal and for the human consumer, but also for microbes. Raw milk kept at roam temperature will be liable to microbial spoilage. After some days, the milk will spontaneously become sour. This is generally due to the activity of lactic acid

  11. Seeing is believing: what experiments with microbes reveal about evolution.

    Science.gov (United States)

    van Ditmarsch, Dave; Xavier, Joao B

    2014-01-01

    Darwin's theory of natural selection is among the most powerful ideas in science, yet evolutionary ideas remain challenged to this day. This is in part because evolution often cannot be directly observed. Simple experiments with microbes can change that by enabling direct observation of evolutionary processes.

  12. Photoheterotrophic microbes in the Arctic Ocean in summer and winter.

    Science.gov (United States)

    Cottrell, Matthew T; Kirchman, David L

    2009-08-01

    Photoheterotrophic microbes, which are capable of utilizing dissolved organic materials and harvesting light energy, include coccoid cyanobacteria (Synechococcus and Prochlorococcus), aerobic anoxygenic phototrophic (AAP) bacteria, and proteorhodopsin (PR)-containing bacteria. Our knowledge of photoheterotrophic microbes is largely incomplete, especially for high-latitude waters such as the Arctic Ocean, where photoheterotrophs may have special ecological relationships and distinct biogeochemical impacts due to extremes in day length and seasonal ice cover. These microbes were examined by epifluorescence microscopy, flow cytometry, and quantitative PCR (QPCR) assays for PR and a gene diagnostic of AAP bacteria (pufM). The abundance of AAP bacteria and PR-containing bacteria decreased from summer to winter, in parallel with a threefold decrease in the total prokaryotic community. In contrast, the abundance of Synechococcus organisms did not decrease in winter, suggesting that their growth was supported by organic substrates. Results from QPCR assays revealed no substantial shifts in the community structure of AAP bacteria and PR-containing bacteria. However, Arctic PR genes were different from those found at lower latitudes, and surprisingly, they were not similar to those in Antarctic coastal waters. Photoheterotrophic microbes appear to compete successfully with strict heterotrophs during winter darkness below the ice, but AAP bacteria and PR-containing bacteria do not behave as superior competitors during the summer.

  13. The high life: Transport of microbes in the atmosphere

    Science.gov (United States)

    Smith, D.J.; Griffin, Dale W.; Jaffe, D.A.

    2011-01-01

    Microbes (bacteria, fungi, algae, and viruses) are the most successful types of life on Earth because of their ability to adapt to new environments, reproduce quickly, and disperse globally. Dispersal occurs through a number of vectors, such as migrating animals or the hydrological cycle, but transport by wind may be the most common way microbes spread. General awareness of airborne microbes predates the science of microbiology. People took advantage of wild airborne yeasts to cultivate lighter, more desirable bread as far back as ancient Egypt by simply leaving a mixture of grain and liquids near an open window. In 1862, Louis Pasteur's quest to disprove spontaneous generation resulted in the discovery that microbes were actually single-celled, living creatures, prevalent in the environment and easily killed with heat (pasteurization). His rudimentary experiments determined that any nutrient medium left open to the air would eventually teem with microbial life because of free-floating, colonizing cells. The same can happen in a kitchen: Opportunistic fungal and bacterial cells cause food items exposed to the air to eventually spoil.

  14. Cooperation and conflict in host-microbe relations.

    Science.gov (United States)

    Ulvestad, Elling

    2009-05-01

    Hosts and microbes associate in a variety of relations along a continuum ranging from symbiotic to pathogenic. Defence mechanisms have been evolutionarily selected in both hosts and microbes to protect the organism's integrity. Such defences have to be utilized with caution. They must be adapted to the tasks at hand; otherwise any symbiotic relation would be impossible. To explain this cautionary use of defences we need to understand how life on Earth evolved into cooperative and competing entities at various levels of organization. The purpose of this article is to review theory and selected mechanisms relating to the evolution and development of host-microbe interactions, with special emphasis on host responses. The rationale is that without theory, extrapolations from misleading observations can dominate and distort, for a significant time, the course of a scientific field. The argument is set forth that social evolution theory provides a conceptual framework for addressing questions relating to interaction between hosts and microbes. The article is a partial summary of arguments presented in my book Defending life - the nature of host-parasite relations.

  15. Fatty Acid-Derived Biofuels and Chemicals Production in Saccharomyces cerevisiae.

    Science.gov (United States)

    Zhou, Yongjin J; Buijs, Nicolaas A; Siewers, Verena; Nielsen, Jens

    2014-01-01

    Volatile energy costs and environmental concerns have spurred interest in the development of alternative, renewable, sustainable, and cost-effective energy resources. Environment-friendly processes involving microbes can be used to synthesize advanced biofuels. These fuels have the potential to replace fossil fuels in supporting high-power demanding machinery such as aircrafts and trucks. From an engineering perspective, the pathway for fatty acid biosynthesis is an attractive route for the production of advanced fuels such as fatty acid ethyl esters, fatty alcohols, and alkanes. The robustness and excellent accessibility to molecular genetics make the yeast Saccharomyces cerevisiae a suitable host for the purpose of bio-manufacturing. Recent advances in metabolic engineering, as well as systems and synthetic biology, have now provided the opportunity to engineer yeast metabolism for the production of fatty acid-derived fuels and chemicals.

  16. Trans Fatty Acids

    Science.gov (United States)

    Doyle, Ellin

    1997-09-01

    Fats and their various fatty acid components seem to be a perennial concern of nutritionists and persons concerned with healthful diets. Advice on the consumption of saturated, polyunsaturated, monounsaturated, and total fat bombards us from magazines and newspapers. One of the newer players in this field is the group of trans fatty acids found predominantly in partially hydrogenated fats such as margarines and cooking fats. The controversy concerning dietary trans fatty acids was recently addressed in an American Heart Association (AHA) science advisory (1) and in a position paper from the American Society of Clinical Nutrition/American Institute of Nutrition (ASCN/AIN) (2). Both reports emphasize that the best preventive strategy for reducing risk for cardiovascular disease and some types of cancer is a reduction in total and saturated fats in the diet, but a reduction in the intake of trans fatty acids was also recommended. Although the actual health effects of trans fatty acids remain uncertain, experimental evidence indicates that consumption of trans fatty acids adversely affects serum lipid levels. Since elevated levels of serum cholesterol and triacylglycerols are associated with increased risk of cardiovascular disease, it follows that intake of trans fatty acids should be minimized.

  17. Microbes in Beach Sands: Integrating Environment, Ecology and Public Health.

    Science.gov (United States)

    Whitman, Richard; Harwood, Valerie J; Edge, Thomas A; Nevers, Meredith; Byappanahalli, Muruleedhara; Vijayavel, Kannappan; Brandão, João; Sadowsky, Michael J; Alm, Elizabeth Wheeler; Crowe, Allan; Ferguson, Donna; Ge, Zhongfu; Halliday, Elizabeth; Kinzelman, Julie; Kleinheinz, Greg; Przybyla-Kelly, Kasia; Staley, Christopher; Staley, Zachery; Solo-Gabriele, Helena M

    2014-09-01

    Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in

  18. Crosstalk of Escherichia coli FadR with global regulators in expression of fatty acid transport genes.

    Directory of Open Access Journals (Sweden)

    Youjun Feng

    Full Text Available Escherichia coli FadR plays two regulatory roles in fatty acid metabolism. FadR represses the fatty acid degradation (fad system and activates the unsaturated fatty acid synthetic pathway. Cross-talk between E. coli FadR and the ArcA-ArcB oxygen-responsive two-component system was observed that resulted in diverse regulation of certain fad regulon β-oxidation genes. We have extended such analyses to the fadL and fadD genes, the protein products of which are required for long chain fatty acid transport and have also studied the role of a third global regulator, the CRP-cAMP complex. The promoters of both the fadL and fadD genes contain two experimentally validated FadR-binding sites plus binding sites for ArcA and CRP-cAMP. Despite the presence of dual binding sites FadR only modestly regulates expression of these genes, indicating that the number of binding sites does not determine regulatory strength. We report complementary in vitro and in vivo studies indicating that the CRP-cAMP complex directly activates expression of fadL and fadD as well as the β-oxidation gene, fadH. The physiological relevance of the fadL and fadD transcription data was validated by direct assays of long chain fatty acid transport.

  19. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

    Science.gov (United States)

    Ma, Wei; Huang, Chuanbo; Zhou, Yuan; Li, Jianwei; Cui, Qinghua

    2017-01-01

    The microbiota colonized on human body is renowned as “a forgotten organ” due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern. PMID:28071710

  20. New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Using a fluorescence microscope and EPMA,abundant microbe "bodies" and clear microbic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor.The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules.According to their morphological features,the microbes are classified into two types:one is named clumpy microbe,which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral,resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe,which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer,leading to potato-shaped nodules with relatively smooth surfaces.It also can be seen that the two types of microbes are intergrown together,resulting in nodules complicated in compositions and shapes.

  1. New evidence of microbe origin for ferromanganese nodules from the East Pacific deep sea floor

    Institute of Scientific and Technical Information of China (English)

    胡文宣; 周怀阳; 顾连兴; 张文兰; 陆现彩; 符琦; 潘建明; 张海生

    2000-01-01

    Using a fluorescence microscope and EPMA, abundant microbe "bodies" and clear mi-crobic fluorescent microstructure are determined in the ferromanganese nodules recently collected from the East Pacific deep sea floor. The microbic fluorescent structure shows a close relation to the formation of the ferromanganese nodules. According to their morphological features, the microbes are classified into two types: one is named clumpy microbe, which takes a bar-shaped manganese mineral as a pillar and grows like fasciculate coral, resulting in irregular cauliflorate nodules with rough surfaces; the other is called filamentous microbe, which grows in very thin arcuate and/or concentric circular laminae composed of a microbe layer and a metal (manganese and iron)-rich layer, leading to potato-shaped nodules with relatively smooth surfaces. It also can be seen that the two types of microbes are intergrown together, resulting in nodules complicated in compositions and shapes.

  2. Metagenomic analysis of Atriplex microbiomes: Investigating Plant-microbe interactions that enhance adaptation to extreme habitats

    Science.gov (United States)

    Cryptic symbiotic microbes influence host adaptation by improving nutrient uptake or stress tolerance. Current technologies for increasing plant productivity, whether for food and fuel production or for restoration and remediation, often utilize approaches that bypass, rather than leverage, microb...

  3. A systems biology approach to studying the role of microbes in human health.

    Science.gov (United States)

    Thiele, Ines; Heinken, Almut; Fleming, Ronan M T

    2013-02-01

    Host-microbe interactions play a crucial role in human health and disease. Of the various systems biology approaches, reconstruction of genome-scale metabolic networks combined with constraint-based modeling has been particularly successful at in silico predicting the phenotypic characteristics of single organisms. Here, we summarize recent studies, which have applied this approach to investigate microbe-microbe and host-microbe metabolic interactions. This approach can be also expanded to investigate the properties of an entire microbial community, as well as single organisms within the community. We illustrate that the constraint-based modeling approach is suitable to model host-microbe interactions at molecular resolution and will enable systematic investigation of metabolic links between the human host and its microbes. Such host-microbe models, combined with experimental data, will ultimately further our understanding of how microbes influence human health.

  4. Fatty Acid Biosynthesis IX

    DEFF Research Database (Denmark)

    Carey, E. M.; Hansen, Heinz Johs. Max; Dils, R.

    1972-01-01

    # 1. I. [I-14C]Acetate was covalently bound to rabbit mammary gland fatty acid synthetase by enzymic transacylation from [I-14C]acetyl-CoA. Per mole of enzyme 2 moles of acetate were bound to thiol groups and up to I mole of acetate was bound to non-thiol groups. # 2. 2. The acetyl-fatty acid...... synthetase complex was isolated free from acetyl-CoA. It was rapidly hydrolysed at 30°C, but hydrolysis was greatly diminished at o°C and triacetic lactone synthesis occurred. In the presence of malonyl-CoA and NADPH, all the acetate bound to fatty acid synthetase was incorporated into long-chain fatty acids....... Hydrolysis of bound acetate and incorporation of bound acetate into fatty acids were inhibited to the same extent by guanidine hydrochloride. # 3. 3. Acetate was also covalently bound to fatty acid synthetase by chemical acetylation with [I-14C]acetic anhydride in the absence of CoASH. A total of 60 moles...

  5. Evolutionary adaptation in three-way interactions between plants, microbes and arthropods

    NARCIS (Netherlands)

    Biere, A.; Tack, A.J.M.

    2013-01-01

    Evolutionary adaptations in interactions between plants, microbes and arthropods are generally studied in interactions that involve only two of these groups, that is, plants and microbes, plants and arthropods or arthropods and microbes. We review the accumulating evidence from a wide variety of

  6. Intracellular plant microbe associations: secretory pathways and the formation of perimicrobial compartments

    NARCIS (Netherlands)

    Ivanov, S.E.; Fedorova, E.; Bisseling, T.

    2010-01-01

    Plants can establish intracellular interactions with symbiotic as well as pathogenic microbes. Such intracellular accommodation of microbes always involves the formation of a host membrane compartment - the interface between the cytoplasm of the host and the microbe. These are the so-called perimicr

  7. Role of bioactive fatty acids in nonalcoholic fatty liver disease.

    Science.gov (United States)

    Juárez-Hernández, Eva; Chávez-Tapia, Norberto C; Uribe, Misael; Barbero-Becerra, Varenka J

    2016-08-02

    Nonalcoholic fatty liver disease (NAFLD) is characterized by fat deposition in hepatocytes, and a strong association with nutritional factors. Dietary fatty acids are classified according to their biochemical properties, which confer their bioactive roles. Monounsaturated fatty acids have a dual role in various human and murine models. In contrast, polyunsaturated fatty acids exhibit antiobesity, anti steatosic and anti-inflammatory effects. The combination of these forms of fatty acids-according to dietary type, daily intake and the proportion of n-6 to n-3 fats-can compromise hepatic lipid metabolism. A chemosensory rather than a nutritional role makes bioactive fatty acids possible biomarkers for NAFLD. Bioactive fatty acids provide health benefits through modification of fatty acid composition and modulating the activity of liver cells during liver fibrosis. More and better evidence is necessary to elucidate the role of bioactive fatty acids in nutritional and clinical treatment strategies for patients with NAFLD.

  8. Microbe-associated immunomodulatory metabolites: Influence on T cell fate and function.

    Science.gov (United States)

    Castro, C N; Freitag, J; Berod, L; Lochner, M; Sparwasser, T

    2015-12-01

    During the past two decades, a growing interest surrounding the interaction between microbe-associated molecular patterns (MAMPs) and pattern recognition receptors has occurred. This attention is now driven alongside bacterial-derived metabolites, which impact immune cell differentiation and function. Hence, this review introduces the term meta-MAMP as a means to classify the microbial derived-metabolites, which influence the immune response by affecting specific cellular processes. We discuss two prominent examples of meta-MAMPs: the first, rapamycin (isolated from Streptomyces), was discovered in the 1970s and since then has been thoroughly studied. The second, soraphen A (isolated from Myxobacteria), was discovered in the early 1990s but only recently identified as a promising immunomodulator. Both meta-MAMPs are similar in their remarkable capacity to modulate T cell fate by targeting key metabolic pathways triggered upon T cell activation. In this context, we highlight the progress made in the field of immunometabolism and the possibility of modulating metabolic pathways such as cellular fatty acid metabolism as a strategy for immunomodulation. We focus on the use of microbial metabolites as auspicious agents for T cell fate modulation.

  9. Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation.

    Science.gov (United States)

    Kaiser, Christina; Kilburn, Matt R; Clode, Peta L; Fuchslueger, Lucia; Koranda, Marianne; Cliff, John B; Solaiman, Zakaria M; Murphy, Daniel V

    2015-03-01

    Plants rapidly release photoassimilated carbon (C) to the soil via direct root exudation and associated mycorrhizal fungi, with both pathways promoting plant nutrient availability. This study aimed to explore these pathways from the root's vascular bundle to soil microbial communities. Using nanoscale secondary ion mass spectrometry (NanoSIMS) imaging and (13) C-phospho- and neutral lipid fatty acids, we traced in-situ flows of recently photoassimilated C of (13) CO2 -exposed wheat (Triticum aestivum) through arbuscular mycorrhiza (AM) into root- and hyphae-associated soil microbial communities. Intraradical hyphae of AM fungi were significantly (13) C-enriched compared to other root-cortex areas after 8 h of labelling. Immature fine root areas close to the root tip, where AM features were absent, showed signs of passive C loss and co-location of photoassimilates with nitrogen taken up from the soil solution. A significant and exclusively fresh proportion of (13) C-photosynthates was delivered through the AM pathway and was utilised by different microbial groups compared to C directly released by roots. Our results indicate that a major release of recent photosynthates into soil leave plant roots via AM intraradical hyphae already upstream of passive root exudations. AM fungi may act as a rapid hub for translocating fresh plant C to soil microbes.

  10. Endophytic and Epiphytic Microbes as Sources of Bioactive Agents

    Directory of Open Access Journals (Sweden)

    David J. Newman

    2015-05-01

    Full Text Available Beginning with the report by Stierle and Strobel in 1993 on taxol(R production by an endophytic fungus 1, it is possible that a number of the agents now used as leads to treatments of diseases in man, are not produced by the plant or invertebrate host from which they were first isolated and identified.They are probably the product of a microbe in, on or around the macroorganism. At times there is an intricate dance between a precursor produced by a microbe, and interactions within the macroorganism, or in certain cases, a fungus, that ends up with the production of a novel agent that has potential as a treatment for a human disease. This report will give examples from insects, plants and marine invertebrates.

  11. Endophytic and Epiphytic Microbes as ``Sources'' of Bioactive Agents

    Science.gov (United States)

    Newman, David; Cragg, Gordon

    2015-05-01

    Beginning with the report by Stierle and Strobel in 1993 on taxol(R) production by an endophytic fungus 1, it is possible that a number of the agents now used as leads to treatments of diseases in man, are not produced by the plant or invertebrate host from which they were first isolated and identified.They are probably the product of a microbe in, on or around the macroorganism. At times there is an intricate “dance” between a precursor produced by a microbe, and interactions within the macroorganism, or in certain cases, a fungus, that ends up with the production of a novel agent that has potential as a treatment for a human disease. This report will give examples from insects, plants and marine invertebrates.

  12. Accumulator-Based Deep-Sea Microbe Gastight Sampling Technique

    Institute of Scientific and Technical Information of China (English)

    HUANG Zhong-hua; LIU Shao-jun; JIN Bo

    2006-01-01

    The accumulator is used as a pressure compensation device to realize deep-sea microbe gastight sampling. Four key states of the accumulator are proposed to describe the pressure compensation process and a corresponding mathematical model is established to investigate the relationship between the results of pressure compensation and the parameters of the accumulator. Simulation results show that during the falling process of the sampler, the accumulator's real opening pressure is greater than its precharge pressure; when the sampling depth is 6000 m and the accumulator's precharge pressure is less than 30 MPa, to increase the accumulator's precharge pressure can improve pressure compensation results obviously. Laboratory experiments at 60 MPa show that the accumulator is an effective and reliable pressure compensation device for deep-sea microbe samplers. The success in sea trial at a depth of 2000 m in the South China Sea shows that the mathematical model and laboratory experiment results are reliable.

  13. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils;

    2015-01-01

    The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly...... and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate...... storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described...

  14. Genetic mechanisms of prebiotic oligosaccharide metabolism in probiotic microbes.

    Science.gov (United States)

    Goh, Yong Jun; Klaenhammer, Todd R

    2015-01-01

    Recent insights into the relationship between the human gut and its resident microbiota have revolutionized our appreciation of this symbiosis and its impact on health and disease development. Accumulating evidence on probiotic and prebiotic interventions has demonstrated promising effects on promoting gastrointestinal health by modulating the microbiota toward the enrichment of beneficial microorganisms. However, the precise mechanisms of how prebiotic nondigestible oligosaccharides are metabolized by these beneficial microbes in vivo remain largely unknown. Genome sequencing of probiotic lactobacilli and bifidobacteria has revealed versatile carbohydrate metabolic gene repertoires dedicated to the catabolism of various oligosaccharides. In this review, we highlight recent findings on the genetic mechanisms involved in the utilization of prebiotic fructooligosaccharides, β-galactooligosaccharides, human milk oligosaccharides, and other prebiotic candidates by these probiotic microbes.

  15. Microbes Drive Evolution of Animals and Plants: the Hologenome Concept

    Directory of Open Access Journals (Sweden)

    Eugene Rosenberg

    2016-03-01

    Full Text Available The hologenome concept of evolution postulates that the holobiont (host plus symbionts with its hologenome (host genome plus microbiome is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.

  16. Predominately Uncultured Microbes as Sources of Bioactive Agents

    Science.gov (United States)

    Newman, David J.

    2016-01-01

    In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving “state of the art” genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules. PMID:27917159

  17. Microbes Drive Evolution of Animals and Plants: the Hologenome Concept.

    Science.gov (United States)

    Rosenberg, Eugene; Zilber-Rosenberg, Ilana

    2016-03-31

    The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel. Copyright © 2016 Rosenberg and Zilber-Rosenberg.

  18. Exploring laser-guided metal deposition through a microbe metabolite

    OpenAIRE

    2009-01-01

    Purpose: The purpose of the paper is to describe exploring laser-guided metal deposition through a microbe metabolite.Design/methodology/approach: A maskless micro-fabrication of laser-guided deposition process through the metabolite of Acidophilic bacteria Thiobacillus ferrooxidans (T.f.) is explored.Findings: The authors have conducted an analysis of the metal deposition process using the point thermal-source of the Nd:YAG laser through the metabolite of Acidophilic bacteria Thiobacillus. A...

  19. MicrobesOnline: an integrated portal for comparative functional genomics

    OpenAIRE

    Joachimiak, Marcin P.

    2014-01-01

    The Virtual Institute for Microbial Stress and Survival (VIMSS, http://vimss.lbl.gov/) funded by the Dept. of Energy's Genomics:GTL Program, is dedicated to using integrated environmental, functional genomic, and comparative sequence and phylogeny data to understand mechanisms by which microbes and microbial communities survive in uncertain environments while carrying out processes of interest for bioremediation and energy generation. To support this work, VIMSS has developed a Web portal, al...

  20. Drone Transport of Microbes in Blood and Sputum Laboratory Specimens.

    Science.gov (United States)

    Amukele, Timothy K; Street, Jeff; Carroll, Karen; Miller, Heather; Zhang, Sean X

    2016-10-01

    Unmanned aerial vehicles (UAVs) could potentially be used to transport microbiological specimens. To examine the impact of UAVs on microbiological specimens, blood and sputum culture specimens were seeded with usual pathogens and flown in a UAV for 30 ± 2 min. Times to recovery, colony counts, morphologies, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identifications of the flown and stationary specimens were similar for all microbes studied.

  1. Microbial electrosynthesis: understanding and strengthening microbe-electrode interactions

    DEFF Research Database (Denmark)

    Tremblay, Pier-Luc; Höglund, Daniel; Ammam, Fariza;

    2014-01-01

    Powering microbes with electrical energy to produce valuable chemicals such as biofuels has recently gained traction as a biosustainable production strategy for the reduction of our dependence to oil. Microbial electrosynthesis (MES) is one of the few bioelectrochemical approaches developed......, and a general lack of knowledge about electron transfer mechanisms have been the main obstacles to MES commercialization todate. Developing genetic systems for known electroautotrophs, screening for better MES chassis organisms and superior electrochemical hardware, establishing alternative MES processes...

  2. Stimulated Growth of Aerobic Microbes Using Calcium Peroxide

    Institute of Scientific and Technical Information of China (English)

    LIU Shejiang; LI Mujin; JIANG Bin; LI Xingang

    2006-01-01

    With continuous and slow oxygen-release characteristic,calcium peroxide (CaO2) has been a new source of supplying oxygen for aerobic microbes in bioremediation of contaminated groundwater.Batch experiments were conducted to evaluate the oxygen-release rate of CaO2 reacting with water,the regulation of high pH,as well as the growth of mixed aerobic microbes in the medium containing CaO2.The results show that the oxygen-release process of CaO2 comprises three phases.In the first phase,dissolved oxygen levels of water increased sharply,and average oxygen-release rates increased as the adding weight of CaO2 increased.However,the rates almost ly.As the necessary components of medium,potassium dihydrogen phosphate (KH2PO4) and ammonium sulphate ((NH4)2SO4) at a certain ratio could regulate pH caused by CaO2 from 12.1 to the range of 6.5-8.5,which is helpful for microbial growth.In addition,diauxic growth curve observed in the medium containing CaO2 suggested that the growth of mixed aerobic microbes could be stimulated by the addition of CaO2.

  3. Single microbe trap and release in sub-microfluidics

    Energy Technology Data Exchange (ETDEWEB)

    Vasdekis, Andreas E. [Swiss Federal Inst. of Technology, Lausanne (Switzerland); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-02-08

    Lab-on-a-chip systems have substantially impacted the way life-sciences are explored; life on earth, however, comprises mostly of microbes, which due to their sub-micron dimensions and high mobility are more challenging to dynamically manipulate on-a-chip. To address this challenge, we developed a high resolution microfluidic system (submicrofluidics) fabricated by direct electron beam lithography that is capable of trapping single microbes and releasing them upon demand. The fabrication method enabled the integration of sub-micron indentations (400 nm) with millimetre-scale fluidic channels rapidly in a single processing step. The larger channels deliver the cell suspension and reagents, while the sub-micron indentations immobilize the cells by locally increasing the hydrodynamic resistance. By volume exclusion, single cell trapping was possible in this system without any surface treatment. By increasing the flow rate, the microbes overcome the trap barrier and pass through the narrow indentation without undergoing lysis with kinetics that depend on their size. The fabrication method and its performance are described, along with microbial characterisations using E. coli.

  4. Fossil genes and microbes in the oldest ice on earth.

    Science.gov (United States)

    Bidle, Kay D; Lee, Sanghoon; Marchant, David R; Falkowski, Paul G

    2007-08-14

    Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is approximately 8 Ma, making it the oldest known ice on Earth. In both samples, radiolabeled substrates were incorporated into macromolecules, and microbes grew in nutrient-enriched meltwaters, but metabolic activity and cell viability were critically compromised with age. Although a 16S rDNA-based community reconstruction suggested relatively low bacterial sequence diversity in both ice samples, metagenomic analyses of community DNA revealed many diverse orthologs to extant metabolic genes. Analyses of five ice samples, spanning the last 8 million years in this region, demonstrated an exponential decline in the average community DNA size with a half-life of approximately 1.1 million years, thereby constraining the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans.

  5. Plant microbe interactions in post genomic era: perspectives and applications

    Directory of Open Access Journals (Sweden)

    Jahangir Imam

    2016-09-01

    Full Text Available Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.

  6. Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications.

    Science.gov (United States)

    Imam, Jahangir; Singh, Puneet K; Shukla, Pratyoosh

    2016-01-01

    Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.

  7. Insights into the Roles of Gut Microbes in Obesity

    Directory of Open Access Journals (Sweden)

    Yolanda Sanz

    2008-01-01

    Full Text Available Obesity is a major public health issue as it enhances the risk of suffering several chronic diseases of increasing prevalence. Obesity results from an imbalance between energy intake and expenditure, associated with a chronic low-grade inflammation. Gut microbes are considered to contribute to body weight regulation and related disorders by influencing metabolic and immune host functions. The gut microbiota as a whole improves the host's ability to extract and store energy from the diet leading to body weight gain, while specific commensal microbes seem to exert beneficial effects on bile salt, lipoprotein, and cholesterol metabolism. The gut microbiota and some probiotics also regulate immune functions, protecting the host form infections and chronic inflammation. In contrast, dysbiosis and endotoxaemia may be inflammatory factors responsible for developing insulin resistance and body weight gain. In the light of the link between the gut microbiota, metabolism, and immunity, the use of dietary strategies to modulate microbiota composition is likely to be effective in controlling metabolic disorders. Although so far only a few preclinical and clinical trials have demonstrated the effects of specific gut microbes and prebiotics on biological markers of these disorders, the findings indicate that advances in this field could be of value in the struggle against obesity and its associated-metabolic disorders.

  8. Amino acids in the rhizosphere: from plants to microbes.

    Science.gov (United States)

    Moe, Luke A

    2013-09-01

    Often referred to as the "building blocks of proteins", the 20 canonical proteinogenic amino acids are ubiquitous in biological systems as the functional units in proteins. Sometimes overlooked are their varying additional roles that include serving as metabolic intermediaries, playing structural roles in bioactive natural products, acting as cosubstrates in enzymatic transformations, and as key regulators of cellular physiology. Amino acids can also serve as biological sources of both carbon and nitrogen and are found in the rhizosphere as a result of lysis or cellular efflux from plants and microbes and proteolysis of existing peptides. While both plants and microbes apparently prefer to take up nitrogen in its inorganic form, their ability to take up and use amino acids may confer a selective advantage in certain environments where organic nitrogen is abundant. Further, certain amino acids (e.g., glutamate and proline) and their betaines (e.g., glycine betaine) serve as compatible solutes necessary for osmoregulation in plants and microbes and can undergo rapid cellular flux. This ability is of particular importance in an ecological niche such as the rhizosphere, which is prone to significant variations in solute concentrations. Amino acids are also shown to alter key phenotypes related to plant root growth and microbial colonization, symbiotic interactions, and pathogenesis in the rhizosphere. This review will focus on the sources, transport mechanisms, and potential roles of the 20 canonical proteinogenic amino acids in the rhizosphere.

  9. Plant root-microbe communication in shaping root microbiomes.

    Science.gov (United States)

    Lareen, Andrew; Burton, Frances; Schäfer, Patrick

    2016-04-01

    A growing body of research is highlighting the impacts root-associated microbial communities can have on plant health and development. These impacts can include changes in yield quantity and quality, timing of key developmental stages and tolerance of biotic and abiotic stresses. With such a range of effects it is clear that understanding the factors that contribute to a plant-beneficial root microbiome may prove advantageous. Increasing demands for food by a growing human population increases the importance and urgency of understanding how microbiomes may be exploited to increase crop yields and reduce losses caused by disease. In addition, climate change effects may require novel approaches to overcoming abiotic stresses such as drought and salinity as well as new emerging diseases. This review discusses current knowledge on the formation and maintenance of root-associated microbial communities and plant-microbe interactions with a particular emphasis on the effect of microbe-microbe interactions on the shape of microbial communities at the root surface. Further, we discuss the potential for root microbiome modification to benefit agriculture and food production.

  10. Microbes as targets and mediators of allelopathy in plants.

    Science.gov (United States)

    Cipollini, Don; Rigsby, Chad M; Barto, E Kathryn

    2012-06-01

    Studies of allelopathy in terrestrial systems have experienced tremendous growth as interest has risen in describing biochemical mechanisms responsible for structuring plant communities, determining agricultural and forest productivity, and explaining invasive behaviors in introduced organisms. While early criticisms of allelopathy involved issues with allelochemical production, stability, and degradation in soils, an understanding of the chemical ecology of soils and its microbial inhabitants has been increasingly incorporated in studies of allelopathy, and recognized as an essential predictor of the outcome of allelopathic interactions between plants. Microbes can mediate interactions in a number of ways with both positive and negative outcomes for surrounding plants and plant communities. In this review, we examine cases where soil microbes are the target of allelopathic plants leading to indirect effects on competing plants, provide examples where microbes play either a protective effect on plants against allelopathic competitors or enhance allelopathic effects, and we provide examples where soil microbial communities have changed through time in response to allelopathic plants with known or potential effects on plant communities. We focus primarily on interactions involving wild plants in natural systems, using case studies of some of the world's most notorious invasive plants, but we also provide selected examples from agriculturally managed systems. Allelopathic interactions between plants cannot be fully understood without considering microbial participants, and we conclude with suggestions for future research.

  11. A metasystem of framework model organisms to study emergence of new host-microbe adaptations.

    Directory of Open Access Journals (Sweden)

    Suresh Gopalan

    Full Text Available An unintended consequence of global industrialization and associated societal rearrangements is new interactions of microbes and potential hosts (especially mammals and plants, providing an opportunity for the rapid emergence of host-microbe adaptation and eventual establishment of new microbe-related diseases. We describe a new model system comprising the model plant Arabidopsis thaliana and several microbes, each representing different modes of interaction, to study such "maladaptations". The model microbes include human and agricultural pathogens and microbes that are commonly considered innocuous. The system has a large knowledge base corresponding to each component organism and is amenable to high-throughput automation assisted perturbation screens for identifying components that modulate host-pathogen interactions. This would aid in the study of emergence and progression of host-microbe maladaptations in a controlled environment.

  12. Uncharted Microbial World: Microbes and Their Activities in the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry.

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  13. Halogenated fatty acids

    DEFF Research Database (Denmark)

    Mu, Huiling; Sundin, Peter; Wesén, Clas

    1997-01-01

    Halogenated fatty acids are the major contributors to organohalogen compounds in lipids of marine mammals, fish, and bivalves. For the initial characterization of these recently noticed compounds, a determination of the halogen concentration has usually been combined with some lipid isolation...... and separation method. This review covers separation by solid phase chromatography, gel permeation chromatography, and liquid-liquid extraction, followed by halogen determination. All studies performed according to this outline have indicated that the major organohalogen compounds are chlorinated fatty acids...... bound in different lipids. For the detection and identification of individual, halogenated fatty acid methyl esters (FAMEs) liberated from the lipids, gas chromatography (GC) has been employed together with detection methods such as electron capture detection, electrolytic conductivity detection (ELCD...

  14. Omega-3 fatty acids (image)

    Science.gov (United States)

    Omega-3 fatty acids are a form of polyunsaturated fat that the body derives from food. Omega-3s (and omega-6s) are known as essential fatty acids (EFAs) because they are important for good health. ...

  15. The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation

    Directory of Open Access Journals (Sweden)

    Christina eEngels

    2016-05-01

    Full Text Available Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol (1,3-PD. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325. Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, Ruminococcus gnavus, Flavonifractor prautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal

  16. Fatty acids of Thiobacillus thiooxidans.

    Science.gov (United States)

    Levin, R A

    1971-12-01

    Fatty acid spectra were made on Thiobacillus thiooxidans cultures both in the presence and absence of organic compounds. Small additions of glucose or acetate had no significant effect either on growth or fatty acid content. The addition of biotin had no stimulatory effect but did result in slight quantitative changes in the fatty acid spectrum. The predominant fatty acid was a C(19) cyclopropane acid.

  17. [Plant-microbe symbioses as an evolutionary continuum].

    Science.gov (United States)

    Provorov, N A

    2009-01-01

    In spite of enormous taxonomic, structural and functional diversity of plant-microbe interactions, they are characterized by a historical succession which allows us to consider different forms of symbioses as the components of an evolutionary continuum. Their ancestral form is represented by arbuscular mycorrhiza (AM) which originated at the outset of terrestrial flora evolution and constituted a key factor for the land colonization by plants. In the course of AM evolution the plant acquired a basal set of genes for regulating the performance of microbes which colonize the root tissues. Later, these genes were repeatedly reorganized to meet the involvement of novel mutualistic symbionts (N2-fixing bacteria, ectomycorrhizal fungi, endophytes and epiphytes) and pathogens into the symbiotic interactions. Form the microbial side, the evolutionary succession of mutualism and antagonism is restricted to the defensive symbioses formed by plants with the ergot fungi, Clavibacter, Bacillus and Pseudomonas bacteria. Involvement of the similar systems for symbiotic interactions may be related to convergent evolution in the distant microorganisms (adaptation to the conservative host defense/regulatory factors), to molecular mimicry (imitation of the mechanisms of interaction used by the more ancient symbionts) or to the horizontal gene transfer. The hypotheses of the successive substitution of symbionts is suggested to address the relationships between AM and N2-fixing nodular symbioses in dicotyledons plants. AM formation is considered as a source of preadaptations responsible for the substitution of glomalean fungi which occupied the plant symbiotic compartments by the actinomycetes Frankia (in Rosid I plants) which were exchanged for the more competitive root nodule bacteria (in legumes). The development of nutritional symbioses with microbes is considered as an ancestral function of plant roots which were later supplemented or substituted with the function of assimilating

  18. Gut microbes may facilitate insect herbivory of chemically defended plants.

    Science.gov (United States)

    Hammer, Tobin J; Bowers, M Deane

    2015-09-01

    The majority of insect species consume plants, many of which produce chemical toxins that defend their tissues from attack. How then are herbivorous insects able to develop on a potentially poisonous diet? While numerous studies have focused on the biochemical counter-adaptations to plant toxins rooted in the insect genome, a separate body of research has recently emphasized the role of microbial symbionts, particularly those inhabiting the gut, in plant-insect interactions. Here we outline the "gut microbial facilitation hypothesis," which proposes that variation among herbivores in their ability to consume chemically defended plants can be due, in part, to variation in their associated microbial communities. More specifically, different microbes may be differentially able to detoxify compounds toxic to the insect, or be differentially resistant to the potential antimicrobial effects of some compounds. Studies directly addressing this hypothesis are relatively few, but microbe-plant allelochemical interactions have been frequently documented from non-insect systems-such as soil and the human gut-and thus illustrate their potential importance for insect herbivory. We discuss the implications of this hypothesis for insect diversification and coevolution with plants; for example, evolutionary transitions to host plant groups with novel allelochemicals could be initiated by heritable changes to the insect microbiome. Furthermore, the ecological implications extend beyond the plant and insect herbivore to higher trophic levels. Although the hidden nature of microbes and plant allelochemicals make their interactions difficult to detect, recent molecular and experimental techniques should enable research on this neglected, but likely important, aspect of insect-plant biology.

  19. The ``Adopt A Microbe'' project: Web-based interactive education connected with scientific ocean drilling

    Science.gov (United States)

    Orcutt, B. N.; Bowman, D.; Turner, A.; Inderbitzen, K. E.; Fisher, A. T.; Peart, L. W.; Iodp Expedition 327 Shipboard Party

    2010-12-01

    We launched the "Adopt a Microbe" project as part of Integrated Ocean Drilling Program (IODP) Expedition 327 in Summer 2010. This eight-week-long education and outreach effort was run by shipboard scientists and educators from the research vessel JOIDES Resolution, using a web site (https://sites.google.com/site/adoptamicrobe) to engage students of all ages in an exploration of the deep biosphere inhabiting the upper ocean crust. Participants were initially introduced to a cast of microbes (residing within an ‘Adoption Center’ on the project website) that live in the dark ocean and asked to select and virtually ‘adopt’ a microbe. A new educational activity was offered each week to encourage learning about microbiology, using the adopted microbe as a focal point. Activities included reading information and asking questions about the adopted microbes (with subsequent responses from shipboard scientists), writing haiku about the adopted microbes, making balloon and fabric models of the adopted microbes, answering math questions related to the study of microbes in the ocean, growing cultures of microbes, and examining the gases produced by microbes. In addition, the website featured regular text, photo and video updates about the science of the expedition using a toy microbe as narrator, as well as stories written by shipboard scientists from the perspective of deep ocean microbes accompanied by watercolor illustrations prepared by a shipboard artist. Assessment methods for evaluating the effectiveness of the Adopt a Microbe project included participant feedback via email and online surveys, website traffic monitoring, and online video viewing rates. Quantitative metrics suggest that the “Adope A Microbe” project was successful in reaching target audiences and helping to encourage and maintain interest in topics related to IODP Expedition 327. The “Adopt A Microbe” project mdel can be adapted for future oceanographic expeditions to help connect the

  20. Hypoxia and fatty liver.

    Science.gov (United States)

    Suzuki, Tomohiro; Shinjo, Satoko; Arai, Takatomo; Kanai, Mai; Goda, Nobuhito

    2014-11-07

    The liver is a central organ that metabolizes excessive nutrients for storage in the form of glycogen and lipids and supplies energy-producing substrates to the peripheral tissues to maintain their function, even under starved conditions. These processes require a considerable amount of oxygen, which causes a steep oxygen gradient throughout the hepatic lobules. Alcohol consumption and/or excessive food intake can alter the hepatic metabolic balance drastically, which can precipitate fatty liver disease, a major cause of chronic liver diseases worldwide, ranging from simple steatosis, through steatohepatitis and hepatic fibrosis, to liver cirrhosis. Altered hepatic metabolism and tissue remodeling in fatty liver disease further disrupt hepatic oxygen homeostasis, resulting in severe liver hypoxia. As master regulators of adaptive responses to hypoxic stress, hypoxia-inducible factors (HIFs) modulate various cellular and organ functions, including erythropoiesis, angiogenesis, metabolic demand, and cell survival, by activating their target genes during fetal development and also in many disease conditions such as cancer, heart failure, and diabetes. In the past decade, it has become clear that HIFs serve as key factors in the regulation of lipid metabolism and fatty liver formation. This review discusses the molecular mechanisms by which hypoxia and HIFs regulate lipid metabolism in the development and progression of fatty liver disease.

  1. Beneficial microbes affect endogenous mechanisms controlling root development

    Science.gov (United States)

    Verbon, Eline H.; Liberman, Louisa M.

    2016-01-01

    Plants have incredible developmental plasticity, enabling them to respond to a wide range of environmental conditions. Among these conditions is the presence of plant growth-promoting rhizobacteria (PGPR) in the soil. Recent studies show that PGPR affect root growth and development within Arabidopsis thaliana root. These effects lead to dramatic changes in root system architecture, that significantly impact aboveground plant growth. Thus, PGPR may promote shoot growth via their effect on root developmental programs. This review focuses on contextualizing root developmental changes elicited by PGPR in light of our understanding of plant-microbe interactions and root developmental biology. PMID:26875056

  2. Role of microbes in the ecology of marine environment

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A.; DeSouza, M.J.B.D.; LokaBharathi, P.A.

    area of the seabed of the Indian Ocean are most promising for the extraction of strategic metals from them. The next article gives a realistic account of researches on coral reefs in the country. It is really unfortunate that coral research which... in the country who has developed interest on corals and coral reefs is the author of the present article Dr. M.V.M. Wafar. His article is followed by an account on microbes which play a very important ecological role in the marine environment, including...

  3. Metabolic engineering of microbes for oligosaccharide and polysaccharide synthesis

    Directory of Open Access Journals (Sweden)

    Chen Rachel

    2006-07-01

    Full Text Available Abstract Metabolic engineering has recently been embraced as an effective tool for developing whole-cell biocatalysts for oligosaccharide and polysaccharide synthesis. Microbial catalysts now provide a practical means to derive many valuable oligosaccharides, previously inaccessible through other methods, in sufficient quantities to support research and clinical applications. The synthesis process based upon these microbes is scalable as it avoids expensive starting materials. Most impressive is the high product concentrations (up to 188 g/L achieved through microbe-catalyzed synthesis. The overall cost for selected molecules has been brought to a reasonable range (estimated $ 30–50/g. Microbial synthesis of oligosaccharides and polysaccharides is a carbon-intensive and energy-intensive process, presenting some unique challenges in metabolic engineering. Unlike nicotinamide cofactors, the required sugar nucleotides are products of multiple interacting pathways, adding significant complexity to the metabolic engineering effort. Besides the challenge of providing the necessary mammalian-originated glycosyltransferases in active form, an adequate uptake of sugar acceptors can be an issue when another sugar is necessary as a carbon and energy source. These challenges are analyzed, and various strategies used to overcome these difficulties are reviewed in this article. Despite the impressive success of the microbial coupling strategy, there is a need to develop a single strain that can achieve at least the same efficiency. Host selection and the manner with which the synthesis interacts with the central metabolism are two important factors in the design of microbial catalysts. Additionally, unlike in vitro enzymatic synthesis, product degradation and byproduct formation are challenges of whole-cell systems that require additional engineering. A systematic approach that accounts for various and often conflicting requirements of the synthesis holds

  4. Fossil genes and microbes in the oldest ice on Earth

    OpenAIRE

    Bidle, Kay D.; Lee, Sanghoon; Marchant, David R.; Falkowski, Paul G

    2007-01-01

    Although the vast majority of ice that formed on the Antarctic continent over the past 34 million years has been lost to the oceans, pockets of ancient ice persist in the Dry Valleys of the Transantarctic Mountains. Here we report on the potential metabolic activity of microbes and the state of community DNA in ice derived from Mullins and upper Beacon Valleys. The minimum age of the former is 100 ka, whereas that of the latter is ≈8 Ma, making it the oldest known ice on Earth. In both sample...

  5. Biodegradation of DTP and PET Fiber by Microbe

    Institute of Scientific and Technical Information of China (English)

    张健飞; 王晓春; 巩继贤; 顾振亚

    2003-01-01

    The degradation of diethylene glycol terephthalate (DTP) and polyethylene terephthalate (PET) fiber by microbe was studied.The degree of DTP degradation was determined by High Performance Liquid Chromatography (HPLC) to be more than 90%.The products after degradation of DTP and PET fiber were various.The degradation of DTP can be described by the first-order reaction model.The degradation of PET fiber was found to be little,but surface erosion of PET fiber could be clearly seen from the SEM photographs indicating there occurred some traces of biodegradation on the PET fiber surface.

  6. Microbes residing in young organic rich Alaskan soils contain older carbon than those residing in old mineral high Arctic soils

    Science.gov (United States)

    Ziolkowski, L. A.; Slater, G. F.; Onstott, T. C.; Whyte, L.; Townsend-Small, A.

    2013-12-01

    Arctic soils range from very organic rich to low carbon and mineral-dominated soils. At present, we do not yet fully understand if all carbon in the Arctic is equally vulnerable to mineralization in a warmer climate. Many studies have demonstrated that ancient carbon is respired when permafrost has thawed, yet our understanding of the active layer and permafrost carbon dynamics is still emerging. In an effort to remedy this disconnect between our knowledge of surface fluxes and below ground processes, we used radiocarbon to examine the microbial carbon dynamics in soil cores from organic rich soils near Barrow, Alaska and mineral soils from the Canadian high Arctic. Specifically, we compared the microbial community using lipid biomarkers, the inputs of carbon using n-alkanes and measured the 14C of both the bulk organic carbon and of the microbial lipids. In theory, the microbial lipids (phospholipid fatty acids, PLFA) represent the viable microbial community, as these lipids are hydrolyzed quickly after cell death. Variations in the PLFA distributions suggested that different microbial communities inhabit organic rich Alaskan soils and those of the Canadian high Arctic. When the PLFA concentrations were converted to cellular concentration, they were within the same order of magnitude (1 to 5 x 108 cells/g dry soil) with slightly higher cell concentrations in the organic rich Alaskan soils. When these cellular concentrations were normalized to the organic carbon content, the Canadian high Arctic soils contained a greater proportion of microbes. Although bulk organic carbon 14C of Alaskan soils indicated more recent carbon inputs into the soil than the Canadian high Arctic soils, the 14C of the PLFA revealed the opposite. For corresponding depth horizons, microbes in Alaskan soils were consuming carbon 1000 to 1500 years older than those in the Canadian high Arctic. Differences between the 14C content of bulk organic carbon and the microbial lipids were much smaller

  7. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities

    Science.gov (United States)

    Akhtar, M. Kalim; Turner, Nicholas J.; Jones, Patrik R.

    2013-01-01

    Aliphatic hydrocarbons such as fatty alcohols and petroleum-derived alkanes have numerous applications in the chemical industry. In recent years, the renewable synthesis of aliphatic hydrocarbons has been made possible by engineering microbes to overaccumulate fatty acids. However, to generate end products with the desired physicochemical properties (e.g., fatty aldehydes, alkanes, and alcohols), further conversion of the fatty acid is necessary. A carboxylic acid reductase (CAR) from Mycobacterium marinum was found to convert a wide range of aliphatic fatty acids (C6–C18) into corresponding aldehydes. Together with the broad-substrate specificity of an aldehyde reductase or an aldehyde decarbonylase, the catalytic conversion of fatty acids to fatty alcohols (C8–C16) or fatty alkanes (C7–C15) was reconstituted in vitro. This concept was applied in vivo, in combination with a chain-length-specific thioesterase, to engineer Escherichia coli BL21(DE3) strains that were capable of synthesizing fatty alcohols and alkanes. A fatty alcohol titer exceeding 350 mg·L−1 was obtained in minimal media supplemented with glucose. Moreover, by combining the CAR-dependent pathway with an exogenous fatty acid-generating lipase, natural oils (coconut oil, palm oil, and algal oil bodies) were enzymatically converted into fatty alcohols across a broad chain-length range (C8–C18). Together with complementing enzymes, the broad substrate specificity and kinetic characteristics of CAR opens the road for direct and tailored enzyme-catalyzed conversion of lipids into user-ready chemical commodities. PMID:23248280

  8. Diaphragmatic function is enhanced in fatty and diabetic fatty rats

    Science.gov (United States)

    Carreira, Serge; Na, Na; Carillion, Aude; Jiang, Cheng; Beuvin, Maud; Lacorte, Jean-Marc; Bonnefont-Rousselot, Dominique; Riou, Bruno; Coirault, Catherine

    2017-01-01

    Background Obesity is associated with a decrease in mortality in the intensive care unit (ICU) (the "obesity paradox"). We hypothesized that obesity may paradoxically improve diaphragmatic function. Methods Diaphragm contractility was prospectively recorded in vitro in adult male Zucker lean (control), fatty, and diabetic fatty rats, at rest, after 12h mechanical ventilation and after fatigue. We analyzed diaphragm morphology, cytokines, and protein expression of the protein kinase signaling pathways. Results Diaphragm active-force (AF) was higher in fatty (96±7mN.mm-2,P = 0.02) but not in diabetic fatty rats (90±17mN.mm-2) when compared with controls (84±8mN.mm-2). Recovery from fatigue was improved in fatty and diabetic fatty groups compared with controls. Ventilator-induced diaphragmatic dysfunction was observed in each group, but AF remained higher in fatty (82±8mN.mm-2,P = 0.03) compared with controls (70±8mN.mm-2). There was neutral lipid droplet accumulation in fatty and diabetic fatty. There were shifts towards a higher cross-sectional-area (CSA) of myosin heavy chain isoforms (MyHC)-2A fibers in fatty and diabetic fatty compared with control rats (P = 0.002 and Pobese rats before and after mechanical ventilation, and is associated with activation of AKT pathway signaling and complex changes in morphology. PMID:28328996

  9. Increased muscle fatty acid oxidation in dairy cows with intensive body fat mobilization during early lactation.

    Science.gov (United States)

    Schäff, C; Börner, S; Hacke, S; Kautzsch, U; Sauerwein, H; Spachmann, S K; Schweigel-Röntgen, M; Hammon, H M; Kuhla, B

    2013-10-01

    The beginning of lactation requires huge metabolic adaptations to meet increased energy demands for milk production of dairy cows. One of the adaptations is the mobilization of body reserves mainly from adipose tissue as reflected by increased plasma nonesterified fatty acid (NEFA) concentrations. The capacity of the liver for complete oxidation of NEFA is limited, leading to an increased formation of ketone bodies, reesterification, and accumulation of triglycerides in the liver. As the skeletal muscle also may oxidize fatty acids, it may help to decrease the fatty acid load on the liver. To test this hypothesis, 19 German Holstein cows were weekly blood sampled from 7 wk before until 5 wk after parturition to analyze plasma NEFA concentrations. Liver biopsies were obtained at d 3, 18, and 30 after parturition and, based on the mean liver fat content, cows were grouped to the 10 highest (HI) and 9 lowest (LO). In addition, muscle biopsies were obtained at d -17, 3, and 30 relative to parturition and used to quantify mRNA abundance of genes involved in fatty acid degradation. Plasma NEFA concentrations peaked after parturition and were 1.5-fold higher in HI than LO cows. Muscle carnitine palmitoyltransferase 1α and β mRNA was upregulated in early lactation. The mRNA abundance of muscle peroxisome proliferator-activated receptor γ (PPARG) increased in early lactation and was higher in HI than in LO cows, whereas the abundance of PPARA continuously decreased after parturition. The mRNA abundance of muscle PPARD, uncoupling protein 3, and the β-oxidative enzymes 3-hydroxyacyl-coenzyme A (CoA) dehydrogenase, very long-chain acyl-CoA dehydrogenase, and 3-ketoacyl-CoA was greatest at d 3 after parturition, whereas the abundance of PPARγ coactivator 1α decreased after parturition. Our results indicate that around parturition, oxidation of fatty acids in skeletal muscle is highly activated, which may contribute to diminish the fatty acid load on the liver. The

  10. Uncharted Microbial World: Microbes and Their Activities in the Environment

    Energy Technology Data Exchange (ETDEWEB)

    Harwood, Caroline; Buckley, Merry

    2007-12-31

    Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymied many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable

  11. Environmental bacteriophages : viruses of microbes in aquatic ecosystems

    Directory of Open Access Journals (Sweden)

    Télesphore eSIME - NGANDO

    2014-07-01

    Full Text Available Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms (http://www.isvm.org/, was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea, as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.

  12. Study of microbes having potentiality for biodegradation of plastics.

    Science.gov (United States)

    Ghosh, Swapan Kumar; Pal, Sujoy; Ray, Sumanta

    2013-07-01

    Plastic is a broad name given to the different types of organic polymers having high molecular weight and is commonly derived from different petrochemicals. Plastics are generally not biodegradable or few are degradable but in a very slow rate. Day by day, the global demand of these polymers is sharply increasing; however, considering their abundance and potentiality in causing different environmental hazards, there is a great concern in the possible methods of degradation of plastics. Recently, there have been some debates at the world stage about the potential degradation procedures of these synthetic polymers and microbial degradation has emerged as one of the potential alternative ways of degradation of plastics. Alternatively, some scientists have also reported many adverse effects of these polymers in human health, and thus, there is an immediate need of a potential screening of some potential microbes to degrade these synthetic polymers. In this review, we have taken an attempt to accumulate all information regarding the chemical nature along with some potential microbes and their enzymatic nature of biodegradation of plastics along with some key factors that affect their biodegradability.

  13. Mg isotope fractionation during microbe-mineral interactions

    Science.gov (United States)

    Kim, Insu; Ryu, Jong-sik; Lee, Kwang-sik; Lee, Dongho

    2014-05-01

    Magnesium is involved in various biogeochemical processes important to the global climate change over geological time-scale. Mg isotopes allow us to directly trace the Mg cycle in the Earth's surface but the factors controlling Mg isotopic compositions have not fully understood yet. Here, we conducted a batch experiment using two bacterial species (Shewanella putrefaciens and Burkholderia fungorum) and three major Mg-bearing minerals (biotite, dolomite and hornblende). All elemental concentrations increased by 336 h and then reached to steady-state values, of which Mg concentrations varied depending on minerals and bacterial species. This result indicates that the mineral dissolution is affect by the presence of microbes, which either provide organic acids or attach onto mineral surface. The Mg isotopic compositions of initial minerals biotite, dolomite and hornblende are -0.35o of biotite, -0.99o of dolomite, and -0.24o of hornblende, in δ26Mg. Similarly, δ26Mg values increased by 336 h and reached to steady-state values, which also varied with minerals and microbes. During dissolution of three minerals, the light isotope of Mg is preferentially incorporated into the dissolved phases and then the dissolved δ26Mg values become consistent with those of minerals with the time.

  14. Plant - microbe interactions under Global Change: the microbial perspective

    Science.gov (United States)

    Richter, Andreas

    2017-04-01

    There is ample evidence that both microorganisms and plants will respond to Global Changes, such as enhanced temperatures, increased nitrogen deposition and atmospheric CO2 concentrations, or biodiversity loss. Plant and microbial activities are linked, amongst other factors, by belowground carbon allocation and aboveground nutrient allocation, which may be altered under Global Changes to different extents. The effect of Global Changes on the interaction of plants and microbes is therefore often difficult to predict. In my talk, I will look at plant-microbe interactions from a microbial perspective. I will ask the question what the direct and indirect (plant-mediated) effects of Global Changes are on microbial activities in soil and what this in turn means for plants and for ecosystem-scale fluxes. I will present results from an in-situ drought experiment, from a long-term soil warming experiment and from a plant diversity experiment, where we investigated microbial growth and turnover, carbon and nutrient use efficiency and gross nutrient transformation rates.

  15. Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds.

    Science.gov (United States)

    Indraningrat, Anak Agung Gede; Smidt, Hauke; Sipkema, Detmer

    2016-05-02

    Sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. However, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. This review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. We discuss the current state-of-the-art by grouping the bioactive compounds produced by sponge-associated microorganisms in four categories: antiviral, antibacterial, antifungal and antiprotozoal compounds. Based on in vitro activity tests, identified targets of potent antimicrobial substances derived from sponge-associated microbes include: human immunodeficiency virus 1 (HIV-1) (2-undecyl-4-quinolone, sorbicillactone A and chartarutine B); influenza A (H1N1) virus (truncateol M); nosocomial Gram positive bacteria (thiopeptide YM-266183, YM-266184, mayamycin and kocurin); Escherichia coli (sydonic acid), Chlamydia trachomatis (naphthacene glycoside SF2446A2); Plasmodium spp. (manzamine A and quinolone 1); Leishmania donovani (manzamine A and valinomycin); Trypanosoma brucei (valinomycin and staurosporine); Candida albicans and dermatophytic fungi (saadamycin, 5,7-dimethoxy-4-p-methoxylphenylcoumarin and YM-202204). Thirty-five bacterial and 12 fungal genera associated with sponges that produce antimicrobials were identified, with Streptomyces, Pseudovibrio, Bacillus, Aspergillus and Penicillium as the prominent producers of antimicrobial compounds. Furthemore culture-independent approaches to more comprehensively exploit the genetic richness of antimicrobial compound-producing pathways from sponge-associated bacteria are addressed.

  16. Fluorogenic Cell-Based Biosensors for Monitoring Microbes

    Science.gov (United States)

    Curtis, Theresa; Salazar, Noe; Tabb, Joel; Chase, Chris

    2010-01-01

    Fluorogenic cell-based sensor systems for detecting microbes (especially pathogenic ones) and some toxins and allergens are undergoing development. These systems harness the natural signaltransduction and amplification cascades that occur in mast cells upon activation with antigens. These systems include (1) fluidic biochips for automated containment of samples, reagents, and wastes and (2) sensitive, compact fluorometers for monitoring the fluorescent responses of mast cells engineered to contain fluorescent dyes. It should be possible to observe responses within minutes of adding immune complexes. The systems have been shown to work when utilizing either immunoglobulin E (IgE) antibodies or traditionally generated rat antibodies - a promising result in that it indicates that the systems could be developed to detect many target microbes. Chimeric IgE antibodies and rat immunoglobulin G (IgG) antibodies could be genetically engineered for recognizing biological and chemical warfare agents and airborne and food-borne allergens. Genetic engineering efforts thus far have yielded (1) CD14 chimeric antibodies that recognize both Grampositive and Gram-negative bacteria and bind to the surfaces of mast cells, eliciting a degranulation response and (2) rat IgG2a antibodies that act similarly in response to low levels of canine parvovirus.

  17. Phytophagous insect-microbe mutualisms and adaptive evolutionary diversification.

    Science.gov (United States)

    Janson, Eric M; Stireman, John O; Singer, Michael S; Abbot, Patrick

    2008-05-01

    Adaptive diversification is a process intrinsically tied to species interactions. Yet, the influence of most types of interspecific interactions on adaptive evolutionary diversification remains poorly understood. In particular, the role of mutualistic interactions in shaping adaptive radiations has been largely unexplored, despite the ubiquity of mutualisms and increasing evidence of their ecological and evolutionary importance. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification, using herbivorous insects and their microbial mutualists as exemplars. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. In this perspective, we examine microbial mutualist mediation of ecological opportunity and ecologically based divergent natural selection for their insect hosts. We also explore the conditions and mechanisms by which microbial mutualists may either facilitate or impede adaptive evolutionary diversification. These include effects on the availability of novel host plants or adaptive zones, modifying host-associated fitness trade-offs during host shifts, creating or reducing enemy-free space, and, overall, shaping the evolution of ecological (host plant) specialization. Although the conceptual framework presented here is built on phytophagous insect-microbe mutualisms, many of the processes and predictions are broadly applicable to other mutualisms in which host ecology is altered by mutualistic interactions.

  18. Environmental bacteriophages: viruses of microbes in aquatic ecosystems.

    Science.gov (United States)

    Sime-Ngando, Télesphore

    2014-01-01

    Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.

  19. Microbes produce nanobacteria-like structures, avoiding cell entombment

    Science.gov (United States)

    Bontognali, Tomaso R. R.; Vasconcelos, Crisógono; Warthmann, Rolf J.; Dupraz, Christophe; Bernasconi, Stefano M.; McKenzie, Judith A.

    2008-08-01

    Microsedimentary structures referred to as nanobacteria-likeparticles were described from modern carbonate environments,where they form in close spatial association with sulfate-reducingbacteria (SRB). However, the exact mechanism of their formation,as well as their paleontological significance, remains controversial.Here we report on an investigation of microbe-mineral interactionsin experimentally produced carbonate globules. The experimentswere carried out under anoxic conditions at 30 °C with Desulfovibriobrasiliensis, a SRB known to mediate dolomite formation. Weobserved that extracellular polymeric substances (EPS) secretedby the microbial community play a key role in the mineralizationprocess. Nanobacteria-like particles represent the early stageof carbonate nucleation within the EPS, which progressivelyevolve to larger globules displaying a grainy texture. We excludedthe possibilities that these structures are fossils of nanobacteria,dissolution surfaces, or artifacts created during sample preparation.D. brasiliensis cells are predominantly located outside of theEPS aggregates where mineral growth takes place. As a result,they remain mobile and are rarely entombed within the mineral.This self-preservation behavior may not be limited to D. brasiliensis.Other microbes may produce, or may have produced during thegeological past, biogenic minerals through a similar process.Mineralization within EPS explains why microbial relics arenot necessarily present in biogenic carbonates.

  20. Next-Generation Beneficial Microbes: The Case of Akkermansia muciniphila

    Directory of Open Access Journals (Sweden)

    Patrice D. Cani

    2017-09-01

    Full Text Available Metabolic disorders associated with obesity and cardiometabolic disorders are worldwide epidemic. Among the different environmental factors, the gut microbiota is now considered as a key player interfering with energy metabolism and host susceptibility to several non-communicable diseases. Among the next-generation beneficial microbes that have been identified, Akkermansia muciniphila is a promising candidate. Indeed, A. muciniphila is inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation. Besides the numerous correlations observed, a large body of evidence has demonstrated the causal beneficial impact of this bacterium in a variety of preclinical models. Translating these exciting observations to human would be the next logic step and it now appears that several obstacles that would prevent the use of A. muciniphila administration in humans have been overcome. Moreover, several lines of evidence indicate that pasteurization of A. muciniphila not only increases its stability but more importantly increases its efficacy. This strongly positions A. muciniphila in the forefront of next-generation candidates for developing novel food or pharma supplements with beneficial effects. Finally, a specific protein present on the outer membrane of A. muciniphila, termed Amuc_1100, could be strong candidate for future drug development. In conclusion, as plants and its related knowledge, known as pharmacognosy, have been the source for designing drugs over the last century, we propose that microbes and microbiomegnosy, or knowledge of our gut microbiome, can become a novel source of future therapies.

  1. Microbes of deep marine sediments as viewed by metagenomics

    Science.gov (United States)

    Biddle, J.

    2015-12-01

    Ten years after the first deep marine sediment metagenome was produced, questions still exist about the nucleic acid sequences we have retrieved. Current data sets, including the Peru Margin, Costa Rica Margin and Iberian Margin show that consistently, data forms larger assemblies at depth due to the reduced complexity of the microbial community. But are these organisms active or preserved? At SMTZs, a change in the assembly statistics is noted, as well as an increase in cell counts, suggesting that cells are truly active. As depth increases, genome sizes are consistently large, suggesting that much like soil microbes, sedimentary microbes may maintain a larger reportorie of genomic potential. Functional changes are seen with depth, but at many sites are not correlated to specific geochemistries. Individual genomes show changes with depth, which raises interesting questions on how the subsurface is settled and maintained. The subsurface does have a distinct genomic signature, including unusual microbial groups, which we are now able to analyze for total genomic content.

  2. Utilizing thermophilic microbe in lignocelluloses based bioethanol production: Review

    Science.gov (United States)

    Sriharti, Agustina, Wawan; Ratnawati, Lia; Rahman, Taufik; Salim, Takiyah

    2017-01-01

    The utilization of thermophilic microbe has attracted many parties, particularly in producing an alternative fuel like ethanol. Bioethanol is one of the alternative energy sources substituting for earth oil in the future. The advantage of using bioethanol is that it can reduce pollution levels and global warming because the result of bioethanol burning doesn't bring in a net addition of CO2 into environment. Moreover, decrease in the reserves of earth oil globally has also contributed to the notion on searching renewable energy resources such as bioethanol. Indonesia has a high biomass potential and can be used as raw material for bioethanol. The utilization of these raw materials will reduce fears of competition foodstuffs for energy production. The enzymes that play a role in degrading lignocelluloses are cellulolytic, hemicellulolytic, and lignolytic in nature. The main enzyme with an important role in bioethanol production is a complex enzyme capable of degrading lignocelluloses. The enzyme can be produced by the thermophilik microbes of the groups of bacteria and fungi such as Trichoderma viride, Clostridium thermocellum, Bacillus sp. Bioethanol production is heavily affected by raw material composition, microorganism type, and the condition of fermentation used.

  3. The structure and dynamics of complex microbe-host interaction networks

    OpenAIRE

    Björk, Johannes

    2016-01-01

    Microbes form intricate and intimate relationships with most animals and plants, many of which are crucial for host development, health and functioning. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialised interactions between a single microbe and host that coevolve are the norm. These symbioses involving just a few s...

  4. Plant traits related to nitrogen uptake influence plant-microbe competition

    OpenAIRE

    Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Mougel, Christophe

    2015-01-01

    Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits ...

  5. The MICROBE Project, A Report from the Interagency Working Group on Microbial Genomics

    Science.gov (United States)

    2001-01-01

    and microalgae ) comprise most of the earth’s biomass, maintain its environments, and hold the key to understanding the history of life on Earth...human pathogens and microbes of relevance to energy production and energy-related bioremediation , reflecting the larger and longer- term investments...algae, difficult-to- culture microbes, and unique protozoa. • microbes involved with bioremediation for improving the environment and bioindicator species

  6. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    DEFF Research Database (Denmark)

    Lloyd, Karen; Bird, Jordan; Schreiber, Lars

    Abstract Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as pr...... such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We ...

  7. Simulation of Neurocomputing Based on Photophobic Reactions of Euglena: Toward Microbe-Based Neural Network Computing

    Science.gov (United States)

    Ozasa, Kazunari; Aono, Masashi; Maeda, Mizuo; Hara, Masahiko

    In order to develop an adaptive computing system, we investigate microscopic optical feedback to a group of microbes (Euglena gracilis in this study) with a neural network algorithm, expecting that the unique characteristics of microbes, especially their strategies to survive/adapt against unfavorable environmental stimuli, will explicitly determine the temporal evolution of the microbe-based feedback system. The photophobic reactions of Euglena are extracted from experiments, and built in the Monte-Carlo simulation of a microbe-based neurocomputing. The simulation revealed a good performance of Euglena-based neurocomputing. Dynamic transition among the solutions is discussed from the viewpoint of feedback instability.

  8. The rhizosphere priming effect explained by microscale interactions among enzyme producing microbes

    Science.gov (United States)

    Kaiser, Christina; Dieckmann, Ulf; Franklin, Oskar

    2017-04-01

    Addition of small amounts of labile carbon (C), for example by root exudations, have been found to accelerate soil organic matter decomposition ('Priming Effect'). Possible explanations that have been suggested so far are that this C increases microbial turnover or - by increasing nitrogen (N) limitation of microbes - triggers increased mining of microbes for nutrients. Individual-based modeling of microbes at the microscale offer a new and alternative explanation for the emergence of the priming effect: Enzyme producing microbes benefit from proximity to other enzyme producing microbes since this increases their return of investment for each enzyme produced. The benefit grows the more microbes are close to each other, such that growth of a patch of microbes becomes a self-enhancing process. Our results show that there is a 'tipping point' - a critical size of such a patch, or number of spatially related microbes, which is necessary to start this process. In a model setting where soil microbes are C limited and thus only grow slowly, the addition of a small amount of labile C in a certain area is sufficient to trigger the emergence of such a growing microbial patch which consequently increases long-term decomposition rates of soil organic matter far beyond the initial labile C input in the model.

  9. Fatty liver in childhood

    Institute of Scientific and Technical Information of China (English)

    Yesim; Ozturk; Ozlem; Bekem; Soylu

    2014-01-01

    Fatty liver is a growing health problem worldwide. It might evolve to nonalcoholic steatohepatitis, cirrhosis and cause hepatocellular carcinoma. This disease, which has increased because of eating habits, changes in food content and lifestyle, affects people from childhood. The most important risk factors are obesity and insulin resistance. Besides these factors, gender, ethnicity, genetic predisposition and some medical problems are also important. Cirrhosis in children is rare but is reported. Nonalcoholic fatty liver disease(NAFLD) has no specific symptoms or signs but should be considered in obese children. NAFLD does not have a proven treatment. Weight loss with family based treatments is the most acceptable management. Exercise and an applicable diet with low glycemic index and appropriate calorie intake are preferred. Drugs are promising but not sufficient in children for today.

  10. The biology of habitat dominance; can microbes behave as weeds?

    Science.gov (United States)

    Cray, Jonathan A; Bell, Andrew N W; Bhaganna, Prashanth; Mswaka, Allen Y; Timson, David J; Hallsworth, John E

    2013-09-01

    Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized--or at least partially vacant--habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes

  11. A perspective: photosynthetic production of fatty acid-based biofuels in genetically engineered cyanobacteria.

    Science.gov (United States)

    Lu, Xuefeng

    2010-01-01

    Biofuels are expected to play a key role in the development of a sustainable, economical and environmentally safe source of energy. Microbes offer great potential for applications in technology based biofuel production. Three fundamental questions need to be addressed in order for the development of microbial synthesis of biofuels to be successful. Firstly, what energy resource platform could be used to make biofuels. Secondly, what type of biofuel is the ideal fuel molecule that should be targeted. Finally, what microbial system could be used to transform energy resources into the targeted biofuel molecules. In this perspective, the potential of using photosynthetic microbes (cyanobacteria in particular) in the solar energy driven conversion of carbon dioxide to fatty acid-based biofuels is explored. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. Detection of circular polarization in light scattered from photosynthetic microbes

    CERN Document Server

    Sparks, William B; Germer, Thomas A; Chen, Feng; DasSarma, Shiladitya; DasSarma, Priya; Robb, Frank T; Manset, Nadine; Kolokolova, Ludmilla; Reid, Neill; Macchetto, F Duccio; Martin, William; 10.1073/pnas.0810215106

    2009-01-01

    The identification of a universal biosignature that could be sensed remotely is critical to the prospects for success in the search for life elsewhere in the universe. A candidate universal biosignature is homochirality, which is likely to be a generic property of all biochemical life. Due to the optical activity of chiral molecules, it has been hypothesized that this unique characteristic may provide a suitable remote sensing probe using circular polarization spectroscopy. Here, we report the detection of circular polarization in light scattered by photosynthetic microbes. We show that the circular polarization appears to arise from circular dichroism of the strong electronic transitions of photosynthetic absorption bands. We conclude that circular polarization spectroscopy could provide a powerful remote sensing technique for generic life searches.

  13. How auxin and cytokinin phytohormones modulate root microbe interactions

    Directory of Open Access Journals (Sweden)

    Stéphane Boivin

    2016-08-01

    Full Text Available A large range of microorganisms can associate with plants, resulting in neutral, friendly or hostile interactions. The ability of plants to recognize compatible and incompatible microorganisms and to limit or promote their colonization is therefore crucial for their survival. Elaborated communication networks determine the degree of association between the host plant and the invading microorganism. Central to these regulations of plant microbe interactions, phytohormones modulate microorganism plant associations and coordinate cellular and metabolic responses associated to the progression of microorganisms across different plant tissues. We review here hormonal regulations, focusing on auxin and cytokinin phytohormones, involved in the interactions between plant roots and soil microorganisms, including bacteria and fungi associations, either beneficial (symbiotic or detrimental (pathogenic. The aim is to highlight similarities and differences in cytokinin/auxin functions amongst various compatible versus incompatible associations.

  14. Microarray tools to unveil viral-microbe interactions in nature

    Directory of Open Access Journals (Sweden)

    Fernando eSantos

    2014-07-01

    Full Text Available The interactions between viruses and their microbial hosts play a central role in the control of microbial communities in nature. However, the study of such interactions within the uncultured majority is technically very challenging. Here, we review how microarray tools can be used to analyze the interactions between viruses and their microbial hosts in nature, away from laboratory pure culture-based models. We show examples of how DNA arrays have been used to study the expression of viral assemblages in natural samples, and to assign viruses to hosts within uncultured communities. Finally, we briefly discuss the possibilities of protein and glycan arrays to gain insight into the ways microbes interact with their viruses.

  15. Receptor kinase signaling pathways in plant-microbe interactions.

    Science.gov (United States)

    Antolín-Llovera, Meritxell; Ried, Martina K; Binder, Andreas; Parniske, Martin

    2012-01-01

    Plant receptor-like kinases (RLKs) function in diverse signaling pathways, including the responses to microbial signals in symbiosis and defense. This versatility is achieved with a common overall structure: an extracytoplasmic domain (ectodomain) and an intracellular protein kinase domain involved in downstream signal transduction. Various surfaces of the leucine-rich repeat (LRR) ectodomain superstructure are utilized for interaction with the cognate ligand in both plant and animal receptors. RLKs with lysin-motif (LysM) ectodomains confer recognitional specificity toward N-acetylglucosamine-containing signaling molecules, such as chitin, peptidoglycan (PGN), and rhizobial nodulation factor (NF), that induce immune or symbiotic responses. Signaling downstream of RLKs does not follow a single pattern; instead, the detailed analysis of brassinosteroid (BR) signaling, innate immunity, and symbiosis revealed at least three largely nonoverlapping pathways. In this review, we focus on RLKs involved in plant-microbe interactions and contrast the signaling pathways leading to symbiosis and defense.

  16. Integrated studies of uncultured microbes in the global ocean (Invited)

    Science.gov (United States)

    Dupont, C.; Rusch, D.; Martiny, A.; Lasken, R.

    2010-12-01

    The Global Ocean Sampling (GOS) initiative at the J. Craig Venter Institute represents the most extensive metagenomic study of a single environment. Early findings highlighted the potential of shotgun metagenomics to expand our knowledge of marine microbial biodiversity and physiology. However, it also became clear that many of the abundant marine microbes remain uncultured, hindering a direct connection between phylogeny and ecophysiology. In two recent studies, a combination of single cell genomics and aggressive assembly of binned metagenomic data have resulted in the acquisition of multiple genomes for two uncultured but globally relevant organisms. Metabolic reconstructions of the whole genomes revealed unique physiological adaptations in marine Prochlorococcus to high nutrient, low Fe regions of the global ocean and illuminated the potential ecological role of the gamma-proteobacterial 16S clade SAR86. The internal reference genomes also facilitate fragment recruitment based biogeographical studies, both at the whole genome level and the protein level.

  17. Harnessing plant-microbe interactions for enhancing farm productivity.

    Science.gov (United States)

    Macdonald, Catriona; Singh, Brajesh

    2014-01-01

    Declining soil fertility and farm productivity is a major global concern in order to achieve food security for a burgeoning world population. It is reported that improving soil health alone can increase productivity by 10-15% and in combination with efficient plant traits, farm productivity can be increased up to 50-60%. In this article we explore the emerging microbial and bioengineering technologies, which can be employed to achieve the transformational increase in farm productivity and can simultaneously enhance environmental outcomes i.e., low green house gas (GHG) emissions. We argue that metagenomics, meta-transcriptomics and metabolomics have potential to provide fundamental knowledge on plant-microbes interactions necessary for new innovations to increase farm productivity. Further, these approaches provide tools to identify and select novel microbial/gene resources which can be harnessed in transgenic and designer plant technologies for enhanced resource use efficiencies.

  18. Arsenic-Microbe-Mineral Interactions in Mining-Affected Environments

    Directory of Open Access Journals (Sweden)

    Karen A. Hudson-Edwards

    2013-10-01

    Full Text Available The toxic element arsenic (As occurs widely in solid and liquid mine wastes. Aqueous forms of arsenic are taken up in As-bearing sulfides, arsenides, sulfosalts, oxides, oxyhydroxides, Fe-oxides, -hydroxides, -oxyhydroxides and -sulfates, and Fe-, Ca-Fe- and other arsenates. Although a considerable body of research has demonstrated that microbes play a significant role in the precipitation and dissolution of these As-bearing minerals, and in the alteration of the redox state of As, in natural and simulated mining environments, the molecular-scale mechanisms of these interactions are still not well understood. Further research is required using traditional and novel mineralogical, spectroscopic and microbiological techniques to further advance this field, and to help design remediation schemes.

  19. Functional metagenomics to decipher food-microbe-host crosstalk.

    Science.gov (United States)

    Larraufie, Pierre; de Wouters, Tomas; Potocki-Veronese, Gabrielle; Blottière, Hervé M; Doré, Joël

    2015-02-01

    The recent developments of metagenomics permit an extremely high-resolution molecular scan of the intestinal microbiota giving new insights and opening perspectives for clinical applications. Beyond the unprecedented vision of the intestinal microbiota given by large-scale quantitative metagenomics studies, such as the EU MetaHIT project, functional metagenomics tools allow the exploration of fine interactions between food constituents, microbiota and host, leading to the identification of signals and intimate mechanisms of crosstalk, especially between bacteria and human cells. Cloning of large genome fragments, either from complex intestinal communities or from selected bacteria, allows the screening of these biological resources for bioactivity towards complex plant polymers or functional food such as prebiotics. This permitted identification of novel carbohydrate-active enzyme families involved in dietary fibre and host glycan breakdown, and highlighted unsuspected bacterial players at the top of the intestinal microbial food chain. Similarly, exposure of fractions from genomic and metagenomic clones onto human cells engineered with reporter systems to track modulation of immune response, cell proliferation or cell metabolism has allowed the identification of bioactive clones modulating key cell signalling pathways or the induction of specific genes. This opens the possibility to decipher mechanisms by which commensal bacteria or candidate probiotics can modulate the activity of cells in the intestinal epithelium or even in distal organs such as the liver, adipose tissue or the brain. Hence, in spite of our inability to culture many of the dominant microbes of the human intestine, functional metagenomics open a new window for the exploration of food-microbe-host crosstalk.

  20. Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

    Science.gov (United States)

    Chen, M.; Kocar, B. D.

    2016-12-01

    Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

  1. New CRISPR–Cas systems from uncultivated microbes

    Science.gov (United States)

    Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

    2016-12-01

    CRISPR–Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR–Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR–Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR–Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR–Cas system. In bacteria, we discovered two previously unknown systems, CRISPR–CasX and CRISPR–CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  2. Effect of Mineral and Microbe Interactions on Biomass Yield

    Science.gov (United States)

    Pena, S. A.; Block, K. A.; Katz, A.; Gottlieb, P.

    2016-12-01

    The ecological feedback of microbes (bacteria and viruses) in association with minerals is virtually unexplored in the context of characterizing how carbon cycles in the terrestrial ecosystem. These interactions include the ability for bacteriophage to control bacteria populations, the ability of minerals to provide a substrate for bacteria growth, and the effect of minerals on bacteriophage viability. We investigate bacteriophage aggregation with minerals in the clay size fraction (virus experiments, bacteriophage Φ6 was suspended with the minerals smectite, illite, kaolinite, and goethite at low divalent cation concentrations so aggregation was in the reaction limited colloidal aggregation (RLCA) regime, at neutral pH and room temperature conditions. Virus remained viable at a 1:1 virus-clay ratio for clays, and at an approximate 100:1 ratio for goethite. However, the number of plaque forming units was reduced by 99%. Electron micrographs show viable as well as partially disassembled virus, similar to the results found by Block et al. 2014. We found that inactivation of a 4 x 1011 cm-3 concentration of bacteriophage Φ6 by smectite, illite, kaolinite, and goethite, required a minimum sediment concentration of 1.5 x 1011 cm-3, 1.4 x 1011 cm-3, 2.5 x 1011 cm-3, and 1.1 x 109 cm-3, respectively. Mineral biofilms were generated by suspension of tropical soil clays with gram-positive and gram-negative microbes and characterized by x-ray diffraction and imaged by electron microscopy (SEM and TEM). Mineral biomass produced by gram negative organisms were subjected to virus infection to determine influence of minerals on community resilience. Lastly, we report biomass yield in each instance to quantify the influence of mineral composition on total biomass production.

  3. Modeling physiological responses of soil microbes to drought (Invited)

    Science.gov (United States)

    Manzoni, S.; Katul, G. G.; Porporato, A. M.; Schaeffer, S. M.; Schimel, J.

    2013-12-01

    Biogeochemical models predict soil carbon (C) under varying environmental conditions, aiming to disentangle the effects of predicted changes in temperature and moisture regimes on C storage. While much work focuses on temperature sensitivity of decomposition, relatively less is known about decomposer responses to changes in soil moisture. Heterotrophic respiration is known to decline as soils become drier, but the underlying physiological mechanisms are not clear and rarely accounted for in models. In particular, we ask: what are the effects of different drought response strategies on C storage potential and the shape of the respiration-moisture relation? We have developed a process-based model to address these questions, including the main physiological responses thought to play a role under varying moisture conditions: i) dormancy, ii) patterns of extra-cellular enzyme production, and iii) osmoregulation. We show that these different drought response strategies play a major role in the long-term partitioning of soil C among stable and labile pools. In very dry conditions, microbes shifting to dormant state tend to favor long-term (steady state) accumulation of stable C at the expenses of microbial biomass, while increasing investment in enzymes leads to accumulation of dissolved organic C, which in turn may partly overcome the diffusion limitations imposed by dry soils. In contrast, entering a dormant state early during a dry down allows microbes to save C by respiring less (due to lowered active biomass), avoid C starvation when substrate diffusion breaks down, and use available C for growth and maintenance rather than osmoregulation. Hence, this strategy explains why little osmolytes are found in microbial biomass subjected to experimental drought. We conclude by highlighting how our results can be implemented in Earth System Models without excessively increasing their complexity.

  4. Climate change driven plant-metal-microbe interactions.

    Science.gov (United States)

    Rajkumar, Mani; Prasad, Majeti Narasimha Vara; Swaminathan, Sandhya; Freitas, Helena

    2013-03-01

    Various biotic and abiotic stress factors affect the growth and productivity of crop plants. Particularly, the climatic and/or heavy metal stress influence various processes including growth, physiology, biochemistry, and yield of crops. Climatic changes particularly the elevated atmospheric CO₂ enhance the biomass production and metal accumulation in plants and help plants to support greater microbial populations and/or protect the microorganisms against the impacts of heavy metals. Besides, the indirect effects of climatic change (e.g., changes in the function and structure of plant roots and diversity and activity of rhizosphere microbes) would lead to altered metal bioavailability in soils and concomitantly affect plant growth. However, the effects of warming, drought or combined climatic stress on plant growth and metal accumulation vary substantially across physico-chemico-biological properties of the environment (e.g., soil pH, heavy metal type and its bio-available concentrations, microbial diversity, and interactive effects of climatic factors) and plant used. Overall, direct and/or indirect effects of climate change on heavy metal mobility in soils may further hinder the ability of plants to adapt and make them more susceptible to stress. Here, we review and discuss how the climatic parameters including atmospheric CO₂, temperature and drought influence the plant-metal interaction in polluted soils. Other aspects including the effects of climate change and heavy metals on plant-microbe interaction, heavy metal phytoremediation and safety of food and feed are also discussed. This review shows that predicting how plant-metal interaction responds to altering climatic change is critical to select suitable crop plants that would be able to produce more yields and tolerate multi-stress conditions without accumulating toxic heavy metals for future food security.

  5. Potential for mercury reduction by microbes in the high arctic.

    Science.gov (United States)

    Poulain, Alexandre J; Ní Chadhain, Sinéad M; Ariya, Parisa A; Amyot, Marc; Garcia, Edenise; Campbell, Peter G C; Zylstra, Gerben J; Barkay, Tamar

    2007-04-01

    The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions.

  6. New CRISPR-Cas systems from uncultivated microbes

    Science.gov (United States)

    Burstein, David; Harrington, Lucas B.; Strutt, Steven C.; Probst, Alexander J.; Anantharaman, Karthik; Thomas, Brian C.; Doudna, Jennifer A.; Banfield, Jillian F.

    2017-02-01

    CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.

  7. Phytochemicals that modulate amino acid and peptide catabolism by caprine rumen microbes

    Science.gov (United States)

    Background: Microbe-derived ionophores and macrolide antibiotics are often added to ruminant diets, and growth promotion and feed efficiency are among the benefits. One mechanism is inhibition of microbes that catabolize amino acids or peptides and produce ammonia. Plants also produce antimicrobial ...

  8. Expression of defensin paralogs across house fly life history: insights into fly-microbe interactions

    Science.gov (United States)

    House flies have a life-long association with microbe-rich environments. Larvae directly ingest bacteria in decaying substrates utilizing them for nutritional purposes. Adult house flies ephemerally associate with microbes, ingesting them either by direct feeding or indirectly during grooming. The h...

  9. Biogeographical diversity of plant associated microbes in arcto-alpine plants

    NARCIS (Netherlands)

    Kumar, Manoj Gopala Krishnan

    2016-01-01

    Terrestrial plants and microbes have co-evolved since the emergence of the former on Earth. Associations with microorganisms can be either beneficial or detrimental for plants. Microbes can be found in the soil surrounding the plant roots, but also in all plant tissues, including seeds. In arcto-alp

  10. Update History of This Database - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us MicrobeDB.jp Update History of This Database Date Update contents 2017/06/29 Archive V2 is r...ion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - MicrobeDB.jp | LSDB Archive ...

  11. Experimental evolution as an underutilized tool for studying beneficial animal-microbe interactions

    Directory of Open Access Journals (Sweden)

    Kim Loan Hoang

    2016-09-01

    Full Text Available Microorganisms play a significant role in the evolution and functioning of the eukaryotes with which they interact. Much of our understanding of beneficial host-microbe interactions stems from studying already established associations; we often infer the genotypic and environmental conditions that led to the existing host-microbe relationships. However, several outstanding questions remain, including understanding how host and microbial (internal traits, and ecological and evolutionary (external processes, influence the origin of beneficial host-microbe associations. Experimental evolution has helped address a range of evolutionary and ecological questions across different model systems; however, it has been greatly underutilized as a tool to study beneficial host-microbe associations. In this review, we suggest ways in which experimental evolution can further our understanding of the proximate and ultimate mechanisms shaping mutualistic interactions between eukaryotic hosts and microbes. By tracking beneficial interactions under defined conditions or evolving novel associations among hosts and microbes with little prior evolutionary interaction, we can link specific genotypes to phenotypes that can be directly measured. Moreover, this approach will help address existing puzzles in beneficial symbiosis research: how symbioses evolve, how symbioses are maintained, and how both host and microbe influence their partner’s evolutionary trajectories. By bridging theoretical predictions and empirical tests, experimental evolution provides us with another approach to test hypotheses regarding the evolution of beneficial host-microbe associations.

  12. Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge

    DEFF Research Database (Denmark)

    Aslam, Shazia N.; Erbs, Gitte; Morrissey, Kate L.

    2009-01-01

    Triggering of defences by microbes has mainly been investigated using single elicitors or microbe-associated molecular patterns (MAMPs), but MAMPs are released in planta as complex mixtures together with endogenous oligogalacturonan (OGA) elicitor. We investigated the early responses in Arabidopsis...

  13. Plant-microbe and plant-insect interactions meet common grounds

    NARCIS (Netherlands)

    Schenk, P.; McGrath, K.C.; Lorito, M.; Pieterse, C.M.J.

    2008-01-01

    Plant–microbe and plant–insect interactions are of global importance for agriculture and of high interest to many plant scientists, microbiologists and entomologists. Traditionally, plant–microbe and plant–insect interactions have been looked at as two separate issues, but in recent years it has bec

  14. Plant-microbe and plant-insect interactions meet common grounds

    NARCIS (Netherlands)

    Schenk, P.; McGrath, K.C.; Lorito, M.; Pieterse, C.M.J.

    2008-01-01

    Plant–microbe and plant–insect interactions are of global importance for agriculture and of high interest to many plant scientists, microbiologists and entomologists. Traditionally, plant–microbe and plant–insect interactions have been looked at as two separate issues, but in recent years it has

  15. Biofilms for Babies: Introducing Microbes and Biofilms to Preschool-Aged Children

    Directory of Open Access Journals (Sweden)

    Jillian M. Couto

    2017-05-01

    Full Text Available Microbes are beneficial to life on our planet as they facilitate natural processes such as global nutrient cycling in our environment. This article details a 30-minute activity to introduce pre-school children ranging from 3 to 5 years of age to microbes and biofilms in the natural environment.

  16. Microbes and animal olfactory communication: Where do we go from here?

    Science.gov (United States)

    Ezenwa, Vanessa O; Williams, Allison E

    2014-09-01

    We know that microbes contribute to the production of odors that some animals use to communicate, but how common is this phenomenon? Recent studies capitalizing on new molecular technologies are uncovering fascinating associations between microbes and odors of wild animals, but causality is difficult to ascertain. Fundamental questions about the nature of these unique host-microbe interactions also remain unanswered. For instance, do microbes benefit from signaling associations with hosts? How does microbial community structure influence signal production? How do hosts regulate microbes in order to generate appropriate signals? Here, we review the current state of knowledge on microbially produced signals in animals and discuss key research foci that can advance our understanding of microbial-based signaling in the animal world. © 2014 WILEY Periodicals, Inc.

  17. Very high gravity ethanol and fatty acid production of Zymomonas mobilis without amino acid and vitamin.

    Science.gov (United States)

    Wang, Haoyong; Cao, Shangzhi; Wang, William Tianshuo; Wang, Kaven Tianyv; Jia, Xianhui

    2016-06-01

    Very high gravity (VHG) fermentation is the mainstream technology in ethanol industry, which requires the strains be resistant to multiple stresses such as high glucose concentration, high ethanol concentration, high temperature and harsh acidic conditions. To our knowledge, it was not reported previously that any ethanol-producing microbe showed a high performance in VHG fermentations without amino acid and vitamin. Here we demonstrate the engineering of a xylose utilizing recombinant Zymomonas mobilis for VHG ethanol fermentations. The recombinant strain can produce ethanol up to 136 g/L without amino acid and vitamin with a theoretical yield of 90 %, which is significantly superior to that produced by all the reported ethanol-producing strains. The intracellular fatty acids of the bacterial were about 16 % of the bacterial dry biomass, with the ratio of ethanol:fatty acids was about 273:1 (g/g). The recombinant strain was achieved by a multivariate-modular strategy tackles with the multiple stresses which are closely linked to the ethanol productivity of Z. mobilis. The over-expression of metB/yfdZ operon enabled the growth of the recombinant Z. mobilis in a chemically defined medium without amino acid and vitamin; and the fatty acids overproduction significantly increased ethanol tolerance and ethanol production. The coupled production of ethanol with fatty acids of the Z. mobilis without amino acid and vitamin under VHG fermentation conditions may permit a significant reduction of the production cost of ethanol and microbial fatty acids.

  18. Microbial engineering for the production of fatty acids and fatty acid derivatives

    Science.gov (United States)

    Stephanopoulos, Gregory; Abidi, Syed Hussain Imam

    2014-07-01

    Some aspects of this invention relate to methods useful for the conversion of a carbon source to a biofuel or biofuel precursor using engineered microbes. Some aspects of this invention relate to the discovery of a key regulator of lipid metabolism in microbes. Some aspects of this invention relate to engineered microbes for biofuel or biofuel precursor production.

  19. Microbial engineering for the production of fatty acids and fatty acid derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Stephanopoulos, Gregory; Abidi, Syed Hussain Imam

    2014-07-01

    Some aspects of this invention relate to methods useful for the conversion of a carbon source to a biofuel or biofuel precursor using engineered microbes. Some aspects of this invention relate to the discovery of a key regulator of lipid metabolism in microbes. Some aspects of this invention relate to engineered microbes for biofuel or biofuel precursor production.

  20. Omega-3 Fatty Acids during Pregnancy

    Science.gov (United States)

    OMEGA-3 FATTY ACIDS DURING PREGNANCY S HARE W ITH W OMEN OMEGA-3 FATTY ACIDS DURING PREGNANCY During pregnancy, your ... the foods you eat and vitamins you take. Omega-3 fatty acids (omega-3s) are an important ...

  1. Microbes versus microbes

    DEFF Research Database (Denmark)

    Jordan, Kieran; Dalmasso, Marion; Zentek, Juergen

    2014-01-01

    Foodborne illness continues as a considerable threat to public health. Despite improved hygiene management systems and increased regulation, pathogenic bacteria still contaminate food, causing sporadic cases of illness and disease outbreaks worldwide. For many centuries, microbial antagonism has...... been used in food processing to improve food safety. An understanding of the mode of action of this microbial antagonism has been gained in recent years and potential applications in food and feed safety are now being explored. This review focuses on the potential opportunities presented...

  2. 赤霉酸降解菌的筛选及其适宜降解条件的确定%Screening of Gibberellic Acid-degrading Strains and the Optimization of Its Degradation Conditions

    Institute of Scientific and Technical Information of China (English)

    李清平; 马丽莉; 唐洁; 黄灏; 姚开

    2012-01-01

    [ Objective] To screen a gibberellic acid-degrading strain and investigate the optimization of its degradation conditions. [ Method] An efficient gibberellic acid-degrading strain G-6 was screened from some domesticated strains tolerant to gibberellic acid ( GA3) by using basal salt medium with gibberellic acid as its only carbon source. In this paper, the effects of various factors on GA3 degradation by G-6 were investigated by single factor test and its condition for GA3 degradation was determined. [ Kesuit] The rate of GA3 degradation was up to 60.62% when the strain was incubated in 250 ml conical flask containing 40 ml mineral medium with 200 mg/L of gibberellic acid, 5. 0% of bacterial suspension and pH 7,0 on a rotary shaker (140 r/min) at 30 X for 120 h. [ Conclusion] The research supplied references for the biodegrada-tion pathway of GA3.%[目的]筛选一株赤霉酸( GA3)降解菌并探讨其适宜的降解备件.[方法]利用仅含赤霉酸为唯一碳源的基础盐培养基,对前期驯化得到的对GA3具有较强耐受性的微生物进行筛选,获得了具有较强降解GA3能力的菌株G-6;采用单因素试验系统考察了不同因素对菌株G-6降解GA3效果的影响,确定了其适宜的降解条件.[结果]在培养时间为120h、培养温度为30℃、初始pH为7.0、接种量(菌悬液OD600=1.000)为5.0% (V/V)、培养基中赤霉酸浓度为200 mg/L、摇床转速为140 r/min、250 ml锥形瓶培养基装量为40 ml的条件下,GA3降解率达到60.62%.[结论]为深入探讨GA3的生物降解途径提供了参考.

  3. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

    Directory of Open Access Journals (Sweden)

    Jenna M. Lang

    2014-12-01

    Full Text Available Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered.We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1 the Average American (AMERICAN: focused on convenience foods, (2 USDA recommended (USDA: emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3 Vegan (VEGAN: excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG

  4. Identification of Soil Microbes Capable of Utilizing Cellobiosan.

    Directory of Open Access Journals (Sweden)

    Jieni Lian

    Full Text Available Approximately 100 million tons of anhydrosugars, such as levoglucosan and cellobiosan, are produced through biomass burning every year. These sugars are also produced through fast pyrolysis, the controlled thermal depolymerization of biomass. While the microbial pathways associated with levoglucosan utilization have been characterized, there is little known about cellobiosan utilization. Here we describe the isolation and characterization of six cellobiosan-utilizing microbes from soil samples. Each of these organisms is capable of using both cellobiosan and levoglucosan as sole carbon source, though both minimal and rich media cellobiosan supported significantly higher biomass production than levoglucosan. Ribosomal sequencing was used to identify the closest reported match for these organisms: Sphingobacterium multivorum, Acinetobacter oleivorans JC3-1, Enterobacter sp SJZ-6, and Microbacterium sps FXJ8.207 and 203 and a fungal species Cryptococcus sp. The commercially-acquired Enterobacter cloacae DSM 16657 showed growth on levoglucosan and cellobiosan, supporting our isolate identification. Analysis of an existing database of 16S rRNA amplicons from Iowa soil samples confirmed the representation of our five bacterial isolates and four previously-reported levoglucosan-utilizing bacterial isolates in other soil samples and provided insight into their population distributions. Phylogenetic analysis of the 16S rRNA and 18S rRNA of strains previously reported to utilize levoglucosan and our newfound isolates showed that the organisms isolated in this study are distinct from previously described anhydrosugar-utilizing microbial species.

  5. Economical evolution: microbes reduce the synthetic cost of extracellular proteins.

    Science.gov (United States)

    Smith, Daniel R; Chapman, Matthew R

    2010-08-24

    Protein evolution is not simply a race toward improved function. Because organisms compete for limited resources, fitness is also affected by the relative economy of an organism's proteome. Indeed, many abundant proteins contain relatively high percentages of amino acids that are metabolically less taxing for the cell to make, thus reducing cellular cost. However, not all abundant proteins are economical, and many economical proteins are not particularly abundant. Here we examined protein composition and found that the relative synthetic cost of amino acids constrains the composition of microbial extracellular proteins. In Escherichia coli, extracellular proteins contain, on average, fewer energetically expensive amino acids independent of their abundance, length, function, or structure. Economic pressures have strategically shaped the amino acid composition of multicomponent surface appendages, such as flagella, curli, and type I pili, and extracellular enzymes, including type III effector proteins and secreted serine proteases. Furthermore, in silico analysis of Pseudomonas syringae, Mycobacterium tuberculosis, Saccharomyces cerevisiae, and over 25 other microbes spanning a wide range of GC content revealed a broad bias toward more economical amino acids in extracellular proteins. The synthesis of any protein, especially those rich in expensive aromatic amino acids, represents a significant investment. Because extracellular proteins are lost to the environment and not recycled like other cellular proteins, they present a greater burden on the cell, as their amino acids cannot be reutilized during translation. We hypothesize that evolution has optimized extracellular proteins to reduce their synthetic burden on the cell.

  6. The Indirect Effect of UV: Some Good News for Microbes?

    Science.gov (United States)

    Rothschild, Lynn J.; Purcell, Diane; Rogoff, Dana; Wilson, Cindy; Brass, James A. (Technical Monitor)

    2002-01-01

    Ultraviolet (UV) radiation is of great concern because its biological effects are predominantly harmful. UV damage may be direct or indirect, the latter mediated through the photochemical production of reactive oxygen species such as hydrogen peroxide. We measured the effect of H2O2 on various microbes both in the lab and in nature. At our study site in Yellowstone National Park, there is a UV-induced diurnal fluctuation of H2O2 extending up to one micron. Levels of DNA synthesis resulting from exposure to H2O2 were measured in several algal mats. Within naturally-occurring concentrations of H2O2, DNA synthesis increased. Laboratory studies showed that similar concentrations of H2O2 induce mitosis. We hypothesize that the low levels of H2O2 encountered in nature are inducing mitotic division. At higher levels of H2O2 a second peak in DNA synthesis was found which we interpret to represent DNA damage repair. These experiments suggest that in nature, the low levels of H2O2 produced may have a mitogenic rather than damaging effect. Assuming early levels of UV radiation were substantially higher at the time protists evolved, differential mitogenic effects could have influenced protistan evolution. With H2O2 likely to be present on such bodies as Mars and Europa, the response of organisms will be concentration-dependent and not linear.

  7. Marine Drugs from Sponge-Microbe Association—A Review

    Directory of Open Access Journals (Sweden)

    Tresa Remya A. Thomas

    2010-04-01

    Full Text Available The subject of this review is the biodiversity of marine sponges and associated microbes which have been reported to produce therapeutically important compounds, along with the contextual information on their geographic distribution. Class Demospongiae and the orders Halichondrida, Poecilosclerida and Dictyoceratida are the richest sources of these compounds. Among the microbial associates, members of the bacterial phylum Actinobacteria and fungal division Ascomycota have been identified to be the dominant producers of therapeutics. Though the number of bacterial associates outnumber the fungal associates, the documented potential of fungi to produce clinically active compounds is currently more important than that of bacteria. Interestingly, production of a few identical compounds by entirely different host-microbial associations has been detected in both terrestrial and marine environments. In the Demospongiae, microbial association is highly specific and so to the production of compounds. Besides, persistent production of bioactive compounds has also been encountered in highly specific host-symbiont associations. Though spatial and temporal variations are known to have a marked effect on the quality and quantity of bioactive compounds, only a few studies have covered these dimensions. The need to augment production of these compounds through tissue culture and mariculture has also been stressed. The reviewed database of these compounds is available at www.niobioinformatics.in/drug.php.

  8. The battle for chitin recognition in plant-microbe interactions.

    Science.gov (United States)

    Sánchez-Vallet, Andrea; Mesters, Jeroen R; Thomma, Bart P H J

    2015-03-01

    Fungal cell walls play dynamic functions in interaction of fungi with their surroundings. In pathogenic fungi, the cell wall is the first structure to make physical contact with host cells. An important structural component of fungal cell walls is chitin, a well-known elicitor of immune responses in plants. Research into chitin perception has sparked since the chitin receptor from rice was cloned nearly a decade ago. Considering the widespread nature of chitin perception in plants, pathogens evidently evolved strategies to overcome detection, including alterations in the composition of cell walls, modification of their carbohydrate chains and secretion of effectors to provide cell wall protection or target host immune responses. Also non-pathogenic fungi contain chitin in their cell walls and are recipients of immune responses. Intriguingly, various mutualists employ chitin-derived signaling molecules to prepare their hosts for the mutualistic relationship. Research on the various types of interactions has revealed different molecular components that play crucial roles and, moreover, that various chitin-binding proteins contain dissimilar chitin-binding domains across species that differ in affinity and specificity. Considering the various strategies from microbes and hosts focused on chitin recognition, it is evident that this carbohydrate plays a central role in plant-fungus interactions.

  9. Engineering plant-microbe symbiosis for rhizoremediation of heavy metals.

    Science.gov (United States)

    Wu, Cindy H; Wood, Thomas K; Mulchandani, Ashok; Chen, Wilfred

    2006-02-01

    The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyperaccumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium, Pseudomonas putida 06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing P. putida endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites.

  10. Exploring laser-guided metal deposition through a microbe metabolite

    Directory of Open Access Journals (Sweden)

    H. Hocheng

    2009-12-01

    Full Text Available Purpose: The purpose of the paper is to describe exploring laser-guided metal deposition through a microbe metabolite.Design/methodology/approach: A maskless micro-fabrication of laser-guided deposition process through the metabolite of Acidophilic bacteria Thiobacillus ferrooxidans (T.f. is explored.Findings: The authors have conducted an analysis of the metal deposition process using the point thermal-source of the Nd:YAG laser through the metabolite of Acidophilic bacteria Thiobacillus. An analytical model adopting the moving point heat source on the substrate and heat transfer conditions is presented. The thermal field generated by the laser input energy is investigated.Practical implications: Though the mechanism of the laser-assisted deposition process is not fully revealed by biologist yet, the current model provides a means of control of the line deposition of metals.Originality/value: Based on the fundamental knowledge of how the line width varies with laser power and scanning speed, more investigation of the mini-scale heat convection and the threshold temperature of chemical reaction is expected in the future for further understanding of this novel metal deposition method triggered and written by laser.

  11. Linking plant nutritional status to plant-microbe interactions.

    Directory of Open Access Journals (Sweden)

    Lilia C Carvalhais

    Full Text Available Plants have developed a wide-range of adaptations to overcome nutrient limitation, including changes to the quantity and composition of carbon-containing compounds released by roots. Root-associated bacteria are largely influenced by these compounds which can be perceived as signals or substrates. Here, we evaluate the effect of root exudates collected from maize plants grown under nitrogen (N, phosphate (P, iron (Fe and potassium (K deficiencies on the transcriptome of the plant growth promoting rhizobacterium (PGPR Bacillus amyloliquefaciens FZB42. The largest shifts in gene expression patterns were observed in cells exposed to exudates from N-, followed by P-deficient plants. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Exudates from P-deficient plants induced bacterial genes involved in chemotaxis and motility whilst exudates released by Fe and K deficient plants did not cause dramatic changes in the bacterial transcriptome during exponential growth phase. Global transcriptional changes in bacteria elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates suggesting that transcriptional profiling of FZB42 associated with metabolomics of N, P, Fe and K-deficient maize root exudates is a powerful approach to better understand plant-microbe interactions under conditions of nutritional stress.

  12. The symbiont side of symbiosis: do microbes really benefit?

    Directory of Open Access Journals (Sweden)

    Justine Rebecca Garcia

    2014-09-01

    Full Text Available Microbial associations are integral to all eukaryotes. Mutualism, the interaction of two species for the benefit of both, is an important aspect of microbial associations, with evidence that multicellular organisms in particular benefit from microbes. However, the microbe’s perspective has largely been ignored, and it is unknown whether most microbial symbionts benefit from their associations with hosts. It has been presumed that microbial symbionts receive host-derived nutrients or a competition-free environment with reduced predation, but there have been few empirical tests, or even critical assessments, of these assumptions. We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. Some symbionts do receive nutrients from their host, but this has not always been linked to a corresponding increase in symbiont fitness. We recommend experiments to test symbiont fitness using current experimental systems of symbiosis and detail considerations for other systems. Incorporating symbiont fitness into symbiosis research will provide insight into the evolution of mutualistic interactions and cooperation in general.

  13. Diet, genes, and microbes: complexities of colon cancer prevention.

    Science.gov (United States)

    Birt, Diane F; Phillips, Gregory J

    2014-01-01

    Colorectal cancer is one of the leading causes of cancer-related deaths in the United States, and generally, as countries climb the economic ladder, their rates of colon cancer increase. Colon cancer was an early disease where key genetic mutations were identified as important in disease progression, and there is considerable interest in determining whether specific mutations sensitize the colon to cancer prevention strategies. Epidemiological studies have revealed that fiber- and vegetable-rich diets and physical activity are associated with reduced rates of colon cancer, while consumption of red and processed meat, or alcoholic beverages, and overconsumption as reflected in obesity are associated with increased rates. Animal studies have probed these effects and suggested directions for further refinement of diet in colon cancer prevention. Recently a central role for the microorganisms in the gastrointestinal tract in colon cancer development is being probed, and it is hypothesized that the microbes may integrate diet and host genetics in the etiology of the disease. This review provides background on dietary, genetic, and microbial impacts on colon cancer and describes an ongoing project using rodent models to assess the ability of digestion-resistant starch in the integration of these factors with the goal of furthering colon cancer prevention.

  14. Microbe-surface interactions in biofouling and biocorrosion processes.

    Science.gov (United States)

    Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

    2005-09-01

    The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

  15. Effects of soya fatty acids on cassava ethanol fermentation.

    Science.gov (United States)

    Xiao, Dongguang; Wu, Shuai; Zhu, Xudong; Chen, Yefu; Guo, Xuewu

    2010-01-01

    Ethanol tolerance is a key trait of microbes in bioethanol production. Previous studies have shown that soya flour contributed to the increase of ethanol tolerance of yeast cells. In this paper, the mechanism of this ethanol tolerance improvement was investigated in cassava ethanol fermentation supplemented with soya flour or defatted soya flour, respectively. Experiment results showed that ethanol tolerance of cells from soya flour supplemented medium increased by 4-6% (v/v) than the control with defatted soya flour. Microscopic observation found that soya flour can retain the cell shape while dramatic elongations of cells were observed with the defatted soya flour supplemented medium. Unsaturated fatty acids (UFAs) compositions of cell membrane were analyzed and the UFAs amounts increased significantly in all tested strains grown in soya flour supplemented medium. Growth study also showed that soya flour stimulated the cell growth rate by approximately tenfolds at 72-h fermentation. All these results suggested that soya fatty acids play an important role to protect yeast cells from ethanol stress during fermentation process.

  16. Engineering Escherichia coli for biodiesel production utilizing a bacterial fatty acid methyltransferase.

    Science.gov (United States)

    Nawabi, Parwez; Bauer, Stefan; Kyrpides, Nikos; Lykidis, Athanasios

    2011-11-01

    The production of low-cost biofuels in engineered microorganisms is of great interest due to the continual increase in the world's energy demands. Biodiesel is a renewable fuel that can potentially be produced in microbes cost-effectively. Fatty acid methyl esters (FAMEs) are a common component of biodiesel and can be synthesized from either triacylglycerol or free fatty acids (FFAs). Here we report the identification of a novel bacterial fatty acid methyltransferase (FAMT) that catalyzes the formation of FAMEs and 3-hydroxyl fatty acid methyl esters (3-OH-FAMEs) from the respective free acids and S-adenosylmethionine (AdoMet). FAMT exhibits a higher specificity toward 3-hydroxy free fatty acids (3-OH-FFAs) than FFAs, synthesizing 3-hydroxy fatty acid methyl esters (3-OH-FAMEs) in vivo. We have also identified bacterial members of the fatty acyl-acyl carrier protein (ACP) thioesterase (FAT) enzyme family with distinct acyl chain specificities. These bacterial FATs exhibit increased specificity toward 3-hydroxyacyl-ACP, generating 3-OH-FFAs, which can subsequently be utilized by FAMTs to produce 3-OH-FAMEs. PhaG (3-hydroxyacyl ACP:coenzyme A [CoA] transacylase) constitutes an alternative route to 3-OH-FFA synthesis; the coexpression of PhaG with FAMT led to the highest level of accumulation of 3-OH-FAMEs and FAMEs. The availability of AdoMet, the second substrate for FAMT, is an important factor regulating the amount of methyl esters produced by bacterial cells. Our results indicate that the deletion of the global methionine regulator metJ and the overexpression of methionine adenosyltransferase result in increased methyl ester synthesis.

  17. Comparison of 16S rRNA gene phylogeny and functional tfdA gene distribution in thirty-one different 2,4-dichlorophenoxyacetic acid and 4-chloro-2-methylphenoxyacetic acid degraders.

    Science.gov (United States)

    Baelum, Jacob; Jacobsen, Carsten S; Holben, William E

    2010-03-01

    31 different bacterial strains isolated using the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole source of carbon, were investigated for their ability to mineralize 2,4-D and the related herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA). Most of the strains mineralize 2,4-D considerably faster than MCPA. Three novel primer sets were developed enabling amplification of full-length coding sequences (CDS) of the three known tfdA gene classes known to be involved in phenoxy acid degradation. 16S rRNA genes were also sequenced; and in order to investigate possible linkage between tfdA gene classes and bacterial species, tfdA and 16S rRNA gene phylogeny was compared. Three distinctly different classes of tfdA genes were observed, with class I tfdA sequences further partitioned into the two sub-classes I-a and I-b based on more subtle differences. Comparison of phylogenies derived from 16S rRNA gene sequences and tfdA gene sequences revealed that most class II tfdA genes were encoded by Burkholderia sp., while class I-a, I-b and III genes were found in a more diverse array of bacteria. Copyright 2010 Elsevier GmbH. All rights reserved.

  18. Enhancement Effect of Gold Nanoparticles on the Bioactivity of Hydrogen-producing Microbe

    Institute of Scientific and Technical Information of China (English)

    LIU Guangzhen; MA Zhanfang; SHEN Jianquan

    2006-01-01

    In order to increase the yield of hydrogen production for hydrogen-producing microbe, the enhancement effect of nanometer- sized gold particles on the activity of hydrogen-producing microbe was studied. The yields of hydrogen production in the system added by gold nanoparticles of 6 nm and 12 nm in diameter were obviously increased by about 17% and 9% in contrast to that in blank system. The experimental results indicate that gold nanoparticles could significantly enhance the bioactivity of hydrogen-producing microbe.

  19. Helping plants to deal with insects: the role of beneficial soil-borne microbes.

    Science.gov (United States)

    Pineda, Ana; Zheng, Si-Jun; van Loon, Joop J A; Pieterse, Corné M J; Dicke, Marcel

    2010-09-01

    Several soil-borne microbes such as mycorrhizal fungi and plant growth-promoting rhizobacteria can help plants to deal with biotic and abiotic stresses via plant growth promotion and induced resistance. Such beneficial belowground microbes interact in a bidirectional way via the plant with aboveground insects such as herbivores, their natural enemies and pollinators. The role of these interactions in natural and agricultural ecosystems is receiving increased attention, and the molecular and physiological mechanisms involved in these interactions should be the focus of more attention. Here, we review the recent discoveries on plant-mediated interactions between beneficial belowground microbes and aboveground insects.

  20. Anaerobic digestion of palm oil mill effluent with lampung natural zeolite as microbe immobilization medium and digested cow manure as starter

    Science.gov (United States)

    Halim, Lenny; Mellyanawaty, Melly; Cahyono, Rochim Bakti; Sudibyo, Hanifrahmawan; Budhijanto, Wiratni

    2017-05-01

    Indonesia is well-known as the world's biggest palm oil producer with 32.5 million tons of annual production. Palm oil processing contributes to 60% wastewater, leading to environmental problem caused by excessive production of wastewater. This wastewater, i.e. Palm Oil Mill Effluent (POME), has high organic content (40,000-60,000 mg COD/L) which is potential for biogas production. However, its low pH value and long chain fatty acid content likely inhibit the anaerobic digestion. Porous media might reduce the inhibitory effect during POME digestion since the media act as both immobilization media for bacteria and as inhibitor adsorbent. Excessive amount of porous media might interfere with the nutrient consumption by microbes. There will be an optimum amount of porous media added, which depends on the wastewater characteristics. This research studied Lampung natural zeolite as immobilization media in digesting POME. The batch experiment was conducted for 40 days with different amount of natural zeolite, i.e. 0; 45; 100; and 200 g/g COD. Digested cow manure was used as the starter inoculum, considering the abundance of anaerobic bacteria therein. Zeolite addition was proven to accelerate COD reduction and stabilized the volatile fatty acid as the intermediate product of anaerobic digestion. The addition of natural zeolite up to 45 g/g COD is considered enough to increase the COD removal (85.695 %), maintain the methane content up to 50%, and enhance the bacteria activity. However, larger amount of natural zeolite lowered the methane production and COD reduction, which indicated nutrient adsorption on to the media and hence caused decreasing nutrient access by the microbes.

  1. Universal ligation-detection-reaction microarray applied for compost microbes

    Directory of Open Access Journals (Sweden)

    Romantschuk Martin

    2008-12-01

    Full Text Available Abstract Background Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones. Results Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array. Conclusion This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.

  2. Insight and analysis problem solving in microbes to machines.

    Science.gov (United States)

    Clark, Kevin B

    2015-11-01

    A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices.

  3. Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes.

    Science.gov (United States)

    Ponce de León, Inés; Montesano, Marcos

    2017-01-01

    Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens.

  4. Scaling Soil Microbe-Water Interactions from Pores to Ecosystems

    Science.gov (United States)

    Manzoni, S.; Katul, G. G.

    2014-12-01

    The spatial scales relevant to soil microbial activity are much finer than scales relevant to whole-ecosystem function and biogeochemical cycling. On the one hand, how to link such different scales and develop scale-aware biogeochemical and ecohydrological models remains a major challenge. On the other hand, resolving these linkages is becoming necessary for testing ecological hypotheses and resolving data-theory inconsistencies. Here, the relation between microbial respiration and soil moisture expressed in water potential is explored. Such relation mediates the water availability effects on ecosystem-level heterotrophic respiration and is of paramount importance for understanding CO2 emissions under increasingly variable rainfall regimes. Respiration has been shown to decline as the soil dries in a remarkably consistent way across climates and soil types (open triangles in Figure). Empirical models based on these respiration-moisture relations are routinely used in Earth System Models to predict moisture effects on ecosystem respiration. It has been hypothesized that this consistency in microbial respiration decline is due to breakage of water film continuity causing in turn solute diffusion limitations in dry conditions. However, this hypothesis appears to be at odds with what is known about soil hydraulic properties. Water film continuity estimated from soil water retention (SWR) measurements at the 'Darcy' scale breaks at far less negative water potential (tools from percolation theory, it is demonstrated that hydrological measurements can be spatially downscaled at a micro-level relevant to microbial activity. Such downscaling resolves the inconsistency between respiration thresholds and hydrological thresholds. This result, together with observations of residual microbial activity well below -15 MPa (dashed back curve in Figure), lends support to the hypothesis that soil microbes are substrate-limited in dry conditions.

  5. Centrality of host cell death in plant-microbe interactions.

    Science.gov (United States)

    Dickman, Martin B; Fluhr, Robert

    2013-01-01

    Programmed cell death (PCD) is essential for proper growth, development, and cellular homeostasis in all eukaryotes. The regulation of PCD is of central importance in plant-microbe interactions; notably, PCD and features associated with PCD are observed in many host resistance responses. Conversely, pathogen induction of inappropriate cell death in the host results in a susceptible phenotype and disease. Thus, the party in control of PCD has a distinct advantage in these battles. PCD processes appear to be of ancient origin, as indicated by the fact that many features of cell death strategy are conserved between animals and plants; however, some of the details of death execution differ. Mammalian core PCD genes, such as caspases, are not present in plant genomes. Similarly, pro- and antiapoptotic mammalian regulatory elements are absent in plants, but, remarkably, when expressed in plants, successfully impact plant PCD. Thus, subtle structural similarities independent of sequence homology appear to sustain operational equivalence. The vacuole is emerging as a key organelle in the modulation of plant PCD. Under different signals for cell death, the vacuole either fuses with the plasmalemma membrane or disintegrates. Moreover, the vacuole appears to play a key role in autophagy; evidence suggests a prosurvival function for autophagy, but other studies propose a prodeath phenotype. Here, we describe and discuss what we know and what we do not know about various PCD pathways and how the host integrates signals to activate salicylic acid and reactive oxygen pathways that orchestrate cell death. We suggest that it is not cell death as such but rather the processes leading to cell death that contribute to the outcome of a given plant-pathogen interaction.

  6. Adaptation Mechanisms in the Evolution of Moss Defenses to Microbes

    Science.gov (United States)

    Ponce de León, Inés; Montesano, Marcos

    2017-01-01

    Bryophytes, including mosses, liverworts and hornworts are early land plants that have evolved key adaptation mechanisms to cope with abiotic stresses and microorganisms. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. In addition, early land plants acquired novel defense mechanisms to protect plant tissues from pre-existing microbial pathogens. Due to its evolutionary stage linking unicellular green algae to vascular plants, the non-vascular moss Physcomitrella patens is an interesting organism to explore the adaptation mechanisms developed in the evolution of plant defenses to microbes. Cellular and biochemical approaches, gene expression profiles, and functional analysis of genes by targeted gene disruption have revealed that several defense mechanisms against microbial pathogens are conserved between mosses and flowering plants. P. patens perceives pathogen associated molecular patterns by plasma membrane receptor(s) and transduces the signal through a MAP kinase (MAPK) cascade leading to the activation of cell wall associated defenses and expression of genes that encode proteins with different roles in plant resistance. After pathogen assault, P. patens also activates the production of ROS, induces a HR-like reaction and increases levels of some hormones. Furthermore, alternative metabolic pathways are present in P. patens leading to the production of a distinct metabolic scenario than flowering plants that could contribute to defense. P. patens has acquired genes by horizontal transfer from prokaryotes and fungi, and some of them could represent adaptive benefits for resistance to biotic stress. In this review, the current knowledge related to the evolution of plant defense responses against pathogens will be discussed, focusing on the latest advances made in the model plant P. patens. PMID:28360923

  7. Cr isotope fractionation in metal-mineral-microbe interactions

    Science.gov (United States)

    Zhang, Qiong; Porcelli, Don; Thompson, Ian; Amor, Ken; Galer, Stephen

    2016-04-01

    Microbes interact with metals and minerals in the environments, altering their physical and chemical state whilst in turn the metals and minerals affect microbial growth, activity and survival. The interactions between Cr, Fe minerals and bacteria were investigated in this study. Cr(VI) reduction experiments by two iron-reducing bacteria, Pseudomonas fluorescens LB 300 and Shewanella oneidensis MR 1, in the presence of two iron oxide minerals, goethite and hematite, were conducted. Both minerals were found to inhibit the Cr(VI) reduction rate by Pseudomonas fluorescens LB 300 but accelerated Shewanella oneidensis MR 1. The Cr isotopic fractionation factor generated by both bacteria was mostly independent of the presence of the minerals, except for hematite with Pseudomonas fluorescens LB 300, where the ɛ was much higher. Aqueous Fe(III) in the solution did not have any detectable impact on either bacterial Cr reduction rates or the isotopic fractionation factors, indicating that the reduction of Cr(VI) occurred prior to that of Fe(III). The presence of aqueous Fe(II) induced a very fast abiotic reduction of Cr, but had little impact on the bacterial Cr reduction rates or its isotope fractionations. The evidence suggests that the different impact that Fe minerals had on the bacteria were related to the way they attached to the minerals and the difference in the reduction mechanism. SEM images confirmed that the attachment of Pseudomonas fluorescens LB 300 on the mineral surfaces were much more tightly packed than that of Shewanella oneidensis MR 1, so reducing mineral-metal interactions.

  8. Nutrient subsidies to belowground microbes impact aboveground food web interactions.

    Science.gov (United States)

    Hines, Jes; Megonigal, J Patrick; Denno, Robert F

    2006-06-01

    Historically, terrestrial food web theory has been compartmentalized into interactions among aboveground or belowground communities. In this study we took a more synthetic approach to understanding food web interactions by simultaneously examining four trophic levels and investigating how nutrient (nitrogen and carbon) and detrital subsidies impact the ability of the belowground microbial community to alter the abundance of aboveground arthropods (herbivores and predators) associated with the intertidal cord grass Spartina alterniflora. We manipulated carbon, nitrogen, and detrital resources in a field experiment and measured decomposition rate, soil nitrogen pools, plant biomass and quality, herbivore density, and arthropod predator abundance. Because carbon subsidies impact plant growth only indirectly (microbial pathways), whereas nitrogen additions both directly (plant uptake) and indirectly (microbial pathways) impact plant primary productivity, we were able to assess the effect of both belowground soil microbes and nutrient availability on aboveground herbivores and their predators. Herbivore density in the field was suppressed by carbon supplements. Carbon addition altered soil microbial dynamics (net potential ammonification, litter decomposition rate, DON [dissolved organic N] concentration), which limited inorganic soil nitrogen availability and reduced plant size as well as predator abundance. Nitrogen addition enhanced herbivore density by increasing plant size and quality directly by increasing inorganic soil nitrogen pools, and indirectly by enhancing microbial nitrification. Detritus adversely affected aboveground herbivores mainly by promoting predator aggregation. To date, the effects of carbon and nitrogen subsidies on salt marshes have been examined as isolated effects on either the aboveground or the belowground community. Our results emphasize the importance of directly addressing the soil microbial community as a factor that influences

  9. Fatty Acid Desaturases, Polyunsaturated Fatty Acid Regulation, and Biotechnological Advances.

    Science.gov (United States)

    Lee, Je Min; Lee, Hyungjae; Kang, SeokBeom; Park, Woo Jung

    2016-01-04

    Polyunsaturated fatty acids (PUFAs) are considered to be critical nutrients to regulate human health and development, and numerous fatty acid desaturases play key roles in synthesizing PUFAs. Given the lack of delta-12 and -15 desaturases and the low levels of conversion to PUFAs, humans must consume some omega-3 and omega-6 fatty acids in their diet. Many studies on fatty acid desaturases as well as PUFAs have shown that fatty acid desaturase genes are closely related to different human physiological conditions. Since the first front-end desaturases from cyanobacteria were cloned, numerous desaturase genes have been identified and animals and plants have been genetically engineered to produce PUFAs such as eicosapentaenoic acid and docosahexaenoic acid. Recently, a biotechnological approach has been used to develop clinical treatments for human physiological conditions, including cancers and neurogenetic disorders. Thus, understanding the functions and regulation of PUFAs associated with human health and development by using biotechnology may facilitate the engineering of more advanced PUFA production and provide new insights into the complexity of fatty acid metabolism.

  10. Fatty Acid Desaturases, Polyunsaturated Fatty Acid Regulation, and Biotechnological Advances

    Directory of Open Access Journals (Sweden)

    Je Min Lee

    2016-01-01

    Full Text Available Polyunsaturated fatty acids (PUFAs are considered to be critical nutrients to regulate human health and development, and numerous fatty acid desaturases play key roles in synthesizing PUFAs. Given the lack of delta-12 and -15 desaturases and the low levels of conversion to PUFAs, humans must consume some omega-3 and omega-6 fatty acids in their diet. Many studies on fatty acid desaturases as well as PUFAs have shown that fatty acid desaturase genes are closely related to different human physiological conditions. Since the first front-end desaturases from cyanobacteria were cloned, numerous desaturase genes have been identified and animals and plants have been genetically engineered to produce PUFAs such as eicosapentaenoic acid and docosahexaenoic acid. Recently, a biotechnological approach has been used to develop clinical treatments for human physiological conditions, including cancers and neurogenetic disorders. Thus, understanding the functions and regulation of PUFAs associated with human health and development by using biotechnology may facilitate the engineering of more advanced PUFA production and provide new insights into the complexity of fatty acid metabolism.

  11. No vacancy: how beneficial microbes cooperate with immunity to provide colonization resistance to pathogens.

    Science.gov (United States)

    Sassone-Corsi, Martina; Raffatellu, Manuela

    2015-05-01

    The mammalian intestine harbors a community of trillions of microbes, collectively known as the gut microbiota, which coevolved with the host in a mutually beneficial relationship. Among the numerous gut microbial species, certain commensal bacteria are known to provide health benefits to the host when administered in adequate amounts and, as such, are labeled "probiotics." We review some of the mechanisms by which probiotics and other beneficial commensals provide colonization resistance to pathogens. The battle for similar nutrients and the bacterial secretion of antimicrobials provide a direct means of competition between beneficial and harmful microbes. Beneficial microbes can also indirectly diminish pathogen colonization by stimulating the development of innate and adaptive immunity, as well as the function of the mucosal barrier. Altogether, we gather and present evidence that beneficial microbes cooperate with host immunity in an effort to shut out pathogens.

  12. 2010 MARINE MICROBES GORDON RESEARCH CONFERENCE (JULY 4-9, 2010 - TILTON SCHOOL, TILTON NH)

    Energy Technology Data Exchange (ETDEWEB)

    David Kirchman

    2010-04-09

    Marine microbes include representatives from all three kingdoms of life and collectively carry out virtually all forms of metabolisms found on the planet. Because of this metabolic and genetic diversity, these microbes mediate many of the reactions making up global biogeochemical cycles which govern the flow of energy and material in the biosphere. The goal of this conference is to bring together approaches and concepts from studies of microbial evolution, genomics, ecology, and oceanography in order to gain new insights into marine microbes and their biogeochemical functions. The integration of scales, from genes to global cycles, will result in a better understanding of marine microbes and of their contribution to the carbon cycle and other biogeochemical processes.

  13. The Antarctic cryptoendolithic microbial ecosystem as a model for studying microbes in shale and coal

    Energy Technology Data Exchange (ETDEWEB)

    Vestal, J.R. (University of Cincinnati, Cincinnati, OH (USA). Dept. of Biological Sciences)

    1991-04-01

    In Antarctica, there exists a complete microbial ecosystem that lives hidden within the pore spaces of sandstone (cryptoendolithic). Studying microbes within this solid matrix has presented certain technical problems which have been overcome. This has allowed studies to be conducted that have shown the effects of the physical and chemical environment on growth and metabolism of the microbes in these rocks. Similar microbial communities have recently been discovered that can exist within the solid matrix of shale and coal. Even though the community and environment are different from the Antarctic microbes, many of the methods and hypotheses regarding their existence are the same. Answers to questions relating how and why these microbes exist in shale and coal may have important implications for coal desulfurization, or degradation of the shale matrix to release hydrocarbons. 40 refs., 1 fig., 1 tab.

  14. The production of ω-hydroxy palmitic acid using fatty acid metabolism and cofactor optimization in Escherichia coli.

    Science.gov (United States)

    Sung, Changmin; Jung, Eunok; Choi, Kwon-Young; Bae, Jin-Hyung; Kim, Minsuk; Kim, Joonwon; Kim, Eun-Jung; Kim, Pyoung Il; Kim, Byung-Gee

    2015-08-01

    Hydroxylated fatty acids (HFAs) are used as important precursors for bulk and fine chemicals in the chemical industry. Here, to overproduce long-chain (C16-C18) fatty acids and hydroxy fatty acid, their biosynthetic pathways including thioesterase (Lreu_0335) from Lactobacillus reuteri DSM20016, β-hydroxyacyl-ACP dehydratase (fabZ) from Escherichia coli, and a P450 system (i.e., CYP153A from Marinobacter aquaeolei VT8 and camA/camB from Pseudomonas putida ATCC17453) were overexpressed. Acyl-CoA synthase (fadD) involved in fatty acid degradation by β-oxidation was also deleted in E. coli BW25113. The engineered E. coli FFA4 strain without the P450 system could produce 503.0 mg/l of palmitic (C16) and 508.4 mg/l of stearic (C18) acids, of which the amounts are ca. 1.6- and 2.3-fold higher than those of the wild type. On the other hand, the E. coli HFA4 strain including the P450 system for ω-hydroxylation could produce 211.7 mg/l of ω-hydroxy palmitic acid, which was 42.1 ± 0.1 % of the generated palmitic acid, indicating that the hydroxylation reaction was the rate-determining step for the HFA production. For the maximum production of ω-hydroxy palmitic acid, NADH, i.e., an essential cofactor for P450 reaction, was overproduced by the integration of NAD(+)-dependent formate dehydrogenase (FDH) from Candida boidinii into E. coli chromosome and the deletion of alcohol dehydrogenase (ADH). Finally, the NADH-level-optimized E. coli strain produced 610 mg/l of ω-hydroxy palmitic acid (ω-HPA), which was almost a threefold increase in its yield compared to the same strain without NADH overproduction.

  15. Study on Microbes and Their Effects on Rare Earth Extraction in Weathering Crust of Granite

    Institute of Scientific and Technical Information of China (English)

    陈炳辉; 毋福海; 刘琥琥

    2001-01-01

    Microbes were cultured from the samples at various depths in a weathering profile of RE-bearing granite in Gonghe RE mine, Guangdong Province. The cultured microbes, existing at a depth of 0.2~12 m and being more plentiful within 3 m in the profile,include bacteria (Bacillus,Enterobacter, Escherichia, Alkaligenes, Neisseria, Staphylococcus and anaerobic bacteria such as Clostridium), fungi (Aspergillus niger, Aspergillus flavus, Penicillium, Mucor and Saccharomycete) and actinomyces. Experiments were made under room temperature by using solutions of the cultured microbes and their metabolites, compared with distilled water and the culture solution without microbes, to leach RE from the sample of the weathering crust. The results are shown by the experiments: (1) The mixed microbes cultured from the profile and their metabolites increase the quantity of RE leached from the sample and reduce the pH of the solutions. (2) The ability to leach RE from the sample varies with various microbes, decreasing in a sequence of fungi (Mucor, saccharomycete, Aspegillus and Penicillium), zymotic bacilli (Enterobacter, Escherichia etc.), Staphylococcus, zymotic Bacillus, actinomyces and Alkaligenes. (3) The RE leached with bacteria is mainly related to the pH value of the solutions influenced by the metabolites of the bacteria; whereas that leached with fungi is mainly related to the adsorption and imbibition of RE by the fungi and the complexing of RE with their metabolites. (4) Compared with that leached with ammonium sulfate, the fractionation of the RE leached with microbes is characterized by higher δCe, lower δEu and lower ratios of NLa/Sm and NGd/Yb. The result of the fractionation of RE accords with the distribution of RE in the various layers of a profile of weathering crust of granite in South China. The experimental results indicate that microbes and their metabolites should play a positive role in the mobilization, migration and fractionation of RE in the

  16. Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions

    OpenAIRE

    Vishal Kumar; Mehak Baweja; Puneet Kumar Singh; Pratyoosh Shukla

    2016-01-01

    Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant–microbe interaction plays an important role to balance the ecosystem. The present review explores plant–microbe interactions using gene editing and system biolo...

  17. Engineering of bio-hybrid materials by electrospinning polymer-microbe fibers

    OpenAIRE

    LIU, Ying; Rafailovich, Miriam H.; Malal, Ram; Cohn, Daniel; Chidambaram, Dev

    2009-01-01

    Although microbes have been used in industrial and niche applications for several decades, successful immobilization of microbes while maintaining their usefulness for any desired application has been elusive. Such a functionally bioactive system has distinct advantages over conventional batch and continuous-flow microbial reactor systems that are used in various biotechnological processes. This article describes the use of polyethylene oxide99-polypropylene oxide67-polyethylene oxide99 tribl...

  18. The impact of beneficial plant-associated microbes on plant phenotypic plasticity.

    Science.gov (United States)

    Goh, Chooi-Hua; Veliz Vallejos, Debora F; Nicotra, Adrienne B; Mathesius, Ulrike

    2013-07-01

    Plants show phenotypic plasticity in response to changing or extreme abiotic environments; but over millions of years they also have co-evolved to respond to the presence of soil microbes. Studies on phenotypic plasticity in plants have focused mainly on the effects of the changing environments on plants' growth and survival. Evidence is now accumulating that the presence of microbes can alter plant phenotypic plasticity in a broad range of traits in response to a changing environment. In this review, we discuss the effects of microbes on plant phenotypic plasticity in response to changing environmental conditions, and how this may affect plant fitness. By using a range of specific plant-microbe interactions as examples, we demonstrate that one way that microbes can alleviate the effect of environmental stress on plants and thus increase plant fitness is to remove the stress, e.g., nutrient limitation, directly. Furthermore, microbes indirectly affect plant phenotypic plasticity and fitness through modulation of plant development and defense responses. In doing so, microbes affect fitness by both increasing or decreasing the degree of phenotypic plasticity, depending on the phenotype and the environmental stress studied, with no clear difference between the effect of prokaryotic and eukaryotic microbes in general. Additionally, plants have the ability to modulate microbial behaviors, suggesting that they manipulate bacteria, enhancing interactions that help them cope with stressful environments. Future challenges remain in the identification of the many microbial signals that modulate phenotypic plasticity, the characterization of plant genes, e.g. receptors, that mediate the microbial effects on plasticity, and the elucidation of the molecular mechanisms that link phenotypic plasticity with fitness. The characterization of plant and microbial mutants defective in signal synthesis or perception, together with carefully designed glasshouse or field experiments that

  19. Effects of Earthworm and Microbe on Soil Nutrients and Heavy Metals

    Institute of Scientific and Technical Information of China (English)

    SHEN Wei-bao; YANG Hong-qiang

    2008-01-01

    Earthworm and microbe are very important soil organisms. They play an important role in the stability of ecosystem and the bioavailability of nutrients and heavy metals in soils. This article reviewed the function of earthworm and microbes in improving soil structure and controlling soil nutrients as well as their effects on the bioavailability of heavy metals in soil through bioabsorption, enrichment, precipitation, dissolution, and oxidation-reduction. The aim is to provide a certain theoretical basis for modern agricultural production.

  20. Microstructured block copolymer surfaces for control of microbe capture and aggregation

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Ryan R [ORNL; Shubert, Katherine R [ORNL; Morrell, Jennifer L. [University of Tennessee, Knoxville (UTK); Lokitz, Bradley S [ORNL; Doktycz, Mitchel John [ORNL; Retterer, Scott T [ORNL

    2014-01-01

    The capture and arrangement of surface-associated microbes is influenced by biochemical and physical properties of the substrate. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe capture. Films of poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA) were patterned on silicon surfaces into line or square grid patterns with 5 m wide features and varied edge spacing. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates captured was dependent on the pattern dimensions. Line patterns with edge spacing of 5 m or less led to the capture of individual microbes with minimal formation of aggregates, while grid patterns with the same spacing also captured individual microbes with further reduction in aggregation. Both geometries allowed for increases in aggregate size distribution with increased in edge spacing. These engineered surfaces combine spatial confinement with affinity-based microbe capture based on exopolysaccharide content to control the degree of microbe aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.

  1. Role of viruses and other microbes in the pathogenesis of type 1 diabetes.

    Science.gov (United States)

    Kondrashova, Anita; Hyöty, Heikki

    2014-01-01

    Type 1 diabetes is caused by an immune-mediated destruction of insulin producing beta-cells in the pancreas. The risk of the disease is determined by interactions between more than 40 different susceptibility genes and yet unidentified environmental factors. The rapidly increasing incidence indicates that these environmental agents have a significant role in the pathogenesis. Microbes have associated with both increased and decreased risk reflecting their possible role as risk or protective factors. Two main hypotheses have been proposed to explain these effects: the hygiene hypothesis suggests that microbial exposures in early childhood stimulate immunoregulatory mechanisms which control autoimmune reactions (analogy with allergy), while the triggering hypothesis suggests that specific microbes damage insulin producing cells. Certain viruses, particularly enteroviruses, are currently the main candidates for such risk microbes. Enteroviruses cause diabetes in animals and have associated with increased risk of type 1 diabetes in epidemiological studies. They have also been detected in the pancreas of diabetic patients. Possible protective effect of microbes has been studied in animal models and in epidemiological studies, where certain enteral microbes (e.g. hepatitis A virus and Helicobacter pylori) and patterns of gut microbiome have associated with low risk of type 1 diabetes. In conclusion, these microbial effects offer attractive possibilities for the development of preventive interventions for type 1 diabetes based on the elimination of triggering agents (e.g. enterovirus vaccines) or use of protective microbes as probiotics.

  2. MicrobesOnline: an integrated portal for comparative and functional genomics

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir; Joachimiak, Marcin; Price, Morgan; Bates, John; Baumohl, Jason; Chivian, Dylan; Friedland, Greg; Huang, Kathleen; Keller, Keith; Novichkov, Pavel; Dubchak, Inna; Alm, Eric; Arkin, Adam

    2011-07-14

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

  3. Combined ESTs from plant-microbe interactions: using GC counting to determine the species of origin.

    Science.gov (United States)

    Huitema, Edgar; Torto, Trudy A; Styer, Allison; Kamoun, Sophien

    2003-01-01

    A diversity of microorganisms establishes intimate associations with plants. Whether pathogenic or symbiotic, such interactions are the result of complex recognition events between plants and microbes, leading to signaling cascades and regulation of countless genes involved in the interaction. A key step in unraveling the mysteries of plant-microbe interactions lies in defining the transcriptional changes that occur in both the host and the microbe during their association. The sum of the transcripts, from both host and microbe, which are produced during their association, has been defined as the interaction transcriptome. One approach to analyze interaction transcriptomes is to perform large-scale sequencing of cDNAs (expressed sequence tags or ESTs) obtained from infected plant tissue and representing a mixture of host and microbe sequences. In some cases, the two organisms have markedly different GC content, allowing most ESTs to be easily distinguished on this basis. In this chapter, we describe a GC counting method to determine the species of origin of ESTs obtained from interactions between plants and oomycetes or other high GC content microbes.

  4. Engineering of bio-hybrid materials by electrospinning polymer-microbe fibers

    Science.gov (United States)

    Liu, Ying; Rafailovich, Miriam H.; Malal, Ram; Cohn, Daniel; Chidambaram, Dev

    2009-01-01

    Although microbes have been used in industrial and niche applications for several decades, successful immobilization of microbes while maintaining their usefulness for any desired application has been elusive. Such a functionally bioactive system has distinct advantages over conventional batch and continuous-flow microbial reactor systems that are used in various biotechnological processes. This article describes the use of polyethylene oxide99-polypropylene oxide67-polyethylene oxide99 triblock polymer fibers, created via electrospinning, to encapsulate microbes of 3 industrially relevant genera, namely, Pseudomonas, Zymomonas, and Escherichia. The presence of bacteria inside the fibers was confirmed by fluorescence microscopy and SEM. Although the electrospinning process typically uses harsh organic solvents and extreme conditions that generally are harmful to bacteria, we describe techniques that overcome these limitations. The encapsulated microbes were viable for several months, and their metabolic activity was not affected by immobilization; thus they could be used in various applications. Furthermore, we have engineered a microbe-encapsulated cross-linked fibrous polymeric material that is insoluble. Also, the microbe-encapsulated active matrix permits efficient exchange of nutrients and metabolic products between the microorganism and the environment. The present results demonstrate the potential of the electrospinning technique for the encapsulation and immobilization of bacteria in the form of a synthetic biofilm, while retaining their metabolic activity. This study has wide-ranging implications in the engineering and use of novel bio-hybrid materials or biological thin-film catalysts. PMID:19667172

  5. MicrobesOnline: an integrated portal for comparative and functional genomics

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir S.; Joachimiak, Marcin P.; Price, Morgan N.; Bates, John T.; Baumohl, Jason K.; Chivian, Dylan; Friedland, Greg D.; Huang, Katherine H.; Keller, Keith; Novichkov, Pavel S.; Dubchak, Inna L.; Alm, Eric J.; Arkin, Adam P.

    2009-09-17

    Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

  6. Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis.

    Science.gov (United States)

    Zhou, Fangyuan; Lou, Qiaozhe; Wang, Bo; Xu, Letian; Cheng, Chihang; Lu, Min; Sun, Jianghua

    2016-02-03

    Insect-microbe interaction is a key area of research in multiplayer symbiosis, yet little is known about the role of microbe-microbe interactions in insect-microbe symbioses. The red turpentine beetle (RTB) has destroyed millions of healthy pines in China and forms context-dependent relationships with associated fungi. The adult-associated fungus Leptographium procerum have played key roles in RTB colonization. However, common fungal associates (L. procerum and Ophiostoma minus) with RTB larvae compete for carbohydrates. Here, we report that dominant bacteria associated with RTB larvae buffer the competition by inhibiting the growth and D-glucose consumption of O. minus. However, they didn't inhibit the growth of L. procerum and forced this fungus to consume D-pinitol before consuming D-glucose, even though D-glucose was available and a better carbon source not only for L. procerum but also for RTB larvae and associated bacteria. This suggests the most frequently isolated bacteria associated with RTB larvae could affect fungal growth and the sequence of carbohydrate consumption. Thus, this regulates carbohydrate allocation in the RTB larva-microbe community, which may in turn benefit RTB larvae development. We also discuss the mechanism of carbohydrate allocation in the RTB larva-microbe community, and its potential contribution to the maintenance of a symbiotic community.

  7. Amino Acid Degradation after Meteoritic Impact Simulation

    Science.gov (United States)

    Bertrand, M.; Westall, F.; vanderGaast, S.; Vilas, F.; Hoerz, F.; Barnes, G.; Chabin, A.; Brack, A.

    2008-01-01

    Amino acids are among the most important prebiotic molecules as it is from these precursors that the building blocks of life were formed [1]. Although organic molecules were among the components of the planetesimals making up the terrestrial planets, large amounts of primitive organic precursor molecules are believed to be exogenous in origin and to have been imported to the Earth via micrometeorites, carbonaceous meteorites and comets, especially during the early stages of the formation of the Solar System [1,2]. Our study concerns the hypothesis that prebiotic organic matter, present on Earth, was synthesized in the interstellar environment, and then imported to Earth by meteorites or micrometeorites. We are particularly concerned with the formation and fate of amino acids. We have already shown that amino acid synthesis is possible inside cometary grains under interstellar environment conditions [3]. We are now interested in the effects of space conditions and meteoritic impact on these amino acids [4-6]. Most of the extraterrestrial organic molecules known today have been identified in carbonaceous chondrite meteorites [7]. One of the components of these meteorites is a clay with a composition close to that of saponite, used in our experiments. Two American teams have studied the effects of impact on various amino acids [8,9]. [8] investigated amino acids in saturated solution in water with pressure ranges between 5.1 and 21 GPa and temperature ranges between 412 and 870 K. [9] studied amino acids in solid form associated with and without minerals (Murchison and Allende meteorite extracts) and pressure ranges between 3 and 30 GPa. In these two experiments, the amino acids survived up to 15 GPa. At higher pressure, the quantity of preserved amino acids decreases quickly. Some secondary products such as dipeptides and diketopiperazins were identified in the [8] experiment.

  8. Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris.

    Science.gov (United States)

    Oberbeckmann, Sonja; Osborn, A Mark; Duhaime, Melissa B

    2016-01-01

    Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem-level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize aquatic plastic debris and members of these biofilm communities are speculated to include pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in selecting for unique microbial communities. This work aimed to characterize microbial biofilm communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communities, and identify seasonal and geographical influences on the communities. A substrate recruitment experiment was established in which PET bottles were deployed for 5-6 weeks at three stations in the North Sea in three different seasons. The structure and composition of the PET-colonizing bacterial/archaeal and eukaryotic communities varied with season and station. Abundant PET-colonizing taxa belonged to the phylum Bacteroidetes (e.g. Flavobacteriaceae, Cryomorphaceae, Saprospiraceae-all known to degrade complex carbon substrates) and diatoms (e.g. Coscinodiscophytina, Bacillariophytina). The PET-colonizing microbial communities differed significantly from free-living communities, but from particle-associated (>3 μm) communities or those inhabiting glass substrates. These data suggest that microbial community assembly on plastics is driven by conventional marine biofilm processes, with the plastic surface serving as raft for attachment, rather than selecting for recruitment of plastic-specific microbial colonizers. A small proportion of taxa, notably, members of the Cryomorphaceae and Alcanivoraceae, were significantly discriminant of PET but not glass surfaces, conjuring the possibility that these groups may directly interact with the PET

  9. Use Issatchenkia Terricola Brewing Technique of Raspberry Wine by Biological Acid-degradation%陆生伊萨酵母生物降酸酿造树莓干型酒工艺研究

    Institute of Scientific and Technical Information of China (English)

    隋韶奕; 张素敏; 连奎; 王雪松

    2014-01-01

    Research using the red raspberry as material and Issatchenkia Terricola as de-acidification yeast during brewing of pure juice wine, the following results were achieved or recorded. We came to a conclusion of the optimum acid-degradation condition by the single factor trial and orthogonal test: Issatchenkia Terricola inoculum size was 3 %, the Brewers yeast inoculum size was 0.08 %, the temperature of de-acidification was 28℃, and de-acidification time was 5 d. Product quality index of raspberry wine is as follow:its colour was ruby, with no obvious suspensions, The palate stable, with a typical aromas of raspberries and harmonious flavour.%以红树莓为原料,利用陆生伊萨酵母(Issatchenkia Terricola)进行生物降酸酿造全汁树莓干型酒。通过正交试验得到了最佳生物降酸条件:陆生伊萨酵母接种量3%、酿酒酵母接种量0.08%、降酸温度为28℃、降酸时间为5 d。经发酵所得树莓干酒色泽为红宝石色,无明显悬浮物,口感圆润淳厚,带有典型的树莓果香及和谐的醇香,无异味。

  10. Fatty acids as biomarkers for food web structure in the eastern North Pacific Ocean

    Science.gov (United States)

    Behrens, J.; Aluwihare, L.; Stephens, B. M.

    2015-12-01

    Resulting from a NSF funded REU program at Scripps Institution of Oceanography in 2015, this research utilized gas chromatography-mass spectrometry (GC-MS) to analyze the fatty acid composition of suspended particulate organic matter (POM) and zooplankton (ZP; primarily copepods). Samples analyzed for this study were collected simultaneously from surface waters approximately 9 miles off the coast of San Diego in June 2015. I was testing the hypothesis that essential fatty acids in ZP should reflect their diet, in particular, distinguishing contributions from a microbial versus traditional food web. Food web structure in this region of the ocean has been shown to be sensitive to climate change on inter-annual and longer timescales. Thus, a proxy that identifies restructuring of food webs would be useful for examining the response of ocean ecosystems to future climate change. Lipids were extracted from ZP and POM using a modified Bligh and Dyer method with sonication. Following saponification free fatty acids and other lipids were further purified using column chromatography. Polar functional groups in lipids were then methylated prior to GC-MS analysis. In addition, 2-dimensional GCxGC with time of flight MS was used to distinguish polyunsaturated fatty acid isomers. My poster will present initial findings of shared fatty acids of zooplankton and POM suspended material from the Northern Pacific collection site. Further research will be focused on analyzing the hydrogen isotope composition of fatty acids in zooplankton and suspended DOM obtained at the collection site to further characterize and increase certainty on the role of microbes and phytoplankton in the region's food-web to distinguish prokaryotic and eukaryotic sources.

  11. Characterization of three novel desaturases involved in the delta-6 desaturation pathways for polyunsaturated fatty acid biosynthesis from Phytophthora infestans.

    Science.gov (United States)

    Sun, Quanxi; Liu, Jiang; Zhang, Qin; Qing, Xiaohe; Dobson, Gary; Li, Xinzheng; Qi, Baoxiu

    2013-09-01

    Phytophthora infestans is the causative agent of potato blight that resulted in the great famine in Ireland in the nineteenth century. This microbe can release large amounts of the C20 very long-chain polyunsaturated fatty acids arachidonic acid (ARA; 20:4Δ(5, 8, 11, 14)) and eicosapentaenoic acid (EPA; 20:5Δ(5, 8, 11, 14, 17)) upon invasion that is known to elicit a hypersensitive response to their host plant. In order to identify enzymes responsible for the biosynthesis of these fatty acids, we blasted the recently fully sequenced P. infestans genome and identified three novel putatively encoding desaturase sequences. These were subsequently functionally characterized by expression in Saccharomyces cerevisiae and confirmed that they encode desaturases with Δ12, Δ6 and Δ5 activity, designated here as PinDes12, PinDes6 and PinDes5, respectively. This, together with the combined fatty acid profiles and a previously identified Δ6 elongase activity, implies that the ARA and EPA are biosynthesized predominantly via the Δ6 desaturation pathways in P. infestans. Elucidation of ARA and EPA biosynthetic mechanism may provide new routes to combating this potato blight microbe directly or by means of conferring resistance to important crops.

  12. Ecological Interactions Between Metals and Microbes That Impact Bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Konopka, Allan E.

    2001-06-01

    Bacterial Community Diversity at a Mixed Waste Contaminated Site The correlation between bacterial population structure and lead, chromium and organic compounds present along a 21.6 m transect was examined. There was a gradient of heavy metal (Cr and Pb) and petroleum hydrocarbon contamination in these soils. A 16S rDNA analysis method and fatty acid methyl esters derived from phospholipids (PLFA) analysis were used to compare microbial communities. Soil microbial DNA was extracted and community fingerprint patterns for each sample location were produced by DGGE separation of the V3 region of the 16S rRNA genes amplified by PCR. Visual analysis of DGGE patterns indicated that sample locations with high concentrations of total toluene (12,000 mg kg-1), xylenes (8,000 mg kg-1), methylene chloride (10,000 mg kg-1), lead (17,000 mg kg-1) and chromium (3,200 mg kg-1) have a different community composition from the community with lower metals (200 mg kg-1) and organics (1200 mg kg-1) content. Microbial biomass, indicated by total phospholipid-P, was greatest in soils with highest organic contamination.

  13. Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms

    Directory of Open Access Journals (Sweden)

    Nurmi ePangesti

    2013-10-01

    Full Text Available Plants are members of complex communities and function as a link between above- and below-ground organisms. Associations between plants and soil-borne microbes commonly occur and have often been found beneficial for plant fitness. Root-associated microbes may trigger physiological changes in the host plant that influence interactions between plants and aboveground insects at several trophic levels. Aboveground, plants are under continuous attack by insect herbivores and mount multiple responses that also have systemic effects on belowground microbes. Until recently, both ecological and mechanistic studies have mostly focused on exploring these below- and above-ground interactions using simplified systems involving both single microbe and herbivore species, which is far from the naturally occurring interactions. Increasing the complexity of the systems studied is required to increase our understanding of microbe - plant - insect interactions and to gain more benefit from the use of non-pathogenic microbes in agriculture. In this review, we explore how colonization by either single non-pathogenic microbe species or a community of such microbes belowground affects plant growth and defense and how this affects the interactions of plants with aboveground insects at different trophic levels. Moreover, we review how plant responses to foliar herbivory by insects belonging to different feeding guilds affect interactions of plants with non-pathogenic soil-borne microbes. The role of phytohormones in coordinating plant growth, plant defenses against foliar herbivores while simultaneously establishing associations with non-pathogenic soil microbes is discussed.

  14. Ozonolysis products of membrane fatty acids activate eicosanoid metabolism in human airway epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Leikauf, G.D.; Zhao, Q.; Zhou, S.; Santrock, J. (Univ. of Cincinnati Medical Center, OH (United States))

    1993-12-01

    When inhaled, ozone reacts at the airway luminal surface with unsaturated fatty acids contained in the extracellular fluid and plasma membrane to form an aldehyde and hydroxyhydroperoxide. The resulting hydroxyhydroperoxide degrades in aqueous systems to yield a second aldehyde and hydrogen peroxide (H2O2). Previously, we demonstrated that ozone can augment eicosanoid metabolism in bovine airway epithelial cells. To examine structure-activity relationships of ozone-fatty acid degradation products on eicosanoid metabolism in human airway epithelial cells, 3-, 6-, and 9-carbon saturated aldehydes and hydroxyhydroperoxides were synthesized and purified. Eicosanoid metabolism was evaluated by determination of total 3H-activity release from confluent cells previously incubated with [3H]arachidonic acid and by identification of specific metabolites with high performance liquid chromatography and radioimmunoassay. The major metabolites detected were prostaglandin E2, prostaglandin F2 alpha, and 15-hydroxyeicosatetraenoic acid. The 9-carbon aldehyde, nonanal, in contrast to 3- or 6-carbon aldehydes, stimulated release at concentrations > or = 100 microM, suggesting that the stimulatory effect increases with increasing chain length. When tested under identical conditions, the 3-, 6-, and 9-carbon hydroxyhydroperoxides were more potent than the corresponding aldehydes. Again, a greater effect was noted when the chain length was increased. One possible explanation for the increased potency of the hydroxyhydroperoxides over the aldehydes could be due to degradation of the hydroxyhydroperoxide into H2O2 and aldehyde. We consider this an unlikely explanation because responses varied with chain length (although each hydroxyhydroperoxide would produce an equivalent amount of H2O2) and because exposure to H2O2 alone or H2O2 plus hexanal produced a response dissimilar to 1-hydroxy-1-hexanehydroperoxide.

  15. Ecological interactions between metals and microbes that impact bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Allan Konopka; Cindy Nakatsu

    2004-03-17

    Distinct microbial communities had been found in contaminated soils that varied in their concentrations of Pb, Cr and aromatic compounds. It is difficult to distinguish between their effects as their presence is highly correlated. Microcosms were constructed in which either Pb{sup +2} or CrO{sub 4}{sup -2} was added at levels that produced acute modest or severe acute effects (50 or 90% reduction). We previously reported on changes in microbial activity and broad patterns of Bacterial community composition. These results showed that addition of an organic energy source selected for a relatively small number of phylotypes and the addition of Pb or Cr(VI) modulated the community response. We sequenced dominant phylotypes from microcosms amended with xylene and Cr(VI) and from those with the simple addition of glucose only. In both cases, the dominant selected phylotypes were diverse. We found a number of distinct Arthrobacter strains, as well as several Pseudomonas spp. In addition, the high GC-content bands belonged to members of the genera Nocardioides and Rhodococcus. The focus of amended microcosm work has now shifted to anaerobic processes. The reduction of Cr(VI) to Cr(III) as a detoxification mechanism is of greater interest, as is the specific role of particular physiological groups of anaerobes in mediating Cr(VI) detoxification. The correlation between microbial activity, community structure, and metal level has been analyzed on 150 mg of soil collected at spatial scales <1, 5, 15 and 50 cm. There was no correlation between metal content and activity level. Soils <1 cm apart could differ in activity 10-fold and extractable Pb and Cr 7-fold. Therefore, we turned to geostatistical analysis. There was spatial periodicity which is likely to reflect the heterogeneous distribution of active microbes and metal contaminants. Variograms indicated that the range of spatial dependence was up to 20 cm. To visualize the spatial relationships between the primary variate

  16. Polythene and Plastics-degrading microbes from the mangrove soil

    Directory of Open Access Journals (Sweden)

    K Kathiresan

    2003-09-01

    Full Text Available Biodegradation of polythene bags and plastic cups was analyzed after 2, 4, 6, and 9 months of incubation in the mangrove soil. The biodegradation of polythene bags was significantly higher (up to 4.21% in 9 months than that of plastic cups (up to 0.25% in 9 months. Microbial counts in the degrading materials were recorded up to 79.67 x 10 4 per gram for total heterotrophic bacteria, and up to 55.33 x 10 2 per gram for fungi. The microbial species found associated with the degrading materials were identified as five Gram positive and two Gram negative bacteria, and eight fungal species of Aspergillus. The species that were predominant were Streptococcus, Staphylococcus, Micrococcus (Gram +ve, Moraxella, and Pseudomonas (Gram -ve and two species of fungi (Aspergillus glaucus and A. niger. Efficacy of the microbial species in degradation of plastics and polythene was analyzed in shaker cultures. Among the bacteria, Pseudomonas species degraded 20.54% of polythene and 8.16% of plastics in one-month period. Among the fungal species, Aspergillus glaucus degraded 28.80% of polythene and 7.26% of plastics in one-month period. This work reveals that the mangrove soil is a good source of microbes capable of degrading polythene and plasticsLa biodegradación de las bolsas de polietileno y vasos de plástico fue analizada después de 2, 4, 6 y 9 meses de incubación en suelo de manglar. La biodegradación de las bolsas fue significativamente más alta (hasta 4.21% en 9 meses que los vasos plásticos (hasta 0.25% en 9 meses. Los conteos microbianos en los materiales degradados mostraron hasta 79.67 x 10(4 por gramo para las bacterias heterotroficas totales, y hasta 55.33 x 10² por gramo para los hongos. Se identificó 5 especies microbianas Gram positivas, 2 Gram negativas, y 8 especies de hongos del género Aspergillus en asociación con materiales degradados. Las especies predominantes fueron Streptococcus, Staphylococcus, Micrococcus (Gram +, Moraxella

  17. Principles of Virus-Microbe Dynamics: From Ecology to Evolution and Back Again

    Science.gov (United States)

    Weitz, Joshua

    Viruses are ubiquitous in the environment and can function like microbial predators, regulating the density and diversity of microbes present in a community. However, efforts to understand the dynamics of complex virus-microbe communities remain in their infancy. In this talk, I present examples of the interplay between evolutionary and ecological dynamics arising due to virus-microbe interactions. I begin by introducing canonical models of virus-microbe population dynamics in the context of observed oscillations of E. coli and associated phage. I then present a series of examples in which novel features observed in time series data arising from phage interactions with E. coli and V. cholerae can be understood when considering both population and evolutionary dynamics together. I conclude by presenting our recent efforts to extend the results of laboratory experiments to an environmental context, with significantly higher diversity of both viruses and microbes. Despite this increase in diversity, I show how network theoretic methods can reveal common principles underlying the dynamic coexistence of complex virus and host communities. Building on these findings, I describe new efforts to infer who infects whom directly from time series of multi-strain communities.

  18. Intestinal microbes influence the survival, reproduction and protein profile of Trichinella spiralis in vitro.

    Science.gov (United States)

    Jiang, Hai-yan; Zhao, Na; Zhang, Qiao-ling; Gao, Jiang-ming; Liu, Li-li; Wu, Teng-Fei; Wang, Ying; Huang, Qing-hua; Gou, Qiang; Chen, Wei; Gong, Peng-tao; Li, Jian-hua; Gao, Ying-jie; Liu, Bo; Zhang, Xi-chen

    2016-01-01

    The interactions between intestinal microbes and parasitic worms play an essential role in the development of the host immune system. However, the effects of gut microbes on Trichinella spiralis are unknown. The aim of this work was to explore microbe-induced alterations in the survival and reproduction of T. spiralis in vitro. To further identify the proteins and genes involved in the response of nematodes to microbes, quantitative proteomic analysis of T. spiralis was conducted by iTRAQ-coupled LCMS/MS technology and quantitative real-time-PCR was used to measure changes in mRNA expression. The results showed Lactobacillus acidophilus, and especially Lactobacillus bulgaricus, significantly enhanced the survival and reproductive rates of nematodes. Salmonella enterica, and especially Escherichia coli O157:H7 (EHEC), had opposite effects. Genetic responses were activated mainly by EHEC. A total of 514 proteins were identified and quantified, and carbohydrate metabolism-related proteins existed in a higher proportion. These findings indicated that some gut bacteria are friendly or harmful to humans and in addition they may have similar beneficial or detrimental effects on parasites. This may be due to the regulation of expression of specific genes and proteins. Our studies provide a basis for developing therapies against parasitic infections from knowledge generated by studying the gut microbes of mammals.

  19. The Control of Auxin Transport in Parasitic and Symbiotic Root–Microbe Interactions

    Directory of Open Access Journals (Sweden)

    Jason Liang Pin Ng

    2015-08-01

    Full Text Available Most field-grown plants are surrounded by microbes, especially from the soil. Some of these, including bacteria, fungi and nematodes, specifically manipulate the growth and development of their plant hosts, primarily for the formation of structures housing the microbes in roots. These developmental processes require the correct localization of the phytohormone auxin, which is involved in the control of cell division, cell enlargement, organ development and defense, and is thus a likely target for microbes that infect and invade plants. Some microbes have the ability to directly synthesize auxin. Others produce specific signals that indirectly alter the accumulation of auxin in the plant by altering auxin transport. This review highlights root–microbe interactions in which auxin transport is known to be targeted by symbionts and parasites to manipulate the development of their host root system. We include case studies for parasitic root–nematode interactions, mycorrhizal symbioses as well as nitrogen fixing symbioses in actinorhizal and legume hosts. The mechanisms to achieve auxin transport control that have been studied in model organisms include the induction of plant flavonoids that indirectly alter auxin transport and the direct targeting of auxin transporters by nematode effectors. In most cases, detailed mechanisms of auxin transport control remain unknown.

  20. Thermo-tolerant phosphate-solubilizing microbes for multi-functional biofertilizer preparation.

    Science.gov (United States)

    Chang, Cheng-Hsiung; Yang, Shang-Shyng

    2009-02-01

    In order to prepare the multi-functional biofertilizer, thermo-tolerant phosphate-solubilizing microbes including bacteria, actinomycetes, and fungi were isolated from different compost plants and biofertilizers. Except Streptomycesthermophilus J57 which lacked pectinase, all isolates possessed amylase, CMCase, chitinase, pectinase, protease, lipase, and nitrogenase activities. All isolates could solubilize calcium phosphate and Israel rock phosphate; various isolates could solubilize aluminum phosphate, iron phosphate, and hydroxyapatite. During composting, biofertilizers inoculated with the tested microbes had a significantly higher temperature, ash content, pH, total nitrogen, soluble phosphorus content, and germination rate than non-inoculated biofertilizer; total organic carbon and carbon-to-nitrogen ratio showed the opposite pattern. Adding these microbes can shorten the period of maturity, improve the quality, increase the soluble phosphorus content, and enhance the populations of phosphate-solubilizing and proteolytic microbes in biofertilizers. Therefore, inoculating thermo-tolerant phosphate-solubilizing microbes into agricultural and animal wastes represents a practical strategy for preparing multi-functional biofertilizer.

  1. Coral reef microbes : the influences of benthic primary producers, nutrient availability, and anthropogenic stressors on community structure and metabolism

    OpenAIRE

    Kelly, Linda Ellen Wegley

    2013-01-01

    Genomic studies of marine microbes have advanced our understanding of community ecology and the vast array of metabolisms microbes utilize for acquiring energy and nutrients in the ocean. The structure of microbial communities overlying coral reefs have been shown to reflect ecosystem health. For example, algal-dominated reefs are inhabited by more pathogen-like microbes. The objective of my PhD thesis was to use metagenomics to investigate the microbial communities associated with the coral ...

  2. Liver cirrhosis and fatty liver

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008075 Effect of Jiangzhi granules on expression of leptin receptor mRNA, P-JAK2 and P-STAT3 in rats with non-alcoholic fatty liver disease. MA Zansong(马赞颂), et al. Dept Gastroenterol, Instit Spleen and Stomach Dis, Longhua Hosp. Shanghai TCM Univ, Shanghai 200032.World Chin J Digestol 2007;15(32):3360-3366. Objective To study the effect of Jiangzhi granules on non-alcoholic fatty liver disease in rats, and on the expression of

  3. Differentiating fatty and non-fatty tissue using photoacoustic imaging

    Science.gov (United States)

    Pan, Leo; Rohling, Robert; Abolmaesumi, Purang; Salcudean, Septimiu; Tang, Shuo

    2014-03-01

    In this paper, we demonstrate a temporal-domain intensity-based photoacoustic imaging method that can differentiate between fatty and non-fatty tissues. PA pressure intensity is partly dependent on the tissue's speed of sound, which increases as temperature increases in non-fatty tissue and decreases in fatty tissue. Therefore, by introducing a temperature change in the tissue and subsequently monitoring the change of the PA intensity, it is possible to distinguish between the two types of tissue. A commercial ultrasound system with a 128-element 5-14 MHz linear array transducer and a tunable ND:YAG laser were used to produce PA images. Ex-vivo bovine fat and porcine liver tissues were precooled to below 10°C and then warmed to room-temperature over ~1 hour period. A thermocouple monitored the temperature rise while PA images were acquired at 0.5°C intervals. The averaged intensity of the illuminated tissue region at each temperature interval was plotted and linearly fitted. Liver samples showed a mean increase of 2.82 %/°C, whereas bovine fat had a mean decrease of 6.24 %/°C. These results demonstrate that this method has the potential to perform tissue differentiation in the temporal-domain.

  4. The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra).

    Science.gov (United States)

    Amato, Katherine R; Leigh, Steven R; Kent, Angela; Mackie, Roderick I; Yeoman, Carl J; Stumpf, Rebecca M; Wilson, Brenda A; Nelson, Karen E; White, Bryan A; Garber, Paul A

    2014-12-01

    In all mammals, growth, development, pregnancy, and lactation increase nutritional demands. Although primate field studies tend to focus on shifts in activity and diet as mechanisms to compensate for these demands, differences in digestive efficiency also are likely to be important. Because the gut microbiota can impact host digestive efficiency, we examined differences in activity budget, diet, and the gut microbial community among adult male (N = 4), adult female (N = 4), and juvenile (N = 5) wild black howler monkeys (Alouatta pigra) across a ten-month period in Palenque National Park, Mexico to determine how adult females and juveniles compensate for increased nutritional demands. Results indicate that adult females and juveniles consumed more protein and energy than adult males. Adult males, adult females, and juveniles also possessed distinct gut microbial communities, unrelated to diet. Juveniles exhibited a gut microbiota characterized by bacteria from the phylum Firmicutes, such as Roseburia and Ruminococcus, and demonstrated high fecal volatile fatty acid content, suggesting increased microbial contributions to host energy balances. Adult females possessed a higher Firmicutes to Bacteroidetes ratio, also suggesting increased energy production, and their gut microbiota was characterized by Lactococcus, which has been associated with folate biosynthesis. On the basis of these patterns, it appears that the gut microbiota differentially contributes to howler monkey nutrition during reproduction and growth. Determining the nutritional and energetic importance of shifts in activity, diet, and the gut microbiota in other nonhuman primate taxa, as well as humans, will transform our understanding of these life history processes and the role of host-microbe relationships in primate evolution. © 2014 Wiley Periodicals, Inc.

  5. Breadand Effervescent Beverage Productions with Local Microbes for the Local Revitalization

    Directory of Open Access Journals (Sweden)

    Manami Watanabe

    2016-06-01

    Full Text Available Local microbes such as yeasts fungi and bacilli, were isolated and used to apply for the food processing (bread making and the production of an effervescent beverage (fruits kvass for promotion of the local revitalization. Our yeast isolates could contribute to make the breads that can sell in alocal bakery shop.  Furthermore, the same yeasts could be used for making the fruit kvass (a Russian effervescent beverage which was fermented by yeast with local fruit products (lemon, dry grape, mandarin orange and apple that were produced in Hiroshima prefecture in Japan. Development of merchandise having the local brand, which was made with only products of Hiroshima prefecture was attempted. Results of these activities demonstrate that the search of local microbes can help to establish the regional brand product related to its local area. They also showed that the local microbes have the potential ability to lead the local revitalization and the local brand product.

  6. Characterization of microbial current production as a function of microbe-electrode-interaction.

    Science.gov (United States)

    Dolch, Kerstin; Danzer, Joana; Kabbeck, Tobias; Bierer, Benedikt; Erben, Johannes; Förster, Andreas H; Maisch, Jan; Nick, Peter; Kerzenmacher, Sven; Gescher, Johannes

    2014-04-01

    Microbe-electrode-interactions are keys for microbial fuel cell technology. Nevertheless, standard measurement routines to analyze the interplay of microbial physiology and material characteristics have not been introduced yet. In this study, graphite anodes with varying surface properties were evaluated using pure cultures of Shewanella oneidensis and Geobacter sulfurreducens, as well as defined and undefined mixed cultures. The evaluation routine consisted of a galvanostatic period, a current sweep and an evaluation of population density. The results show that surface area correlates only to a certain extent with population density and anode performance. Furthermore, the study highlights a strain-specific microbe-electrode-interaction, which is affected by the introduction of another microorganism. Moreover, evidence is provided for the possibility of translating results from pure culture to undefined mixed species experiments. This is the first study on microbe-electrode-interaction that systematically integrates and compares electrochemical and biological data.

  7. [Origin of the plague microbe Yersinia pestis: structure of the process of speciation].

    Science.gov (United States)

    Suntsov, V V

    2012-01-01

    The origin and evolution of the plague microbe Yersinia pestis are considered in the context of propositions of modern Darwinism. It was shown that the plague pathogen diverged from the pseudotuberculous microbe Yersinia pseudotuberculosis O:1b in the mountain steppe landscapes of Central Asia in the Sartan: 22000-15000 years ago. Speciation occurred in the tarbagan (Marmota sibirica)--flea (Oropsylla silantiewi) parasitic system. The structure of the speciation process included six stages: isolation, genetic drift, enhancement of intrapopulational polymorphism, the beginning of pesticin synthesis (genetic conflict and emergence of hiatus), specialization (stabilization of characteristics), and adaptive irradiation (transformation of the monotypic species Y. pestis tarbagani into a polytypic species). The scenario opens up wide prospects for construction of the molecular phylogeny of the plague microbe Y. pestis and for investigation of the biochemical and molecular-genetic aspects of "Darwinian" evolution of pathogens from many other nature-focal infections.

  8. Wars between microbes on roots and fruits [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Ben Lugtenberg

    2017-03-01

    Full Text Available Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.

  9. 2008 Marine Microbes Gordon Research Conference (July 13-17, 2008)

    Energy Technology Data Exchange (ETDEWEB)

    David Kirchman

    2009-09-16

    Marine microbes are very abundant and diverse. They play significant roles in all element cycles, both quantitatively and qualitatively. However, they are little known, as the continuous series of surprising discoveries in the last few years shows. In the present conference the main focus will be on how these microbes interact: with other cells of their own species, with other microbes and with large living beings, from biofilms to symbiants. Another important topic will be the exploration of marine microbial diversity based on the recently developed sequencing approaches and on efforts to obtain marine organisms in pure cultures. This conference will be the third in the Marine Microorganisms series. We hope it will contribute to enlarge the community of marine microbiologists and help in pointing the future directions of research even more than the two previous meetings.

  10. Expression of fatty acid synthase in nonalcoholic fatty liver disease.

    Science.gov (United States)

    Dorn, Christoph; Riener, Marc-Oliver; Kirovski, Georgi; Saugspier, Michael; Steib, Kathrin; Weiss, Thomas S; Gäbele, Erwin; Kristiansen, Glen; Hartmann, Arndt; Hellerbrand, Claus

    2010-03-25

    Nonalcoholic fatty liver disease (NAFLD) is characterized by hepatic lipid accumulation which starts with simple hepatic steatosis and may progress toward inflammation (nonalcoholic steatohepatitis [NASH]). Fatty acid synthase (FASN) catalyzes the last step in fatty acid biosynthesis, and thus, it is believed to be a major determinant of the maximal hepatic capacity to generate fatty acids by de novo lipogenesis. The aim of this study was to analyze the correlation between hepatic steatosis and inflammation with FASN expression. In vitro incubation of primary human hepatocytes with fatty acids dose-dependently induced cellular lipid-accumulation and FASN expression, while stimulation with TNF did not affect FASN levels. Further, hepatic FASN expression was significantly increased in vivo in a murine model of hepatic steatosis without significant inflammation but not in a murine NASH model as compared to control mice. Also, FASN expression was not increased in mice subjected to bile duct ligation, an experimental model characterized by severe hepatocellular damage and inflammation. Furthermore, FASN expression was analyzed in 102 human control or NAFLD livers applying tissue micro array technology and immunohistochemistry, and correlated significantly with the degree of hepatic steatosis, but not with inflammation or ballooning of hepatocytes. Quantification of FASN mRNA expression in human liver samples confirmed significantly higher FASN levels in hepatic steatosis but not in NASH, and expression of SREBP1, which is the main transcriptional regulator of FASN, paralleled FASN expression levels in human and experimental NAFLD. In conclusion, the transcriptional induction of FASN expression in hepatic steatosis is impaired in NASH, while hepatic inflammation in the absence of steatosis does not affect FASN expression, suggesting that FASN may serve as a new diagnostic marker or therapeutic target for the progression of NAFLD.

  11. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City.

    Science.gov (United States)

    Maritz, Julia M; Sullivan, Steven A; Prill, Robert J; Aksoy, Emre; Scheid, Paul; Carlton, Jane M

    2017-01-01

    Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with-and potential exchange of-microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes.

  12. Methods to Prevent or Treat Refractory Diseases by Focusing on Intestinal Microbes Using LPS and Macrophages.

    Science.gov (United States)

    Soma, Gen-Ichiro; Inagawa, Hiroyuki

    2015-08-01

    Intestinal microbes are known to influence host homeostasis by producing various substances. Recently, the presence of a diverse range of intestinal microbiota has been shown to play a key role in the maintenance of health, along with influencing the host's innate immunity towards various diseases. For example, fecal microbiota transplantation (FMT) from healthy individuals was remarkably effective in cases of refractory Clostridium difficile colitis. Conversely, decreased number of intestinal microbes resulting from the oral administration of antibiotics reportedly suppressed the antitumor effects of immunotherapy or anticancer drugs. Furthermore, it has been shown that a change in the intestinal environment triggered by oral administration of antibiotics resulted in increased number of drug-resistant microbes causing nosocomial infections. Intestinal microbes are also shown to be effective in cancer treatment as they activate macrophages at the site of cancer. One of the effects of intestinal microbes on hosts that has been gaining increasing attention is the biological regulation caused by the lipopolysaccharides (LPS) produced by Gram-negative bacteria. Among the intestinal microbiota present in the host, Gram-negative bacteria form the most dominant flora. The administration of antibiotics leads to a decreased number of intestinal microbes, as well as to suppression of cancer immunotherapy effects or anticancer drug effects, and this deterioration has been shown to be improved by oral administration of LPS. In this article, we discuss the functions of intestinal microbiota, that is currently undergoing a paradigm shift in relation to maintenance of health and the validity of LPS as a possible target for bio-treatment in the future.

  13. Companion animals symposium: role of microbes in canine and feline health.

    Science.gov (United States)

    Kil, D Y; Swanson, K S

    2011-05-01

    Whether in an ocean reef, a landfill, or a gastrointestinal tract (GIT), invisible communities of highly active and adaptable microbes prosper. Over time, mammals have developed a symbiosis with microbes that are important inhabitants not only in the GIT, but also in the mouth, skin, and urogenital tract. In the GIT, the number of commensal microbes exceeds the total number of host cells by at least 10 times. The GIT microbes play a critical role in nutritional, developmental, defensive, and physiologic processes in the host. Recent evidence also suggests a role of GIT microbes in metabolic phenotype and disease risk (e.g., obesity, metabolic syndrome) of the host. Proper balance is a key to maintaining GIT health. Balanced microbial colonization is also important for other body regions such as the oral cavity, the region with the greatest prevalence of disease in dogs and cats. A significant obstruction to studying microbial populations has been the lack of tools to identify and quantify microbial communities accurately and efficiently. Most of the current knowledge of microbial populations has been established by traditional cultivation methods that are not only laborious, time-consuming, and often inaccurate, but also greatly limited in scope. However, recent advances in molecular-based techniques have resulted in a dramatic improvement in studying microbial communities. These DNA-based high-throughput technologies have enabled us to more clearly characterize the identity and metabolic activity of microbes living in the host and their association with health and diseases. Despite this recent progress, however, published data pertaining to microbial communities of dogs and cats are still lacking in comparison with data in humans and other animals. More research is required to provide a more detailed description of the canine and feline microbiome and its role in health and disease.

  14. Microbe-ID: an open source toolbox for microbial genotyping and species identification

    Directory of Open Access Journals (Sweden)

    Javier F. Tabima

    2016-08-01

    Full Text Available Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org and provided a working implementation for the genus Phytophthora (phytophthora-id.org. In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

  15. 40 CFR 721.3720 - Fatty amide.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Fatty amide. 721.3720 Section 721.3720... Fatty amide. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as a fatty amide (PMN P-91-87) is subject to reporting under this...

  16. Maastricht essential fatty acid birth cohort

    NARCIS (Netherlands)

    Van der Wurff, Inge; De Groot, Renate; Stratakis, Nikos; Gielen, Marij; Hornstra, Gerard; Zeegers, Maurice

    2016-01-01

    The Maastricht Essential Fatty Acid Birth cohort (MEFAB) was established in 1989 to study the changes in fatty acid concentration during pregnancy and how this related to the fatty acid concentrations of the neonate. The original sample contains data of 1203 subjects. Some participants whom particip

  17. License - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp License License to Use This Database Last updated : 2017/06/29 You may use this... database in compliance with the terms and conditions of the license described below. The license specifies the lice...nse terms regarding the use of this database and the requirements you must follow in using this database. The lice...se as follows: MicrobeDB.jp © Ken Kurokawa (Center for Information Biology, National Institute of Genetics) lice... Creative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, you are lice

  18. Giving microbes their due--animal life in a microbially dominant world.

    Science.gov (United States)

    McFall-Ngai, Margaret J

    2015-06-01

    The new technology of next-generation sequencing is changing our perceptions of the form and function of the biological world. The emerging data reveal an array of microbes that is more vast and more central to all biological processes than previously appreciated. Further, evidence is accumulating that the alliances of microbes with one another and with constituents of the macrobiological world are critical for the health of the biosphere. This contribution summarizes the basic arguments as to why, when considering the biochemical adaptations of animals, we should integrate the roles of their microbial partners.

  19. Prediction of highly expressed genes in microbes based on chromatin accessibility

    DEFF Research Database (Denmark)

    Willenbrock, Hanni; Ussery, David

    2007-01-01

    BACKGROUND: It is well known that gene expression is dependent on chromatin structure in eukaryotes and it is likely that chromatin can play a role in bacterial gene expression as well. Here, we use a nucleosomal position preference measure of anisotropic DNA flexibility to predict highly expressed...... and ribosomal RNA are encoded by DNA having significantly lower position preference values than other genes in fast-replicating microbes. CONCLUSION: This insight into DNA structure-dependent gene expression in microbes may be exploited for predicting the expression of non-translated genes such as non...

  20. Diverse Roles of Lysin-Motif (LysM Proteins in Mediating Plant-Microbe Interactions

    Directory of Open Access Journals (Sweden)

    Jinrong WAN

    2015-08-01

    Full Text Available Lysin-motif (LysM is a protein domain initially identified in a phage protein responsible for binding peptidoglycan, an important component of bacterial cell walls. LysM-containing proteins are distributed in diverse organisms, ranging from microbes to plants and animals (including human beings. Recent studies demonstrated that this group of proteins plays different roles in mediating plant-microbe interactions, leading to defense, symbiosis, or suppression of host defense. These roles are probably related to their potential ability to recognize and bind a specific signal molecule, such as chitooligosaccharides, peptidoglycan, nodulation factors (NFs, and mycorrhization factors (MFs.

  1. The Use of Stuffed Microbes in an Undergraduate Microbiology Course Increases Engagement and Student Learning

    Directory of Open Access Journals (Sweden)

    Ginny Webb

    2015-08-01

    Full Text Available Student engagement, attention, and attendance during a microbiology lecture are crucial for student learning.  In addition, it is challenging to cover a large number of infectious diseases during a one-semester introductory microbiology course.  The use of visual aids helps students retain the information presented during a lecture.  Here, I discuss the use of stuffed, plush microbes as visual aids during an introductory microbiology course.  The incorporation of these stuffed microbes during a microbiology lecture results in an increase in engagement, interest, attendance, and retention of material.

  2. Threats, Challenges, and Promise of Marine Microbes: A NOAA Perspective with Emphasis on Ecological Forecasting

    Science.gov (United States)

    Sandifer, P. A.

    2012-12-01

    Fully functioning ecosystems, as well as healthy humans, depend on robust and diverse communities of microbes. The diversity of microbes in the marine environment is estimated to be huge, dwarfing diversity of other life forms, and crucial for many ecosystem processes. Despite the ubiquity and extreme importance of microbial life in the sea - from the air-surface interface to the deepest abyss and sediments - we know relatively little about this biotic component that may compose a large proportion of the total biomass on the planet. As the nation's principal steward of marine living resources, NOAA is both responsible for and vitally interested in marine microbes, from a variety of perspectives. These include (1) health threats to humans and other organisms and how these may be affected by climate change and ecosystem alteration; (2) detoxification of organic pollutants such as hydrocarbons (e.g., in the Deep Water Horizon oil catastrophe); (3) production of valuable natural products including potential new pharmaceuticals; (4) roles in biogeochemical cycles (e.g., for carbon, nitrogen, phosphorus, iron, etc.) and how human activities may affect these roles; (5) development and deployment of new methods to detect and quantify certain marine microbes, and incorporation of these into ocean observing systems; (6) development of Earth System models that include much improved understanding of microbial functional diversity and microbially mediated biogeochemical processes; (7) dynamics of bacterial, phyto- and zooplankton blooms, including for harmful algae and bacteria; (8) effects of climate change factors (e.g., temperature, CO2 concentrations, ocean acidification, changes in habitats and species distribution, etc.) on marine microbes; and others. Many of these topics likely will be discussed by others in this session. This presentation will focus primarily on NOAA's activities in addressing health threats emanating from a variety of microbes in the marine

  3. Acute fatty liver in pregnancy.

    NARCIS (Netherlands)

    Tan, A.; Krieken, J.H.J.M. van; Peters, W.H.M.; Steegers, E.A.P.

    2002-01-01

    When confronted with liver abnormalities during the third trimester of pregnancy, one should consider acute fatty liver of pregnancy. The differential diagnosis with (pre-)eclampsia and HELLP syndrome is sometimes difficult. In these cases a liver biopsy is helpful though rarely performed during pre

  4. Generation of fad2 transgenic mice that produce omega-6 fatty acids

    Institute of Scientific and Technical Information of China (English)

    CHEN Qing; LIU Qing; WU ZhiFang; WANG ZongYi; GOU KeMian

    2009-01-01

    Fatty acid desaturase-2 (FAD2)introduces a double bond in position △12 in oleic acid (18:1)to form linoleic acid (18:2 n-6)in higher plants and microbes.A new transgenic expression cassette,containing CMV promoter/fad2 cDNA/SV40 polyA,was constructedto produce transgenic mice.Among 63 healthy offspring,10 founders (15.9%)integrated the cotton fad2 transgene into their genomes,as demonstrated by PCR and Southern blotting analysis.All founder mice were fertile and heterozygous fad2 female and nontransgenic littermates were used for fatty acid analysis using gas chromatography.One fad2 transgenic line showed substantial differences in the fatty acid profiles and the level of linoleic acid was increased 19% (P<0.05)in transgenic muscles compared to their nontransgenic littermates.Moreover,it exhibited an 87% and a 9% increase (P<0.05)in arachidonic acid (20:4 n-6)in muscles and liver,compared to their nontransgenic littermates.The results indicate that the plant fad2 gene can be functionally expressed in transgenic mice and may playan active role in conversion of oleic acid into linoleic acid.

  5. Generation of fad2 transgenic mice that produce omega-6 fatty acids

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Fatty acid desaturase-2 (FAD2) introduces a double bond in position 12 in oleic acid (18:1) to form linoleic acid (18:2 n-6) in higher plants and microbes. A new transgenic expression cassette, containing CMV promoter/fad2 cDNA/SV40 polyA, was constructedto produce transgenic mice. Among 63 healthy offspring, 10 founders (15.9%) integrated the cotton fad2 transgene into their genomes, as demonstrated by PCR and Southern blotting analysis. All founder mice were fertile and heterozygous fad2 female and nontransgenic littermates were used for fatty acid analysis using gas chromatography. One fad2 transgenic line showed substantial differences in the fatty acid profiles and the level of linoleic acid was increased 19% (P<0.05) in transgenic muscles compared to their nontransgenic littermates. Moreover, it exhibited an 87% and a 9% increase (P<0.05) in arachidonic acid (20:4 n-6) in muscles and liver, compared to their nontransgenic littermates. The results indicate that the plant fad2 gene can be functionally expressed in transgenic mice and may playan active role in conversion of oleic acid into linoleic acid.

  6. Two-way plant mediated interactions between root-associated microbes and insects: from ecology to mechanisms

    NARCIS (Netherlands)

    Pangesti, N.P.D.; Pineda Gomez, A.M.; Pieterse, C.M.J.; Dicke, M.; Loon, van J.J.A.

    2013-01-01

    Plants are members of complex communities and function as a link between above- and below-ground organisms. Associations between plants and soil-borne microbes commonly occur and have often been found beneficial for plant fitness. Root-associated microbes may trigger physiological changes in the hos

  7. Characterization of microbes in prosthetic joint specimens by culture-independent molecular methods

    DEFF Research Database (Denmark)

    Thomsen, Trine Rolighed; Xu, Yijuan; Rudkjøbing, Vibeke Børsholt

    (qPCR). In order to reveal possible heterogeneous distribution of the microbes, multiple biopsies were taken from wounds, biofilm was scraped from internal and external catheter surfaces, and during revision arthroplasty several specimen types (joint fluid, tissue biopsy, bone biopsy and prosthesis...

  8. Antibacterial activities of silver nanoparticles and antibiotic-adsorbed silver nanoparticles against biorecycling microbes.

    Science.gov (United States)

    Khurana, Chandni; Vala, Anjana K; Andhariya, Nidhi; Pandey, O P; Chudasama, Bhupendra

    2014-09-20

    Silver nanoparticles have a huge share in nanotechnology based products used in clinical and hygiene products. Silver nanoparticles leaching from these medical and domestic products will eventually enter terrestrial ecosystems and will interact with the microbes present in the land and water. These interactions could be a threat to biorecycling microbes present in the Earth's crust. The antimicrobial action towards biorecycling microbes by leached silver nanoparticles from medical waste could be many times greater compared to that of silver nanoparticles leached from other domestic products, since medical products may contain traditional antibiotics along with silver nanoparticles. In the present article, we have evaluated the antimicrobial activities of as-synthesized silver nanoparticles, antibiotics - tetracycline and kanamycin, and antibiotic-adsorbed silver nanoparticles. The antimicrobial action of silver nanoparticles with adsorbed antibiotics is 33-100% more profound against the biorecycling microbes B. subtilis and Pseudomonas compared to the antibacterial action of silver nanoparticles of the same concentration. This study indicates that there is an immediate and urgent need for well-defined protocols for environmental exposure to silver nanoparticles, as the use of silver nanoparticles in nanotechnology based products is poorly restricted.

  9. Microscopic study of migration of microbes in food-packaging paper and board.

    Science.gov (United States)

    Suominen, I; Suihko, M L; Salkinoja-Salonen, M

    1997-08-01

    The microbiological barrier properties of food-packaging paperboards, coated with polyethylene, mineral pigment or a biodegradable polymer and of high-density paper were examined with confocal laser scanning microscopy. The results show that the spatial distribution of microscopically observable bacterial cells was uneven inside the paperboard. The concentration in the interface between the polyethylene coating and the cellulose fibers was 100-200 times higher than inside the cellulose matrix. The bacteria in the interface and the mineral coating layer grew in response to access to food and moisture, whereas no growth was observed inside the fiber web, not even after extended exposure for up to 90 days. The paper and paperboards studied contained soluble nutrients (C:N:P 54:9:1 to 309:3:1) and no measurable antimicrobial activity. The factor limiting growth and migration of bacteria inside the fiber web was most likely limited access to free water, even under conditions of extensive wetting. The studied paperboards functioned as efficient barriers against translocation of microbes. The microbes residing between the paperboard and its polymer coating facing food, was the only potential site from which microbes could leak into food. This emphasizes the need for high hygienic quality of surface-sizing chemicals. Mineral-coating pigments were a source of microbes and their application behind the PE coating facing food is contraindicated.

  10. Plant interactions with microbes and insects: from molecular mechanisms to ecology

    NARCIS (Netherlands)

    Pieterse, C.M.J.; Dicke, M.

    2007-01-01

    Plants are members of complex communities and interact both with antagonists and beneficial organisms. An important question in plant defense-signaling research is how plants integrate signals induced by pathogens, beneficial microbes and insects into the most appropriate adaptive response. Molecula

  11. Disease - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...sion V2 10.18908/lsdba.nbdc01181-007.V002 Update History V1 - Description of data contents The PDO annotatio...iption Download License Update History of This Database Site Policy | Contact Us Disease - MicrobeDB.jp | LSDB Archive ...

  12. GOLD - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...2 10.18908/lsdba.nbdc01181-008.V002 Update History V1 - Description of data contents Annotation results of p... Download License Update History of This Database Site Policy | Contact Us GOLD - MicrobeDB.jp | LSDB Archive ...

  13. Do volatiles produced by nectar-dwelling microbes affect honey bee preferences?

    Science.gov (United States)

    The microbiome of plants mediates many interactions in natural and managed systems. Among these, plant-pollinator interactions are important for ensuring high crop yields, pollinator health and successful plant reproduction. Despite initial work demonstrating effects of floral microbes on pollinatio...

  14. Microbes inside—from diversity to function: the case of Akkermansia

    NARCIS (Netherlands)

    Belzer, C.; Vos, de W.M.

    2012-01-01

    The human intestinal tract is colonized by a myriad of microbes that have developed intimate interactions with the host. In healthy individuals, this complex ecosystem remains stable and resilient to stressors. There is significant attention on the understanding of the composition and function of th

  15. [A review of the role and function of microbes in coral reef ecosystem].

    Science.gov (United States)

    Zhou, Jin; Jin, Hui; Cai, Zhong-Hua

    2014-03-01

    Coral reef is consisted with several kinds of reef-associated organisms, including coral, fish, benthos, algae and microbes, which is an important marine ecosystem. Coral reef lives in the oligotrophic environment, has very highly primary productivity and net productivity, and is called "tropical rain forest in ocean". In corals, diverse microorganisms exert a significant influence on biogeochemical and ecological processes, including food webs, organism life cycles, and nutrient cycling. With the development of molecular biology, the role of microorganisms in a coral system is becoming more outstanding. In this article, we reviewed current understanding on 1) the onset of coral-bacterial associations; 2) the characteristics of microbes in coral (specificity, plasticity and co-evolution) ; 3) the role and signal regulation of microbes in the health and disease of coral; and 4) the response mechanism of microbes for global climatic change and consequent effects, such as temperature rise, ocean acidification and eutrophication. The aims of this article were to summarize the latest theories and achievements, clear the mechanism of microbial ecology in coral reefs and provide a theoretical reference for better protection and maintaining the coral's biodiversity.

  16. Biodiversity of Soil Microbes from Rhizosphere at Wamena Biological Garden (WBiG, Jayawijaya, Papua

    Directory of Open Access Journals (Sweden)

    SRI WIDAWATI

    2005-01-01

    Full Text Available The isolation, identification and population of soil microbes from rizosphere at WBiG had been done in the Soil Laboratories Microbiology, Microbiology Division, Research Center of Biology, Indonesian Institute of Sciences (LIPI, Bogor. The soil was collected randomly from 16 sites in WBiG, and taken from 0-15 cm depth. Isolates of microbes were identified by Bergeys manual method for bacteria; Ellis method for fungi, and the morphology of isolate method for Actinomycetes. The population of microbes was estimated by plate count method. The result of isolation, identification and population soil microbes from 16 samples in WBiG showed that 20 isolates of bacteria (Azotobacter sp., Accinetobacter sp. , Bacillus sp., Citrobacter sp., Flavobacterium sp., Klebsiella sp., Nitrosomonas sp., Pseudomonas sp., Rhizobium sp., Thiobacillus sp., Azospirillum sp., Azotobacter chrococcum, Bacillus panthothenticus, Chromobacterium violaceum, C.lividum, Escherrrichia coli, Flavobacterium breve, Klebsiella aerogenes, Spaerotillus natans, and Staphylococcus epidermidis; nine isolates of fungi (Aspergillus niger, Bisporomyces, Monilia sp., Cephalospharium sp., Verticillum sp., Giocladium sp., Penicillium sp., Nelicocephalum sp., and Cuninghamella sp., and seven isolates of Actinomycetes (Streptomyces, Streptosporangium, Nocardia, Thermomonospora, Thermoactinomyces, Micromonospora, Mycobacterium. The population of Bacillus (108-109, Rhizobium (106-107, Azospirillum (106-107, and Thiobacillus (104 -109 were founded all of soil samples.

  17. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    Energy Technology Data Exchange (ETDEWEB)

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  18. Microbes inside—from diversity to function: the case of Akkermansia

    NARCIS (Netherlands)

    Belzer, C.; Vos, de W.M.

    2012-01-01

    The human intestinal tract is colonized by a myriad of microbes that have developed intimate interactions with the host. In healthy individuals, this complex ecosystem remains stable and resilient to stressors. There is significant attention on the understanding of the composition and function of th

  19. Long-range transport of airborne microbes over the global tropical and subtropical ocean

    KAUST Repository

    Mayol, Eva

    2017-07-28

    The atmosphere plays a fundamental role in the transport of microbes across the planet but it is often neglected as a microbial habitat. Although the ocean represents two thirds of the Earth\\'s surface, there is little information on the atmospheric microbial load over the open ocean. Here we provide a global estimate of microbial loads and air-sea exchanges over the tropical and subtropical oceans based on the data collected along the Malaspina 2010 Circumnavigation Expedition. Total loads of airborne prokaryotes and eukaryotes were estimated at 2.2 × 1021 and 2.1 × 1021 cells, respectively. Overall 33-68% of these microorganisms could be traced to a marine origin, being transported thousands of kilometres before re-entering the ocean. Moreover, our results show a substantial load of terrestrial microbes transported over the oceans, with abundances declining exponentially with distance from land and indicate that islands may act as stepping stones facilitating the transoceanic transport of terrestrial microbes.The extent to which the ocean acts as a sink and source of airborne particles to the atmosphere is unresolved. Here, the authors report high microbial loads over the tropical Atlantic, Pacific and Indian oceans and propose islands as stepping stones for the transoceanic transport of terrestrial microbes..

  20. Nitrogen source and concentration affect utilization of glucose by mixed ruminal microbes in vitro

    Science.gov (United States)

    Availability of ruminally degradable protein (RDP) changes the utilization of carbohydrates by ruminal microbes. However, the effects are not well described, though such information is needed to understand the potential impact on nutrient supplies for ruminants. The objective of this study was to co...

  1. Biomineralization of phototrophic microbes in silica-enriched hot springs in South China

    Institute of Scientific and Technical Information of China (English)

    PENG XiaoTong; ZHOU HuaiYang; WU ZhiJun; JIANG Lei; TANG Song; YAO HuiQiang; CHEN GuangQian

    2007-01-01

    Microbial mats in two hot springs in South China were sampled for the research of mineralization of microbes and its mechanism by the methods of geology and modern biology. The results show that hot spring microbes have the key capability for enrichment of Si, Al, Fe, Ca and other elements, and the microbes are also crucial for the formation of SiO2, CaCO3, clay and so on. The extracellular polymeric substances (EPS) play important roles in the process of mineralization of hot spring microbes, which mainly takes place in the layer of EPS outside cell wall or sheath of cyanobacteria. The sheath outside cell wall, which keeps the normal metabolism of cyanobacteria during the process of mineralization on its surface, is also considerable for the biomineralization of cyanobacteria. According to structure and mineralization characteristics of two microbial mats, the process of mineralization can be divided into three stages, namely, early surface mineralization, middle degradation mineralization, and late desquamation of mineral. The above conclusions are significant for comprehension of the process of mineralization, the process of deposition and the preservation of microfossil in modern and ancient extreme environments.

  2. Prominent Human Health Impacts from Several Marine Microbes: History, Ecology, and Public Health Implications

    Directory of Open Access Journals (Sweden)

    P. K. Bienfang

    2011-01-01

    Full Text Available This paper overviews several examples of important public health impacts by marine microbes and directs readers to the extensive literature germane to these maladies. These examples include three types of dinoflagellates (Gambierdiscus spp., Karenia brevis, and Alexandrium fundyense, BMAA-producing cyanobacteria, and infectious microbes. The dinoflagellates are responsible for ciguatera fish poisoning, neurotoxic shellfish poisoning, and paralytic shellfish poisoning, respectively, that have plagued coastal populations over time. Research interest on the potential for marine cyanobacteria to contribute BMAA into human food supplies has been derived by BMAA's discovery in cycad seeds and subsequent implication as the putative cause of amyotrophic lateral sclerosis/parkinsonism dementia complex among the Chamorro people of Guam. Recent UPLC/MS analyses indicate that recent reports that BMAA is prolifically distributed among marine cyanobacteria at high concentrations may be due to analyte misidentification in the analytical protocols being applied for BMAA. Common infectious microbes (including enterovirus, norovirus, Salmonella, Campylobacter, Shigella, Staphylococcus aureus, Cryptosporidium, and Giardia cause gastrointestinal and skin-related illness. These microbes can be introduced from external human and animal sources, or they can be indigenous to the marine environment.

  3. Evaluation of Factors Affecting Uricase Production by the Screened Wild/Natural Microbes

    Directory of Open Access Journals (Sweden)

    Harinath Dwivedi

    2012-01-01

    Full Text Available Gout is a metabolic disorder due to the deposition of uric acid crystals within articular or periarticular tissues. Uricase (urate oxidase catalyzes the oxidation of less water soluble uric acid (7 mg/dl to a compound allantoin which is more water soluble(11g/L at 40°C resulting into the ease of excretion of uric acid. The objective of the work was to develop a new method for screening of microbes for uricase production and estimation of uricase thereof. This was achieved by utilizing the fact that uric acid dissolves on being acted upon by uricase. The proposed method is a novel, inexpensive, simple and sensitive technique for screening and estimation of uricase. Biomass and uricase production at different stages of microbial growth curve for the uricase producing microbe was studied. Effects of different medium components affecting uricase production by microbes were studied using Placket Burman statistical design. Addition of uric acid in the nutrient medium was found to be effective in increasing the uricase production by microbes growing in the medium.

  4. Spatially-Correlated Mass Spectrometric Analysis of Microbe-Mineral Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Jill R. Scott; Beizhan Yan; Daphne L. Stoner

    2006-11-01

    A new methodology for examining the interactions of microbes with heterogeneous minerals is presented. Imaging laser-desorption Fourier transform mass spectrometry was used to examine the colonization patterns of Burkholderia vietnamiensis (Burkholderia cepacia) G4 on a heterogeneous basalt sample. Depth-profile imaging found that the bacterium preferentially colonized the plagioclase mineral phases within the basalt.

  5. Using a “Microbe Minute” to Improve Class Attendance and Increase Course Interest

    Directory of Open Access Journals (Sweden)

    Kathleen A. Feldman

    2013-08-01

    Full Text Available Previous studies have shown a positive correlation between lecture attendance and exam performance (2. Teaching an introductory microbiology class in a large lecture format to 200–375 students at 8:00 a.m. has unique challenges. In particular, due to the early morning lecture, students tend to arrive late and some cease attending after the first few weeks of class, since lecture PowerPoint slides are provided on the class website. Additionally, student interest in the subject may be low since it is a required course. Many introductory level textbooks focus on large concepts but minimize discussion of interesting microorganisms, particularly pathogens. To address these issues, a “Microbe Minute” was added to the start of the class period (1. The “Microbe Minute” consists of four PowerPoint slides focusing on an interesting microorganism. The class starts exactly at 8:00 a.m. and copies of the slides are not provided to the students. Spending the first five minutes of an undergraduate introductory microbiology class discussing an interesting microbe can improve class attendance, foster discussion, and increase course interest, which ultimately benefits both the students and the instructor. The “Microbe Minute” can be implemented in any undergraduate or graduate-level microbiology or biology course from the introductory to the advanced level. It is particularly useful in a large lecture format but can also be used for a small classroom.

  6. Experimental Activities in Primary School to Learn about Microbes in an Oral Health Education Context

    Science.gov (United States)

    Mafra, Paulo; Lima, Nelson; Carvalho, Graça S.

    2015-01-01

    Experimental science activities in primary school enable important cross-curricular learning. In this study, experimental activities on microbiology were carried out by 16 pupils in a Portuguese grade-4 classroom (9-10?years old) and were focused on two problem-questions related to microbiology and health: (1) do your teeth carry microbes? (2) why…

  7. Divergent utilization patterns of grass fructan, inulin, and other nonfiber carbohydrates by ruminal microbes

    Science.gov (United States)

    Fructans are an important nonfiber carbohydrate in cool-season grasses. Their fermentation by ruminal microbes is not well described, though such information is needed to understand their nutritional value to ruminants. Our objective was to compare kinetics and product formation of orchardgrass fruc...

  8. Investigating the context-dependency of plant-soil-AMF-microbe interactions along a pollution gradient

    Science.gov (United States)

    Glassman, S. I.; Casper, B. B.

    2010-12-01

    Background/Question/Methods Investigating how arbuscular mycorrhizal fungi (AMF)-plant interactions vary with edaphic conditions provides an opportunity to test the context-dependency of interspecific interactions, which is currently recognized as a major avenue of future research. We study plant-mycorrhiza symbiotic relationships along a gradient of heavy metal contamination at a recently revegetated “Superfund” site on Blue Mountain, in Palmerton, Pennsylvania. We investigated the interactions involving the native mycorrhizal fungi, non-mycorrhizal soil microbes, soil, and two plant species (a C3 and C4 grass) along the contamination gradient. The native C3 study species Deschampsia flexuosa, is dominant along the gradient and established naturally; the C4 Sorghastrum nutans, is native to Pennsylvania but not to the site and was introduced during restoration. Because C4 grasses are obligate mycotrophs, we expected S. nutans to have a different effect on and response to the soil symbiont community than the C3 grass. We carried out a full factorial greenhouse experiment using field-collected seeds of D. flexuosa and S. nutans, soil, AMF spores, and non-mycorrhizal microbes from both high and low contaminated ends of the gradient. After 11 weeks of growth in the greenhouses, we harvested above and belowground plant biomass, and quantified AMF root colonization and AMF sporulation. Results/Conclusions Our results indicate that context-dependent function is an important factor driving specific ecological interactions between plants and soil microbes. We found that soil origin significantly affected plant growth. Plants from both species grew much larger in soil from low contaminated (LC) origin than high contaminated (HC) origin. Furthermore, we found that the efficacy of AMF in promoting plant growth depended on AMF origin. Specifically, AMF from LC improved growth of D. flexuosa best in either soil background and improved survivorship of S. nutans in HC soil

  9. Differences in codon bias cannot explain differences in translational power among microbes

    Directory of Open Access Journals (Sweden)

    Dethlefsen Les

    2005-01-01

    Full Text Available Abstract Background Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level and degree of codon bias among genes of Escherichia coli and other bacteria capable of rapid growth is commonly attributed to selection for high translational power. Conversely, the absence of such a correlation in some slowly growing microbes has been interpreted as the absence of selection for translational power. Because codon bias caused by translational selection varies between rapidly growing and slowly growing microbes, we investigated whether observed differences in translational power among microbes could be explained entirely by differences in the degree of codon bias. Although the data are not available to estimate the effect of codon bias in other species, we developed an empirically-based mathematical model to compare the translation rate of E. coli to the translation rate of a hypothetical strain which differs from E. coli only by lacking codon bias. Results Our reanalysis of data from the scientific literature suggests that translational power can differ by a factor of 5 or more between E. coli and slowly growing microbial species. Using empirical codon-specific in vivo translation rates for 29 codons, and several scenarios for extrapolating from these data to estimates over all codons, we find that codon bias cannot account for more than a doubling of the translation rate in E. coli, even with unrealistic simplifying assumptions that exaggerate the effect of codon bias. With more realistic assumptions, our best estimate is that codon bias accelerates translation in E. coli by no more than

  10. Cooperation, competition, and coalitions in enzyme-producing microbes: Social evolution and nutrient depolymerization rates

    Directory of Open Access Journals (Sweden)

    Henry Joseph Folse

    2012-09-01

    Full Text Available Extracellular enzymes represent a public good for microbial communities, as they break down complex molecules into simple molecules that microbes can take up. These communities are vulnerable to cheating by microbes that do not produce enzymes, but benefit from those produced by others. However, extracellular enzymes are ubiquitous and play an important role in the depolymerization of nutrients. We developed a multi-genotype, multi-nutrient model of a community of exoenzyme-producing microbes, in order to investigate the relationship between diversity, social interactions, and nutrient depolymerization. We focused on coalitions between complementary types of microbes and their implications for spatial pattern formation and nutrient depolymerization. The model included polymers containing carbon, nitrogen, or phosphorus, and eight genotypes of bacteria, which produced different subsets of the three enzymes responsible for hydrolyzing these polymers. We allowed social dynamics to emerge from a mechanistic model of enzyme production, action, and diffusion. We found that diversity was maximized at high rates of either diffusion or enzyme production (but not both. Conditions favoring cheating also favored the emergence of coalitions. We characterized the spatial patterns formed by different interactions, showing that same-type cooperation leads to aggregation, but between-type cooperation leads to an interwoven, filamentous pattern. Contrary to expectations based on niche complementarity, we found that nutrient depolymerization declined with increasing diversity due to a negative competitive effect of coalitions on generalist producers, leading to less overall enzyme production. This decline in depolymerization was stronger for non-limiting nutrients in the system. This study shows that social interactions among microbes foraging for complementary resources can influence microbial diversity, microbial spatial distributions, and rates of nutrient

  11. Plant traits related to nitrogen uptake influence plant-microbe competition.

    Science.gov (United States)

    Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Philippot, Laurent; Mougel, Christophe

    2015-08-01

    Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more

  12. Cooperation, competition, and coalitions in enzyme-producing microbes: social evolution and nutrient depolymerization rates.

    Science.gov (United States)

    Folse, Henry J; Allison, Steven D

    2012-01-01

    Extracellular enzymes represent a public good for microbial communities, as they break down complex molecules into simple molecules that microbes can take up. These communities are vulnerable to cheating by microbes that do not produce enzymes, but benefit from those produced by others. However, extracellular enzymes are ubiquitous and play an important role in the depolymerization of nutrients. We developed a multi-genotype, multi-nutrient model of a community of exoenzyme-producing microbes, in order to investigate the relationship between diversity, social interactions, and nutrient depolymerization. We focused on coalitions between complementary types of microbes and their implications for spatial pattern formation and nutrient depolymerization. The model included polymers containing carbon, nitrogen, or phosphorus, and eight genotypes of bacteria, which produced different subsets of the three enzymes responsible for hydrolyzing these polymers. We allowed social dynamics to emerge from a mechanistic model of enzyme production, action, and diffusion. We found that diversity was maximized at high rates of either diffusion or enzyme production (but not both). Conditions favoring cheating also favored the emergence of coalitions. We characterized the spatial patterns formed by different interactions, showing that same-type cooperation leads to aggregation, but between-type cooperation leads to an interwoven, filamentous pattern. Contrary to expectations based on niche complementarity, we found that nutrient depolymerization declined with increasing diversity due to a negative competitive effect of coalitions on generalist producers, leading to less overall enzyme production. This decline in depolymerization was stronger for non-limiting nutrients in the system. This study shows that social interactions among microbes foraging for complementary resources can influence microbial diversity, microbial spatial distributions, and rates of nutrient depolymerization.

  13. Polyunsaturated fatty acids and epilepsy.

    Science.gov (United States)

    Taha, Ameer Y; Burnham, W McIntyre; Auvin, Stéphane

    2010-08-01

    Omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) are dietary fatty acids that are involved in a myriad of physiologic processes in the brain. There is some evidence suggesting that PUFAs-and particularly omega-3 PUFAs-may have anticonvulsant effects, both in humans and in animals. In the present review, we assess the evidence related to the antiseizure properties of the n-3 PUFAs, discuss their possible mechanism(s) of action, and make recommendations for future clinical trials. In general, the available data from cell cultures and whole animal studies support the idea that the n-3 PUFAs have antiseizure properties. Future clinical trials involving the n-3 PUFAs should involve higher doses and longer periods of administration in order to definitively assess their possible antiseizure effects.

  14. Nonalcoholic Fatty Liver Disease Treatment

    Directory of Open Access Journals (Sweden)

    M Sadeghian

    2014-04-01

    Full Text Available Nonalcoholic fatty liver disease (NAFLD is increasing in pediatric age group parallel to the growing prevalence of obesity and overweight all around the world. So changing in life style and   interventions on obesogenic environment is cornerstone of NAFLD therapy in obese children. Some experts recommend that children and adolescents be encouraged to follow a low-fat, low-glycemic-index diet that includes eating a minimum of 5 servings of vegetables and fruits daily, engaging in physical activity for at least 1 hour daily, and minimizing television/computer time to 2 hours daily.  In spite of effectiveness of weight loss and exercise in improvement NAFLD, this goal is very difficult to be achieved and pharmacological approaches have become necessary. Pharmacologic therapies against one or more specific factors and/or molecules involved in the development of NAFLD (i.e., insulin resistance, free fatty acid lipid toxicity, and oxidative stress also might slow the progression of NAFLD to NASH or cirrhosis.  On this basis, insulin sensitizers, antioxidants, cytoprotective agents, and dietary supplementations have been evaluated in pediatric clinical trials but there is no approved pharmacologic therapy for NAFLD or NASH. Not all obese children affected by NAFLD. Diet modification and regular exercise beside to serial medical follow up highly suggested for this group of children. Normal weight and thin children with NAFLD or NASH should be investigated appropriately in a logical manner based on causes of primary liver steatosis in children and treatment of underlying disease can cause improvement fatty liver in these patients.   Keywords: Non-alcoholic fatty liver disease; Non-alcoholic steatohepatitis; Children; Steatosis; Treatment

  15. The possible interplanetary transfer of microbes: assessing the viability of Deinococcus spp. under the ISS Environmental conditions for performing exposure experiments of microbes in the Tanpopo mission.

    Science.gov (United States)

    Kawaguchi, Yuko; Yang, Yinjie; Kawashiri, Narutoshi; Shiraishi, Keisuke; Takasu, Masako; Narumi, Issay; Satoh, Katsuya; Hashimoto, Hirofumi; Nakagawa, Kazumichi; Tanigawa, Yoshiaki; Momoki, Yoh-Hei; Tanabe, Maiko; Sugino, Tomohiro; Takahashi, Yuta; Shimizu, Yasuyuki; Yoshida, Satoshi; Kobayashi, Kensei; Yokobori, Shin-Ichi; Yamagishi, Akihiko

    2013-10-01

    To investigate the possible interplanetary transfer of life, numerous exposure experiments have been carried out on various microbes in space since the 1960s. In the Tanpopo mission, we have proposed to carry out experiments on capture and space exposure of microbes at the Exposure Facility of the Japanese Experimental Module of the International Space Station (ISS). Microbial candidates for the exposure experiments in space include Deinococcus spp.: Deinococcus radiodurans, D. aerius and D. aetherius. In this paper, we have examined the survivability of Deinococcus spp. under the environmental conditions in ISS in orbit (i.e., long exposure to heavy-ion beams, temperature cycles, vacuum and UV irradiation). A One-year dose of heavy-ion beam irradiation did not affect the viability of Deinococcus spp. within the detection limit. Vacuum (10(-1) Pa) also had little effect on the cell viability. Experiments to test the effects of changes in temperature from 80 °C to -80 °C in 90 min (± 80 °C/90 min cycle) or from 60 °C to -60 °C in 90 min (± 60 °C/90 min cycle) on cell viability revealed that the survival rate decreased severely by the ± 80 °C/90 min temperature cycle. Exposure of various thicknesses of deinococcal cell aggregates to UV radiation (172 nm and 254 nm, respectively) revealed that a few hundred micrometer thick aggregate of deinococcal cells would be able to withstand the solar UV radiation on ISS for 1 year. We concluded that aggregated deinococcal cells will survive the yearlong exposure experiments. We propose that microbial cells can aggregate as an ark for the interplanetary transfer of microbes, and we named it 'massapanspermia'.

  16. Distributions of fatty acids in a stalagmite related to paleoclimate change at Qingjiang in Hubei, southern China

    Institute of Scientific and Technical Information of China (English)

    XIE Shucheng; HUANG Junhua; WANG Hongmei; YI Yi; HU Chaoyong; CAI Yanjun; CHENG Hai

    2005-01-01

    Fatty acids extracted from a subtropical stalagmite at Qingjiang in Southern China's Hubei Province were analysed using gas chromatography-mass spectrometry. These n-alkanoic acids range from C14 to C26 in carbon number, maximizing at C16, with a second dominance at C22. In contrast to the stalagmite analysed, the overlying soils are characterized by the dominance of heavy-molecular-weight homologues (>C20). The n-fatty acids in the stalagmite were proposed to be contributed by both the soil ecosystems and the microbes harboring in the percolating water and the cave. The ratios of unsaturated to saturated n-fatty acids (C16:1/C16:0,C18:1/C18:0) appear to show trends comparable with the oxygen isotope records of the stalagmite carbonate, with enhanced values associated with the cold episode such as Heinrich event 1. This paleoclimate-dependent record of the n-fatty acids might reflect microbial changes in physiology and activity in response to the temperature. This record shows somewhat difference from the previous paleoclimate signal extracted from n-alkanols and n-alkan-2-ones of the same stalagmite. The acid record fails to document the well-known Younger Dryas event which was effectively shown by the latter two biomarkers derived from soil ecosystems. This discrepancy might result from the changing biogeochemical impact on different lipid fractions as well as the varied organism populations in different ecosystems.

  17. Aspirin increases mitochondrial fatty acid oxidation.

    Science.gov (United States)

    Uppala, Radha; Dudiak, Brianne; Beck, Megan E; Bharathi, Sivakama S; Zhang, Yuxun; Stolz, Donna B; Goetzman, Eric S

    2017-01-08

    The metabolic effects of salicylates are poorly understood. This study investigated the effects of aspirin on fatty acid oxidation. Aspirin increased mitochondrial long-chain fatty acid oxidation, but inhibited peroxisomal fatty acid oxidation, in two different cell lines. Aspirin increased mitochondrial protein acetylation and was found to be a stronger acetylating agent in vitro than acetyl-CoA. However, aspirin-induced acetylation did not alter the activity of fatty acid oxidation proteins, and knocking out the mitochondrial deacetylase SIRT3 did not affect the induction of long-chain fatty acid oxidation by aspirin. Aspirin did not change oxidation of medium-chain fatty acids, which can freely traverse the mitochondrial membrane. Together, these data indicate that aspirin does not directly alter mitochondrial matrix fatty acid oxidation enzymes, but most likely exerts its effects at the level of long-chain fatty acid transport into mitochondria. The drive on mitochondrial fatty acid oxidation may be a compensatory response to altered mitochondrial morphology and inhibited electron transport chain function, both of which were observed after 24 h incubation of cells with aspirin. These studies provide insight into the pathophysiology of Reye Syndrome, which is known to be triggered by aspirin ingestion in patients with fatty acid oxidation disorders. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Simulated Microbe Removal around Finger Rings Using Different Hand Sanitation Methods

    Science.gov (United States)

    Alur, Archana A; Rane, Madhavi J; Scheetz, James P; Lorenz, Douglas J; Gettleman, Lawrence

    2009-01-01

    Aim It is our opinion that the CDC and the WHO have underestimated cross-contamination under examination gloves in dental clinics while wearing jewelry, such as finger rings. These agencies only “recommend” removing jewelry, and only washing hands for 15 seconds with soap and warm water before donning gloves. This study examined several washing procedures and finger rings using simulated microbes. Methodology A gloved rubber hand manikin was made and fitted with a fresh disposable vinyl glove. Four fingers were fitted with rings or no ring, dusted with simulated microbes, and washed with a scrub brush for 5, 15, and 25 seconds under 20°C and 40°C water alone, or with liquid hand soap. Light levels (in lux) of fluorescent powder before and after washing were measured and delta scores calculated for changes in light levels, equivalent to effectiveness of hand washing procedures. A full-factorial, 3-factor analysis of variance (ANOVA) was used to test for differences among levels of the three study factors—time, temperature, and soap use. Tukey's post hoc honestly significant difference (HSD) test was applied to significant factors to examine pair-wise differences between factor levels. Results It was found that the longer the hands with rings were washed with a scrub brush under flowing water, the more simulated microbes were removed. By 25 seconds, all methods were essentially the same. Simulated microbes were more difficult to remove from the palm compared to the back of the hand. The liquid hand soap used in this study was more effective with warm water than cold. When given a choice of washing with cold water up to 15 seconds, it would be preferable not to use soap to remove simulated microbes. Qualitatively, the outer surface of finger rings were more effectively cleaned than the crevice below the ring, and the ring with a stone setting appeared to accumulate and retain simulated microbes more than other rings. Conclusion The most effective treatment was

  19. Simulated microbe removal around finger rings using different hand sanitation methods.

    Science.gov (United States)

    Alur, Archana A; Rane, Madhavi J; Scheetz, James P; Lorenz, Douglas J; Gettleman, Lawrence

    2009-09-01

    It is our opinion that the CDC and the WHO have underestimated cross-contamination under examination gloves in dental clinics while wearing jewelry, such as finger rings. These agencies only "recommend" removing jewelry, and only washing hands for 15 seconds with soap and warm water before donning gloves. This study examined several washing procedures and finger rings using simulated microbes. A gloved rubber hand manikin was made and fitted with a fresh disposable vinyl glove. Four fingers were fitted with rings or no ring, dusted with simulated microbes, and washed with a scrub brush for 5, 15, and 25 seconds under 20 degrees C and 40 degrees C water alone, or with liquid hand soap. Light levels (in lux) of fluorescent powder before and after washing were measured and delta scores calculated for changes in light levels, equivalent to effectiveness of hand washing procedures. A full-factorial, 3-factor analysis of variance (ANOVA) was used to test for differences among levels of the three study factors-time, temperature, and soap use. Tukey's post hoc honestly significant difference (HSD) test was applied to significant factors to examine pair-wise differences between factor levels. It was found that the longer the hands with rings were washed with a scrub brush under flowing water, the more simulated microbes were removed. By 25 seconds, all methods were essentially the same. Simulated microbes were more difficult to remove from the palm compared to the back of the hand. The liquid hand soap used in this study was more effective with warm water than cold. When given a choice of washing with cold water up to 15 seconds, it would be preferable not to use soap to remove simulated microbes. Qualitatively, the outer surface of finger rings were more effectively cleaned than the crevice below the ring, and the ring with a stone setting appeared to accumulate and retain simulated microbes more than other rings. The most effective treatment was washing with warm water

  20. MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

    Directory of Open Access Journals (Sweden)

    Feng Xueyang

    2012-08-01

    Full Text Available Abstract Background Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. Results We have developed a semi-automatic, web-based platform (MicrobesFlux for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language. Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. Conclusion MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG

  1. Electrogenicity of hepatocellular fatty acid uptake.

    Science.gov (United States)

    Elsing, C; Kassner, A; Gajdzik, L; Graf, J; Stremmel, W

    1998-08-18

    Sensitivity of cellular fatty acids uptake to the membrane potential difference is still a matter of controversy. For direct evaluation of potential sensitivity the effect of changing membrane potential on uptake of a fluorescent long chain fatty acid derivative, 12-NBD-stearate, in isolated rat hepatocytes, was examined. Changes in membrane potential were achieved by patch clamp procedures. Fatty acid influx was simultaneously determined by recording of cell fluorescence. Hyperpolarization from -30 to -70 mV accelerated fatty acid influx whereas depolarization to +50 mV reduced uptake. After obtaining equilibrium hyperpolarization increased cell fluorescence, whereas depolarization pushed NBD-stearate out of cells. Potential sensitivity of uptake was dependent on the fatty acid concentrations in the medium with most prominent effects at low unbound concentrations. These data show that, at low fatty acid concentrations, uptake is, in part, driven by an intracellular negative electric membrane potential.

  2. Fatty acid content of selected seed oils.

    Science.gov (United States)

    Orhan, Ilkay; Sener, Bilge

    2002-01-01

    Fatty acid content of selected seed oils from world-wide edible fruits, Ceratonia ciliqua (carob) from Caesalpiniaceae family, Diospyros kaki (persimmon) from Ebenaceae family, Zizyphus jujuba (jujube) from Rhamnaceae family, and Persea gratissima (avocado pear) from Lauraceae family, were determined by capillary gas chromatography- mass spectrometry (GC-MS) to find new natural sources for essential fatty acids. Among the seed oils analyzed, Ceratonia ciliqua has been found to have the highest essential fatty acid content.

  3. Pathophysiology of Non Alcoholic Fatty Liver Disease

    Science.gov (United States)

    Petta, Salvatore; Gastaldelli, Amalia; Rebelos, Eleni; Bugianesi, Elisabetta; Messa, Piergiorgio; Miele, Luca; Svegliati-Baroni, Gianluca; Valenti, Luca; Bonino, Ferruccio

    2016-01-01

    The physiopathology of fatty liver and metabolic syndrome are influenced by diet, life style and inflammation, which have a major impact on the severity of the clinicopathologic outcome of non-alcoholic fatty liver disease. A short comprehensive review is provided on current knowledge of the pathophysiological interplay among major circulating effectors/mediators of fatty liver, such as circulating lipids, mediators released by adipose, muscle and liver tissues and pancreatic and gut hormones in relation to diet, exercise and inflammation. PMID:27973438

  4. Fatty Acids in Veterinary Medicine and Research

    OpenAIRE

    Rutland, Catrin S.; Mostyn, Alison; Simpson, Siobhan

    2017-01-01

    Fatty acid regulation is an essential process for all animals. A number of studies have shown that diet affects the levels/availability of fatty acids in the body but increasingly evidence shows that disease states can alter the amounts within the body too. Fatty acid levels and availability have been altered by a number of diseases, disorders and reactions including inflammatory responses, heart disease and heart failure and wound repair. They are also essential during the growth and develop...

  5. Solution Structure and Backbone Dynamics of Human Liver Fatty Acid Binding Protein: Fatty Acid Binding Revisited

    OpenAIRE

    Cai, Jun; Lücke, Christian; Chen, Zhongjing; Qiao, Ye; Klimtchuk, Elena; Hamilton, James A.

    2012-01-01

    Liver fatty acid binding protein (L-FABP), a cytosolic protein most abundant in liver, is associated with intracellular transport of fatty acids, nuclear signaling, and regulation of intracellular lipolysis. Among the members of the intracellular lipid binding protein family, L-FABP is of particular interest as it can i), bind two fatty acid molecules simultaneously and ii), accommodate a variety of bulkier physiological ligands such as bilirubin and fatty acyl CoA. To better understand the p...

  6. Veal fatty acid composition of different breeds

    Directory of Open Access Journals (Sweden)

    Ivica Kos

    2010-01-01

    Full Text Available Veal fatty acid composition in M. Longissimus thoracis was investigated in different calf breeds (Simmental, Holstein, Simmental x Holstein. Calves were reared on the same farm under identical feeding and handling conditions. Simmental calves had higher polyunsaturated fatty acid (PUFA but lower saturated fatty acid (SFA and monounsaturated fatty acid (MUFA values than Holstein and crossbreed calves (P<0,05. The PUFA/SFA ratio was the highest in Simmental calves and the lowest in Holstein calves. Simmental calves also had the highest n-6/n-3 ratio while the crossbreed calves had the lowest n-6/n-3 ratio.

  7. Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease.

    Science.gov (United States)

    Babickova, Janka; Gardlik, Roman

    2015-10-28

    The intestinal microbiome is a dynamic system of interactions between the host and its microbes. Under physiological conditions, a fine balance and mutually beneficial relationship is present. Disruption of this balance is a hallmark of inflammatory bowel disease (IBD). Whether an altered microbiome is the consequence or the cause of IBD is currently not fully understood. The pathogenesis of IBD is believed to be a complex interaction between genetic predisposition, the immune system and environmental factors. In the recent years, metagenomic studies of the human microbiome have provided useful data that are helping to assemble the IBD puzzle. In this review, we summarize and discuss current knowledge on the composition of the intestinal microbiota in IBD, host-microbe interactions and therapeutic possibilities using bacteria in IBD. Moreover, an outlook on the possible contribution of bacteriophages in the pathogenesis and therapy of IBD is provided.

  8. Isolation and identification of microbes from biofilm of Urinary catheters and antimicrobial Susceptibility evaluation

    Institute of Scientific and Technical Information of China (English)

    ABalasubramanian; KChairman; AJARanjit Singh; GAlagumuthu

    2012-01-01

    Objective: Bacterial species colonize indwelling catheters as biofilm induce complications in patients care. Methods: From the biofilm matrix seven species of microbes were isolated. The predominant bacteria seen in catheters were E.coli, (27 percent) P.mirabilis (20 percent) and S.epidermis (18 percent). Results: The biomass of microbes associated with the biofilm was estimated. The mean dry weight of biomass of bacteria associated with a catheter that was used for over a month time was in the range 2.5±0.04g - 3.1 ± 0.6g. Conclusion: But it was found to colonize the microtitre plate to attain a peak growth at 84h. P.mirabilis isolated from the biofilm was able to tolerate the antibiotics tetracycline, Penicillin, Kanamycin and Gentamycin at a dose level of 20μg/ml. The study indicated that the catheter has to be replaced if biofilm formation was noticed.

  9. Effect of Microbes Contamination in Quality of Compounding Antitubeculosis Drugs in Bandung

    Directory of Open Access Journals (Sweden)

    Angga P. Kautsar

    2013-06-01

    Full Text Available Based on The Indonesia’s TBC profile from WHO, total of TBC new cases in year 2011 is 313.601 cases and 8.9% involve children under age of 15. TBC cure rate for pediatric patient was influenced primarily by the quality of antituberculosis medicine given. Consideration of drug delivery in the form of compounded medicine because the dose can be calculated and adjust base on weight and age of the pediatric patient. The qualities of compounded medicine need to be monitored in order to increase the expected therapeutic effect and to prevent TBC treatment failure. Survey has been carried out in the level of microbe contaminations test using Total Plate Count Method (TPC. From the TPC test, all of the microbe contaminations tests (100% show qualified levels of contaminations. Both of the results, the qualities of compounded medicine shows 82% categorize as good and 18% as very good.

  10. Glycine uptake in heath plants and soil microbes responds to elevated temperature, CO2 and drought

    DEFF Research Database (Denmark)

    Andresen, Luise C.; Michelsen, Anders; Jonasson, Sven

    2009-01-01

    may increase plant root exudation of dissolved organic compounds such as amino acids, and the release of amino acids during decomposition of organic matter. Such free amino acids in soil serve as substrates for soil microorganisms and are also acquired as nutrients directly by plants. We investigated...... the magnitude of the response to the potential climate change treatments on uptake of organic nitrogen in an in situ pulse labelling experiment with 15N13C2-labelled glycine (amino acid) injected into the soil. In situ root nitrogen acquisition by grasses responded significantly to the climate change treatments...... the responses to single factors treatments. The soil microbes were superior to plants in the short-term competition for the added glycine, as indicated by an 18 times larger 15N recovery in the microbial biomass compared to the plant biomass. The soil microbes acquired glycine largely as an intact compound (87...

  11. Invited review: Microbe-mediated aflatoxin decontamination of dairy products and feeds.

    Science.gov (United States)

    Kim, Sejeong; Lee, Heeyoung; Lee, Soomin; Lee, Jeeyeon; Ha, Jimyeong; Choi, Yukyung; Yoon, Yohan; Choi, Kyoung-Hee

    2017-02-01

    Aspergillus flavus, Aspergillus parasiticus, and Aspergillus nomius contaminate corn, sorghum, rice, peanuts, tree nuts, figs, ginger, nutmeg, and milk. They produce aflatoxins, especially aflatoxin B1, which is classified as a Group 1 carcinogen by the International Agency for Research on Cancer. Many studies have focused on aflatoxin removal from food or feed, especially via microbe-mediated mechanisms-either adsorption or degradation. Of the lactic acid bacteria, Lactobacillus rhamnosus GG efficiently binds aflatoxin B1, and a peptidoglycan in the bacterium cell wall plays an important role. This ability of L. rhamnosus GG should be applied to the removal of aflatoxin B1. Aflatoxin can be removed using other aflatoxin-degrading microorganisms, including bacterial and fungal strains. This review explores microbe-associated aflatoxin decontamination, which may be used to produce aflatoxin-free food or feed. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. Electron and scanning probe microscopy study of S-layers of plague microbes

    Science.gov (United States)

    Konnov, Nikolai P.; Baiburin, Vil B.; Djatlov, Ivan A.; Antonova, Oksana A.; Volkov, Uryi P.

    1999-01-01

    Microscopy investigations of S-layers of plague microbes have been carried out. A protein forming S-layer was isolated, purified and its biochemical properties were studied. Images of plague cells with and without S-layer and images of isolated S-layer protein arrays on solid supports were obtained by transmission electron microscopy. An isolated protein forming the layer is self-assembled into crystalline structure with hexagonal pores are of regular size about 4 - 8 nm, which was observed by transmission electron micrographs. The STM images of plague microbes with S-layer and without one and the STM and AFM images of isolated S-layer protein arrays on mica surface were obtained.

  13. Towards a General Equation for the Survival of Microbes Transferred between Solar System Bodies

    Science.gov (United States)

    Fries, M.; Steele, A.

    2014-01-01

    It should be possible to construct a general equation describing the survival of microbes transferred between Solar System bodies. Such an equation will be useful for constraining the likelihood of transfer of viable organisms between bodies throughout the lifetime of the Solar System, and for refining Planetary Protection constraints placed on future missions. We will discuss the construction of such an equation, present a plan for definition of pertinent factors, and will describe what research will be necessary to quantify those factors. Description: We will examine the case of microbes transferred between Solar System bodies as residents in meteorite material ejected from one body (the "intial body") and deposited on another (the "target body"). Any microbes transferred in this fashion will experience four distinct phases between their initial state on the initial body, up to the point where they colonize the target body. Each of these phases features phenomena capable of reducing or exterminating the initial microbial population. They are: 1) Ejection: Material is ejected from the initial body, imparting shock followed by rapid desiccation and cooling. 2) Transport: Material travels through interplanetary space to the target body, exposing a hypothetical microbial population to extended desiccation, irradiation, and temperature extremes. 3) Infall: Material is deposited on the target body, diminishing the microbial population through shock, mass loss, and heating. 4) Adaptation: Any microbes which survive the previous three phases must then adapt to new chemophysical conditions of the target body. Differences in habitability between the initial and target bodies dominate this phase. A suitable general-form equation can be assembled from the above factors by defining the initial number of microbes in an ejected mass and applying multiplicitive factors based on the physical phenomena inherent to each phase. It should be possible to present the resulting equation

  14. Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry.

    Science.gov (United States)

    Stasulli, Nikolas M; Shank, Elizabeth A

    2016-09-02

    The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical 'maps' that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.

  15. Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease

    Science.gov (United States)

    Babickova, Janka; Gardlik, Roman

    2015-01-01

    The intestinal microbiome is a dynamic system of interactions between the host and its microbes. Under physiological conditions, a fine balance and mutually beneficial relationship is present. Disruption of this balance is a hallmark of inflammatory bowel disease (IBD). Whether an altered microbiome is the consequence or the cause of IBD is currently not fully understood. The pathogenesis of IBD is believed to be a complex interaction between genetic predisposition, the immune system and environmental factors. In the recent years, metagenomic studies of the human microbiome have provided useful data that are helping to assemble the IBD puzzle. In this review, we summarize and discuss current knowledge on the composition of the intestinal microbiota in IBD, host-microbe interactions and therapeutic possibilities using bacteria in IBD. Moreover, an outlook on the possible contribution of bacteriophages in the pathogenesis and therapy of IBD is provided. PMID:26525290

  16. Isolation of microbe for asymmetric reduction of prochiral aromatic ketone and its reaction characters

    Institute of Scientific and Technical Information of China (English)

    YANG Zhonghua; ZENG Rong; WANG Yu; WANG Guanghui; YAO Shanjing

    2007-01-01

    The favorable microbes for the asymmetric reduction of prochiral aromatic ketones was isolated from soil using acetophenone as the sole carbon source,when the asymmetric reduction of acetophenone (ACP) to chiral α-phenethyl alcohol (PEA) was chosen as the model reaction.Two microbe strains with excellent catalytic activity were obtained.They were Geotrichum candidum and Pichia pastoris identified by bacteria identification.The product of the asymmetric reduction of ACP catalyzed by Pichia pastoris was mainly R-PEA and that by Geotrichum candidum was mainly S-PEA.The yield and enantiomeric excesses (e.e.) could respectively reach 75% and 90% for Pichiapastoris,and 80% and 70% for Geotrichum candidum,much higher than those catalyzed by baker's yeast.

  17. Controls over nutrient flow through plants and microbes in Arctic tundra. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Schimel, J.

    1994-02-01

    Ecosystem productivity in the Arctic is strongly controlled by N availability to plants. Thus, disturbances to the Arctic system are likely to have their greatest impacts by altering the supply of nutrients to plants. Thus, to understand the dynamics of Arctic tundra, a complete understanding of the controls on N cycling in tundra soils is necessary. This project focused on understanding nutrient dynamics in arctic tussock tundra, specifically evaluating the role of microbial uptake and competition for nutrients as a control on plant N-uptake. The project consisted of several major components: Short- and long-term partitioning of NH{sub 4}{sup +} in tussock tundra (1990--1991); Measurement of NH{sub 4}{sup +} uptake rates by Eriophorum vaginatum and by soil microbes; Determination of microbial NH{sub 4}{sup +} and NO{sub 3}{minus} uptake kinetics; and Determination of the partitioning of NH{sub 4}{sup +} and amino acids between E. vaginatum and soil microbes.

  18. Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays

    Energy Technology Data Exchange (ETDEWEB)

    Frank F. Roberto

    2008-08-01

    Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

  19. Synthesis of Calcium Silicate (Casio3 Using Calcium Fluoride, Quartz and Microbes

    Directory of Open Access Journals (Sweden)

    B. Gopal Krishna

    2015-09-01

    Full Text Available Microbes like bacteria, algae, fungi and virus play an important role to catalyst chemical reactions. In Nature, ores or minerals of different compounds are formed due to microbial environment and other factors like weathering. Microbial environment is also instrumental in forming calcium containing silicate minerals. Chemical reactions occur under microbial environment because microbes have the ability to control or modify different factors like pH, chemical potential and temperature during reactions. In this paper, synthesis of calcium silicate (CaSiO3 using calcium fluoride (CaF2 and quartz (SiO2 under microbial environment in a laboratory is being adopted to produce the required material. XRD technique is used to confirm the formation of CaSiO3.

  20. Intake of fatty acids in Western Europe with emphasis on trans fatty acids: The TRANSFAIR study

    NARCIS (Netherlands)

    Hulshof, K.F.A.M; Erp van - Baart, M.A.; Anttolainen, M.; Becker, W.; Church, S.M.; Couet, C.; Hermann-Kunz, E.; Kesteloot, H.; Leth, T.; Martins, I.; Moreiras, O.; Moschandreas, J.; Pizzoferrato, L.; Rimestad, A.H.; Thorgeirsdottir, H.; Amelsvoort, J.M.M. van; Aro, A.; Kafatos, A.G.; Lanzmann-Petithory, D.; Poppel, G. van

    1999-01-01

    Objective: To assess the intake of trans fatty acids (TFA) and other fatty acids in 14 Western European countries. Design and subjects: A maximum of 100 foods per country were sampled and centrally analysed. Each country calculated the intake of individual trans and other fatty acids, clusters of fa

  1. Intake of fatty acids in Western Europe with emphasis on trans fatty acids: The TRANSFAIR study

    NARCIS (Netherlands)

    Hulshof, K.F.A.M; Erp van - Baart, M.A.; Anttolainen, M.; Becker, W.; Church, S.M.; Couet, C.; Hermann-Kunz, E.; Kesteloot, H.; Leth, T.; Martins, I.; Moreiras, O.; Moschandreas, J.; Pizzoferrato, L.; Rimestad, A.H.; Thorgeirsdottir, H.; Amelsvoort, J.M.M. van; Aro, A.; Kafatos, A.G.; Lanzmann-Petithory, D.; Poppel, G. van

    1999-01-01

    Objective: To assess the intake of trans fatty acids (TFA) and other fatty acids in 14 Western European countries. Design and subjects: A maximum of 100 foods per country were sampled and centrally analysed. Each country calculated the intake of individual trans and other fatty acids, clusters of

  2. Ultrasensitive bioluminescent determinations of adenosine triphosphate (ATP) for investigating the energetics of host-grown microbes

    Science.gov (United States)

    Hanks, J. H.; Dhople, A. M.

    1975-01-01

    Stability and optimal concentrations of reagents were studied in bioluminescence assay of ATP levels. Luciferase enzyme was prepared and purified using Sephadex G-100. Interdependencies between enzyme and luciferin concentrations in presence of optimal Mg are illustrated. Optimal ionic strength was confirmed to be 0.05 M for the four buffers tested. Adapted features of the R- and H-systems are summarized, as well as the percentages of ATP pools released from representative microbes by heat and chloroform.

  3. Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil

    Science.gov (United States)

    Luo, Jinming; Bai, Yaohui; Liang, Jinsong; Qu, Jiuhui

    2014-01-01

    Microbes have great potential for arsenic (As) and antimony (Sb) bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb) in a high As (range from 34.11 to 821.23 mg kg−1) and Sb (range from 226.67 to 3923.07 mg kg−1) contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA) of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3) were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R2 = 0.871) and aioA-like (R2 = 0.675) gene abundance and As concentration, and indicated that intracellular As(V) reduction and As(III) oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment. PMID:25299175

  4. NCBI - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...2 10.18908/lsdba.nbdc01181-009.V002 Update History V1 - Description of data contents The RDF data of several...ports in NCBI Assembly. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us NCBI - MicrobeDB.jp | LSDB Archive ...

  5. Ortholog - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ersion V2 10.18908/lsdba.nbdc01181-010.V002 Update History V1 - Description of data contents Microbial ortho...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...

  6. BRC - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...10.18908/lsdba.nbdc01181-001.V002 Update History V1 10.18908/lsdba.nbdc01181-001.V001 - Description of data ...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

  7. Peculiarities of microelemental homeostasis at microbal-inflammatory nephropathies in children

    Directory of Open Access Journals (Sweden)

    I. A. Melnikova

    2012-01-01

    Full Text Available The content of essential (Zn, Se, Cu and toxic (Pb, Cd microelements in blood serum and daily urine of 120 children from 3 to 15years old with microbal-inflammatory nephropathies was determined. The deficit of essential (Zn, Se, Cu and excess of toxic (Pb microelements in children with acute and chronic pyelonephritis at different periods of the disease were revealed.

  8. [Application of the BACspreader™ Microbe Dispersion Counter in drug susceptibility test on Mycobacterium tuberculosis].

    Science.gov (United States)

    Jiang, Y; Li, J; Zhang, Y Y; Wu, J; Wang, L L; Yu, C L; Shen, X; Zhu, G F

    2017-04-12

    Objective: To evaluate the application of the BACspreader™ Microbe Dispersion Counter in drug susceptibility test (DST) on Mycobacterium tuberculosis (MTB). Methods: The MTB strains were dispersed and diluted to 1.0 McFarland standard turbidity, by means of BACspreader™ Microbe Dispersion Counter and manual grinding method, respectively. The bacterial dispersion effect and bacterial activity were tested by microscope and colony counting method. During Jan. 2015 to June 2015, a total of 726 isolates of MTB were collected in all district tuberculosis hospitals of Shanghai. The bacterial suspension dispersed by instrument and manual grinding, were inoculated in slant medium for DST (Proportion Method), and then incubated in 37 ℃ incubator for 28 days and the DST results were reported. The effects of the 2 different bacterial dispersion methods were compared by comparing DST results and counting the bacterial colony which grew in high and low concentration control media. Paired chi-square test was used for statistical analysis, and the significance level was 0.05. Results: Compared to the manual grinding method, the MTB colony could be better dispersed by BACspreader™ Microbe Dispersion Counter, without reducing the bacterial activity. The DST results of 726 mycobacterial isolates were the same by different bacterial dispersion methods. The count of bacterial colony growing in high concentration control medium was significantly different between of the 2 dispersion methods (χ(2)=8.0, PDispersion Counter, and 4.3% by manual grinding method; the difference being significant between the 2 dispersion methods (χ(2)=674, PDispersion Counter had better countability in low concentration control slants, and had more significant contrast between high and low concentration control slants, which was useful to determine the DST results. Introducing the BACspreader™ Microbe Dispersion Counter to MTB DST could automate the DST process, make the testing results objective

  9. Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union.

    Science.gov (United States)

    Brodmann, Theodor; Endo, Akihito; Gueimonde, Miguel; Vinderola, Gabriel; Kneifel, Wolfgang; de Vos, Willem M; Salminen, Seppo; Gómez-Gallego, Carlos

    2017-01-01

    Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to improve health outcomes is of particular interest because growing evidence points to the importance of gut microbiota in human health. As well, some recently isolated microorganisms have promise for use as probiotics, although in-depth assessment of their safety is necessary. Recent examples of microorganisms calling for more detailed evaluation include Bacteroides xylanisolvens, Akkermansia muciniphila, fructophilic lactic acid bacteria (FLAB), and Faecalibacterium prausnitzii. This paper discusses each candidate's safety evaluation for novel food or novel food ingredient approval according to European Union (EU) regulations. The factors evaluated include their beneficial properties, antibiotic resistance profiling, history of safe use (if available), publication of the genomic sequence, toxicological studies in agreement with novel food regulations, and the qualified presumptions of safety. Sufficient evidences have made possible to support and authorize the use of heat-inactivated B. xylanisolvens in the European Union. In the case of A. muciniphila, the discussion focuses on earlier safety studies and the strain's suitability. FLAB are also subjected to standard safety assessments, which, along with their proximity to lactic acid bacteria generally considered to be safe, may lead to novel food authorization in the future. Further research with F. prausnitzii will increase knowledge about its safety and probiotic properties and may lead to its future use as novel food. Upcoming changes in EUU Regulation 2015/2283 on novel food will facilitate the authorization of future novel products and might increase the presence of novel microbes in the food market.

  10. Mechanism(s) of Electricity Production by Shewanella and other Microbes: Understanding and Optimization

    Science.gov (United States)

    2013-08-23

    Zhou. 2009. Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein...the activities of microbes acting as catalysts on the cathodes of MFC systems. During this time, we published over *** reviewed papers, presented...Production and Metal Oxide Reduction by Shewanella oneidensis MR-1 Wild Type and Mutants. Applied and Environmental Microbiology 73:7003-7012. 8. El

  11. Microbiology and Biodegradation: Deep Ultraviolet Microscopy for the Detection, Quantification, and Characterization of Microbes

    Science.gov (United States)

    2016-06-14

    possible. Since then the instrument development, spectroscopic theory /analysis, and scientific understanding have been supported by NASA, Army, DTRA...the use of the DUV spectral system to gain insights into the past cultivation history of microbes. In order to accomplish these goals, improvements...development, spectroscopic theory /analysis, and scientific understanding have been supported by NASA, Army, DTRA, Navy, etc. and led to instruments such as

  12. Mechanisms of Heavy Metal Sequestration in Soils: Plant-Microbe Interactions and Organic Matter Aging

    Energy Technology Data Exchange (ETDEWEB)

    Teresa W.-M. Fan; Richard M. Higashi; David Crowley; Andrew N. Lane: Teresa A. Cassel; Peter G. Green

    2004-12-31

    For stabilization of heavy metals at contaminated sites, the three way interaction among soil organic matter (OM)-microbes-plants, and their effect on heavy metal binding is critically important for long-term sustainability, a factor that is poorly understood at the molecular level. Using a soil aging system, the humification of plant matter such as wheat straw was probed along with the effect on microbial community on soil from the former McClellan Air Force Base.

  13. PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes.

    Directory of Open Access Journals (Sweden)

    Shaun W Lim

    Full Text Available Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS. This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.

  14. Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil.

    Science.gov (United States)

    Luo, Jinming; Bai, Yaohui; Liang, Jinsong; Qu, Jiuhui

    2014-01-01

    Microbes have great potential for arsenic (As) and antimony (Sb) bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb) in a high As (range from 34.11 to 821.23 mg kg-1) and Sb (range from 226.67 to 3923.07 mg kg-1) contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA) of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3) were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R2 = 0.871) and aioA-like (R2 = 0.675) gene abundance and As concentration, and indicated that intracellular As(V) reduction and As(III) oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment.

  15. Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union

    Directory of Open Access Journals (Sweden)

    Theodor Brodmann

    2017-09-01

    Full Text Available Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to improve health outcomes is of particular interest because growing evidence points to the importance of gut microbiota in human health. As well, some recently isolated microorganisms have promise for use as probiotics, although in-depth assessment of their safety is necessary. Recent examples of microorganisms calling for more detailed evaluation include Bacteroides xylanisolvens, Akkermansia muciniphila, fructophilic lactic acid bacteria (FLAB, and Faecalibacterium prausnitzii. This paper discusses each candidate's safety evaluation for novel food or novel food ingredient approval according to European Union (EU regulations. The factors evaluated include their beneficial properties, antibiotic resistance profiling, history of safe use (if available, publication of the genomic sequence, toxicological studies in agreement with novel food regulations, and the qualified presumptions of safety. Sufficient evidences have made possible to support and authorize the use of heat-inactivated B. xylanisolvens in the European Union. In the case of A. muciniphila, the discussion focuses on earlier safety studies and the strain's suitability. FLAB are also subjected to standard safety assessments, which, along with their proximity to lactic acid bacteria generally considered to be safe, may lead to novel food authorization in the future. Further research with F. prausnitzii will increase knowledge about its safety and probiotic properties and may lead to its future use as novel food. Upcoming changes in EUU Regulation 2015/2283 on novel food will facilitate the authorization of future novel products and might increase the presence of novel microbes in the food market.

  16. A Hair & a Fungus: Showing Kids the Size of a Microbe

    Science.gov (United States)

    Richter, Dana L.

    2013-01-01

    A simple method is presented to show kids the size of a microbe--a fungus hypha--compared to a human hair. Common household items are used to make sterile medium on a stove or hotplate, which is dispensed in the cells of a weekly plastic pill box. Mold fungi can be easily and safely grown on the medium from the classroom environment. A microscope…

  17. A Hair & a Fungus: Showing Kids the Size of a Microbe

    Science.gov (United States)

    Richter, Dana L.

    2013-01-01

    A simple method is presented to show kids the size of a microbe--a fungus hypha--compared to a human hair. Common household items are used to make sterile medium on a stove or hotplate, which is dispensed in the cells of a weekly plastic pill box. Mold fungi can be easily and safely grown on the medium from the classroom environment. A microscope…

  18. Fungal innate immunity induced by bacterial microbe-associated molecular patterns (MAMPs)

    DEFF Research Database (Denmark)

    Ip Cho, Simon; Sundelin, Thomas; Erbs, Gitte

    2016-01-01

    Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal-bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposing...... for further interactions with beneficial or pathogenic bacteria, and constitute a fungal innate immune response with similarities to those of plants and animals....

  19. Generation of reactive oxygen species by lethal attacks from competing microbes

    OpenAIRE

    Dong, Tao G.; Dong, Shiqi; Catalano, Christy; Moore, Richard; Liang, Xiaoye; Mekalanos, John J.

    2015-01-01

    How microbes respond to lethal attacks from competing species is not fully understood. Here, we investigated the response of Escherichia coli to attacks from the type VI secretion system (T6SS), bacteriophage P1vir, and polymyxin B. We report that generation of reactive oxygen species (ROS) is a general outcome of potentially lethal activities mediated by contact-dependent or contact-independent interactions of aggressive competing bacterial species and phage. An ROS response gene, soxS, is h...

  20. Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans.

    Science.gov (United States)

    Scott, Timothy A; Quintaneiro, Leonor M; Norvaisas, Povilas; Lui, Prudence P; Wilson, Matthew P; Leung, Kit-Yi; Herrera-Dominguez, Lucia; Sudiwala, Sonia; Pessia, Alberto; Clayton, Peter T; Bryson, Kevin; Velagapudi, Vidya; Mills, Philippa B; Typas, Athanasios; Greene, Nicholas D E; Cabreiro, Filipe

    2017-04-20

    Fluoropyrimidines are the first-line treatment for colorectal cancer, but their efficacy is highly variable between patients. We queried whether gut microbes, a known source of inter-individual variability, impacted drug efficacy. Combining two tractable genetic models, the bacterium E. coli and the nematode C. elegans, we performed three-way high-throughput screens that unraveled the complexity underlying host-microbe-drug interactions. We report that microbes can bolster or suppress the effects of fluoropyrimidines through metabolic drug interconversion involving bacterial vitamin B6, B9, and ribonucleotide metabolism. Also, disturbances in bacterial deoxynucleotide pools amplify 5-FU-induced autophagy and cell death in host cells, an effect regulated by the nucleoside diphosphate kinase ndk-1. Our data suggest a two-way bacterial mediation of fluoropyrimidine effects on host metabolism, which contributes to drug efficacy. These findings highlight the potential therapeutic power of manipulating intestinal microbiota to ensure host metabolic health and treat disease. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. Tiny Microbes, Big Yields: enhancing food crop production with biological solutions.

    Science.gov (United States)

    Trivedi, Pankaj; Schenk, Peer M; Wallenstein, Matthew D; Singh, Brajesh K

    2017-08-25

    Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microbial technology, their efficacy and consistency under the broad range of real-world conditions need to be improved. While the optimization of microbial biofertilizers and biopesticides is advancing rapidly to enable use in various soils, crop varieties and environments, crop breeding programmes have yet to incorporate the selection of beneficial plant-microbe interactions to breed 'microbe-optimized plants'. Emerging efforts exploring microbiome engineering could lead to microbial consortia that are better suited to support plants. The combination of all three approaches could be integrated to achieve maximum benefits and significantly improved crop yields to address food security. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  2. Effect of inoculating microbes in municipal solid waste composting on characteristics of humic acid.

    Science.gov (United States)

    Wei, Zimin; Xi, Beidou; Zhao, Yue; Wang, Shiping; Liu, Hongliang; Jiang, Youhai

    2007-06-01

    Municipal solid waste (MSW) compost contains a significant amount of humic substances. In this study, the compost consisted of residual MSW with the metal, plastic and glass removed. In order to enhance degradation processes and the degree of composting humification, complex microorganisms (Bacillus casei, Lactobacillus buchneri and Candida rugopelliculosa) and ligno-cellulolytic (Trichoderma and White-rot fungi) microorganisms were respectively inoculated in the composting process. During the MSW composting, humic acid (HA) was extracted and purified. Elements (C, N, H, O) and spectroscopic characteristics of the HA were determined using elementary analyzer, UV, Fourier transform infrared (FTIR), and fluorescence spectroscopy. The elements analysis, UV, FTIR and fluorescence spectra all led to the same conclusion, that is inoculations with microbes led to a greater degree of aromatization of HA than in the control process (CK) with no inoculation microbes. This indicated that inoculation with microbes in composting would improve the degree humification and maturation processes, in the following order: lingo-cellulolytic>complex microorganisms>CK. And mixed inoculation of MSW with complex microorganisms and lingo-cellulolytic during composting gave a greater degree of HA aromatization than inoculation with complex microorganisms or lingo-cellulolytic alone. But comparing with the HA of soil, the HA of MSW compost revealed a lower degree of aromatization.

  3. Enzymes from solvent-tolerant microbes: useful biocatalysts for non-aqueous enzymology.

    Science.gov (United States)

    Gupta, Anshu; Khare, S K

    2009-01-01

    Solvent-tolerant microbes are a newly emerging class that possesses the unique ability to thrive in the presence of organic solvents. Their enzymes adapted to mediate cellular and metabolic processes in a solvent-rich environment and are logically stable in the presence of organic solvents. Enzyme catalysis in non-aqueous/low-water media is finding increasing applications for the synthesis of industrially important products, namely peptides, esters, and other trans-esterification products. Solvent stability, however, remains a prerequisite for employing enzymes in non-aqueous systems. Enzymes, in general, get inactivated or give very low rates of reaction in non-aqueous media. Thus, early efforts, and even some recent ones, have aimed at stabilization of enzymes in organic media by immobilization, surface modifications, mutagenesis, and protein engineering. Enzymes from solvent-tolerant microbes appear to be the choicest source for studying solvent-stable enzymes because of their unique ability to survive in the presence of a range of organic solvents. These bacteria circumvent the solvent's toxic effects by virtue of various adaptations, e.g. at the level of the cytoplasmic membrane, by degradation and transformation of solvents, and by active excretion of solvents. The recent screening of these exotic microbes has generated some naturally solvent-stable proteases, lipases, cholesterol oxidase, cholesterol esterase, cyclodextrin glucanotransferase, and other important enzymes. The unique properties of these novel biocatalysts have great potential for applications in non-aqueous enzymology for a range of industrial processes.

  4. A simple separation method for downstream biochemical analysis of aquatic microbes.

    Science.gov (United States)

    Garrison, Cody E; Bochdansky, Alexander B

    2015-04-01

    In order to study the chemical composition of aquatic microbes it is necessary to obtain completely separated fractions of subpopulations. Size separation by filtration is usually unsuccessful because the smaller group of organisms contaminates the larger fractions due to being trapped on filter surfaces of nominally much larger pore sizes. Here we demonstrate that a simple sucrose density separation method allowed us to separate microorganisms of even subtle size differences and to determine their bulk biochemical composition (proteins, polysaccharides+nucleic acids, and lipids). Both autotrophs and heterotrophs (through anaplerotic pathways) were labeled with (14)C-bicarbonate for biochemical fractionation. We provided proof of concept that eukaryotic microbes could be cleanly separated from prokaryotes in cultures and in field samples, enabling detection of differences in their biochemical makeup. We explored methodological issues regarding separation mechanisms, fixation, and pre-concentration via tangential flow filtration of oligotrophic marine waters where abundances of microorganisms are comparably low. By selecting an appropriate centrifugal force, two processes (i.e., isopycnal and rate-zonal separation) can be exploited simultaneously resulting in finely-separated density fractions, which also resulted in size separation. Future applications of this method include exploration of the stoichiometric, biochemical and genetic differences among subpopulations of microbes in a wide variety of aquatic environments. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. [Effects of different organic fertilizers on the microbes in rhizospheric soil of flue-cured tobacco].

    Science.gov (United States)

    Zhang, Yun-Wei; Xu, Zhi; Tang, Li; Li, Yan-Hong; Song, Jian-Qun; Xu, Jian-Qin

    2013-09-01

    A field experiment was conducted to study the effects of applying different organic fertilizers (refined organic fertilizer and bio-organic fertilizer) and their combination with 20% reduced chemical fertilizers on the microbes in rhizospheric soil of flue-cured tobacco, the resistance of the tobacco against bacterial wilt, and the tobacco yield and quality. As compared with conventional chemical fertilization (CK), applying refined organic fertilizer (ROF) or bio-organic fertilizer (BIO) in combining with 20% reduced chemical fertilization increased the bacterial number and the total microbial number in the rhizospheric soil significantly. Applying BIO in combining with 20% reduced chemical fertilization also increased the actinomyces number in the rhizospheric soil significantly, with an increment of 44.3% as compared with that under the application of ROF in combining with 20% reduced chemical fertilization, but decreased the fungal number. As compared with CK, the ROF and BIO increased the carbon use capacity of rhizospheric microbes significantly, and the BIO also increased the capacity of rhizospheric microbes in using phenols significantly. Under the application of ROF and BIO, the disease incidence and the disease index of bacterial wilt were decreased by 4% and 8%, and 23% and 15.9%, and the proportions of high grade tobacco leaves increased significantly by 10.5% and 9.7%, respectively, as compared with those in CK. BIO increased the tobacco yield and its output value by 17.1% and 18.9% , respectively, as compared with ROF.

  6. The Effect of Antibacterial Formula Hand Cleaners on the Elimination of Microbes on Hands

    Science.gov (United States)

    Coleman, J. R.

    2002-05-01

    : The purpose of this project is to find out which one of the antibacterial hand cleanser (antibacterial bar soap, antibacterial liquid hand soap, and liquid hand sanitizer) is more effective in eliminating microbes. If antibacterial- formula liquid hand soap is used on soiled hands, then it will be more effective in eliminating microbes. Germs are microorganisms that cause disease and can spread from person-to-person. Bacteria are a kind of microbe, an example of which is Transient Flora that is often found on hands. Hand washing prevents germs from spreading to others. During the procedure, swabs were used to take samples before and after the soiled hands had been washed with one of the antibacterial hand cleansers. Nutrient Easygel was poured into petri dishes to harden for 1 day, and then samples were swabbed on the gel. The Petri dishes were placed in an incubator for 24 hours, and then data was recorded accordingly. The antibacterial liquid hand soap was sufficient in eliminating the majority of bacteria. The hands had 65% of the bacteria on them, and after the liquid hand soap was used only 37% of the bacteria remained.

  7. Some Case Studies on Metal-Microbe Interactions to Remediate Heavy Metals- Contaminated Soils in Korea

    Science.gov (United States)

    Chon, Hyo-Taek

    2015-04-01

    Conventional physicochemical technologies to remediate heavy metals-contaminated soil have many problems such as low efficiency, high cost and occurrence of byproducts. Recently bioremediation technology is getting more and more attention. Bioremediation is defined as the use of biological methods to remediate and/or restore the contaminated land. The objectives of bioremediation are to degrade hazardous organic contaminants and to convert hazardous inorganic contaminants to less toxic compounds of safe levels. The use of bioremediation in the treatment of heavy metals in soils is a relatively new concept. Bioremediation using microbes has been developed to remove toxic heavy metals from contaminated soils in laboratory scale to the contaminated field sites. Recently the application of cost-effective and environment-friendly bioremediation technology to the heavy metals-contaminated sites has been gradually realized in Korea. The merits of bioremediation include low cost, natural process, minimal exposure to the contaminants, and minimum amount of equipment. The limitations of bioremediation are length of remediation, long monitoring time, and, sometimes, toxicity of byproducts for especially organic contaminants. From now on, it is necessary to prove applicability of the technologies to contaminated sites and to establish highly effective, low-cost and easy bioremediation technology. Four categories of metal-microbe interactions are generally biosorption, bioreduction, biomineralization and bioleaching. In this paper, some case studies of the above metal-microbe interactions in author's lab which were published recently in domestic and international journals will be introduced and summarized.

  8. Microbe-aliphatic hydrocarbon interactions in soil: implications for biodegradation and bioremediation.

    Science.gov (United States)

    Stroud, J L; Paton, G I; Semple, K T

    2007-05-01

    Aliphatic hydrocarbons make up a substantial portion of organic contamination in the terrestrial environment. However, most studies have focussed on the fate and behaviour of aromatic contaminants in soil. Despite structural differences between aromatic and aliphatic hydrocarbons, both classes of contaminants are subject to physicochemical processes, which can affect the degree of loss, sequestration and interaction with soil microflora. Given the nature of hydrocarbon contamination of soils and the importance of bioremediation strategies, understanding the fate and behaviour of aliphatic hydrocarbons is imperative, particularly microbe-contaminant interactions. Biodegradation by microbes is the key removal process of hydrocarbons in soils, which is controlled by hydrocarbon physicochemistry, environmental conditions, bioavailability and the presence of catabolically active microbes. Therefore, the aims of this review are (i) to consider the physicochemical properties of aliphatic hydrocarbons and highlight mechanisms controlling their fate and behaviour in soil; (ii) to discuss the bioavailability and bioaccessibility of aliphatic hydrocarbons in soil, with particular attention being paid to biodegradation, and (iii) to briefly consider bioremediation techniques that may be applied to remove aliphatic hydrocarbons from soil.

  9. Effects of amoebae on the growth of microbes isolated from moisture-damaged buildings.

    Science.gov (United States)

    Yli-Pirilä, Terhi; Kusnetsov, Jaana; Hirvonen, Maija-Riitta; Seuri, Markku; Nevalainen, Aino

    2006-04-01

    Dampness, moisture, and mold in buildings are associated with adverse health outcomes. In addition to fungi and bacteria, amoebae have been found in moisture-damaged building materials. Amoebae and a growing list of bacteria have been shown to have mutual effects on each other's growth, but the interactions between amoebae and microbes common in moisture-damaged buildings have not been reported. We co-cultivated the amoeba Acanthamoeba polyphaga with bacteria and fungi isolated from moisture-damaged buildings in laboratory conditions for up to 28 days. The microbes selected were the bacteria Streptomyces californicus, Bacillus cereus, and Pseudomonas fluorescens, and the fungi Stachybotrys chartarum, Aspergillus versicolor, and Penicillium spinulosum. Fungi and bacteria generally benefited from the presence of the amoebae, whereas the growth of amoebae was hindered by Streptomyces californicus, Stachybotrys chartarum, and Bacillus cereus. Pseudomonas fluorescens slightly enhanced amoebae viability. Amoebae were indifferent to the presence of Aspergillus versicolor and Penicillium spinulosum. Thus, our results show that amoebae can alter the survival and growth of some microbes in moisture-damaged buildings.

  10. Biochemical and Molecular Mechanisms of Plant-Microbe-Metal Interactions: Relevance for Phytoremediation

    Science.gov (United States)

    Ma, Ying; Oliveira, Rui S.; Freitas, Helena; Zhang, Chang

    2016-01-01

    Plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. Plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. Some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (PGPMs), may alleviate metal phytotoxicity and stimulate plant growth indirectly via the induction of defense mechanisms against phytopathogens, and/or directly through the solubilization of mineral nutrients (nitrogen, phosphate, potassium, iron, etc.), production of plant growth promoting substances (e.g., phytohormones), and secretion of specific enzymes (e.g., 1-aminocyclopropane-1-carboxylate deaminase). PGPM can also change metal bioavailability in soil through various mechanisms such as acidification, precipitation, chelation, complexation, and redox reactions. This review presents the recent advances and applications made hitherto in understanding the biochemical and molecular mechanisms of plant–microbe interactions and their role in the major processes involved in phytoremediation, such as heavy metal detoxification, mobilization, immobilization, transformation, transport, and distribution. PMID:27446148

  11. Phylogenetic and functional diversity of nitrogen cycling microbes in coastal sediments

    Directory of Open Access Journals (Sweden)

    Xiaoli Zhang

    2013-07-01

    Full Text Available The coastal zone contains diverse habitats which are usually characterized by strong environmental gradients (e.g. salinity, nutrients and pollutants. This makes the coastal zone an ideal experimental laboratory for describing microbial diversity and testing hypotheses on community structure, function and control. Coastal sediment is of significance in nutrient regeneration and transformation involving different assemblages of microbes in the nitrogen cycle. This review focuses on 16S rRNA gene-based phylogenetic diversity and the key enzyme encoding gene-based (e.g. nifH, amoA, narG, nirS, nirK, nosZ, nrfA, hzo and hzs functional diversity of nitrogen fixing, ammonia oxidizing and anaerobic ammonia oxidation (Anammox bacteria as well as bacteria and fungi involved in denitrification and dissimilatory nitrate reduction to ammonium (DNRA. Characteristics of community composition and diversity of nitrogen cycling microbes in different habitats (e.g. estuarine, intertidal flats, seagrass or seaweed beds, mangroves, salt marsh, coral reefs, and shallow seas, and their spatiotemporal patterns under benthic pollution or bioturbation are reviewed. Future directions for a better understanding diversity of nitrogen cycling microbes are suggested, such as culture methods and technologies, and single-cell sequencing, etc.

  12. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast.

    Science.gov (United States)

    Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

    2011-08-30

    Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.

  13. Baseline survey of root-associated microbes of Taxus chinensis (Pilger Rehd.

    Directory of Open Access Journals (Sweden)

    Qian Zhang

    Full Text Available Taxol (paclitaxel a diterpenoid is one of the most effective anticancer drugs identified. Biosynthesis of taxol was considered restricted to the Taxus genera until Stierle et al. discovered that an endophytic fungus isolated from Taxus brevifolia could independently synthesize taxol. Little is known about the mechanism of taxol biosynthesis in microbes, but it has been speculated that its biosynthesis may differ from plants. The microbiome from the roots of Taxus chinensis have been extensively investigated with culture-dependent methods to identify taxol synthesizing microbes, but not using culture independent methods.,Using bar-coded high-throughput sequencing in combination with a metagenomics approach, we surveyed the microbial diversity and gene composition of the root-associated microbiomefrom Taxus chinensis (Pilger Rehd. High-throughput amplicon sequencing revealed 187 fungal OTUs which is higher than any previously reported fungal number identified with the culture-dependent method, suggesting that T. chinensis roots harbor novel and diverse fungi. Some operational taxonomic units (OTU identified were identical to reported microbe strains possessing the ability to synthesis taxol and several genes previously associated with taxol biosynthesis were identified through metagenomics analysis.

  14. Commensal Microbes and Hair Follicle Morphogenesis Coordinately Drive Treg Migration into Neonatal Skin.

    Science.gov (United States)

    Scharschmidt, Tiffany C; Vasquez, Kimberly S; Pauli, Mariela L; Leitner, Elizabeth G; Chu, Kevin; Truong, Hong-An; Lowe, Margaret M; Sanchez Rodriguez, Robert; Ali, Niwa; Laszik, Zoltan G; Sonnenburg, Justin L; Millar, Sarah E; Rosenblum, Michael D

    2017-04-12

    Regulatory T cells (Tregs) are required to establish immune tolerance to commensal microbes. Tregs accumulate abruptly in the skin during a defined window of postnatal tissue development. However, the mechanisms mediating Treg migration to neonatal skin are unknown. Here we show that hair follicle (HF) development facilitates the accumulation of Tregs in neonatal skin and that upon skin entry these cells localize to HFs, a primary reservoir for skin commensals. Further, germ-free neonates had reduced skin Tregs indicating that commensal microbes augment Treg accumulation. We identified Ccl20 as a HF-derived, microbiota-dependent chemokine and found its receptor, Ccr6, to be preferentially expressed by Tregs in neonatal skin. The Ccl20-Ccr6 pathway mediated Treg migration in vitro and in vivo. Thus, HF morphogenesis, commensal microbe colonization, and local chemokine production work in concert to recruit Tregs into neonatal skin, thereby establishing this tissue Treg niche early in life. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Microbes on-air: gut and tissue microbiota as targets in type 2 diabetes.

    Science.gov (United States)

    Serino, Matteo; Blasco-Baque, Vincent; Burcelin, Remy

    2012-10-01

    Each individual can be distinguished by the heterogeneity of the trillions of microbes inhabiting his gastrointestinal tract. This concept, together with the role that gut microbiota is considered to play in the induction of metabolic diseases, paves the way for the development of personalized medicine. By exploiting our unique animal model of metabolic adaptation to a high-fat diet, we have recently shown that differential gut microbiota lead to different metabolic phenotypes--metabotypes. Moreover, we have also reported that a given metabotype can be distinguished by different profiles of gut microbes, symptomatic of the complexity of the regulation of host physiology by gut microbiota. Furthermore, in an effort to find bacterial predictors of type 2 diabetes (T2D), we discovered that in a healthy population, subjects who subsequently developed T2D had increased blood levels of bacterial 16S rDNA well before. In addition, tissue (blood) microbiota, mainly characterized by Proteobacteria (up to 90%), has been discovered both in healthy individuals and in diabetic patients. Altogether, our results confirm the presence of gut microbes and propose tissue microbiota as new targets for the innovative treatment of T2D.

  16. How do natural, uncultivated microbes interact with organic matter? Insights from single cell genomics and metagenomics

    Science.gov (United States)

    Lloyd, K. G.; Bird, J.; Schreiber, L.; Petersen, D.; Kjeldsen, K.; Schramm, A.; Stepanauskas, R.; Jørgensen, B. B.

    2013-12-01

    Since most of the microbes in marine sediments remain uncultured, little is known about the mechanisms by which these natural communities degrade organic matter (OM). Likewise, little is known about the make-up of labile OM in marine sediments beyond general functional classes such as proteins, carbohydrates, and lipids, measured as monomers. However, microbes have complex interactions with specific polymers within these functional classes, which can be indicated by a microbe's enzymatic toolkit. We found that four single cell genomes of archaea have very different peptidase compositions than four single cells of bacteria, suggesting that archaea and bacteria may play different roles in OM degradation. We also found that predicted extracellular cysteine peptidases, which require chemically reducing conditions, were common in IMG database metagenomes from marine sediments, and absent in those from seawater. This suggests that the pathways, and not just the rates, of OM degradation may differ between seawater and sediments. By comparing enzyme classes in different organisms, or in different types of marine environments, we present an emerging view of the microbial potential for specific carbon remineralization pathways in marine sediments. In addition, the methods we present hold promise for characterizing OM degradation in any environment where genomic information is available.

  17. Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential.

    Science.gov (United States)

    Haldar, Shyamalina; Sengupta, Sanghamitra

    2015-01-01

    Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration.

  18. INTERACTIONS AMONG PHOSPHATE AMENDMENTS, MICROBES AND URANIUM MOBILITY IN CONTAMINATED SEDIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Knox, A

    2007-08-30

    The use of sequestering agents for the transformation of radionuclides in low concentrations in contaminated soils/sediments offers considerable potential for long-term environmental cleanup. This study evaluated the influence of four phosphate amendments and two microbial amendments on U availability. The synchrotron X-ray fluorescence mapping of the untreated U-contaminated sediment showed that U was closely associated with Mn. All tested phosphate amendments reduced aqueous U concentration more than 90%, likely due to formation of insoluble phosphate precipitates. The addition of A. piechaudii and P. putida alone were found to reduce U concentrations 63% and 31% respectively. Uranium sorption in phosphate treatments was significantly reduced in the presence of microbes. However, increased microbial activity in the treated sediment led to reduction of phosphate effectiveness. The average U concentration in 1 M MgCl{sub 2} extract from U amended sediment was 437 {micro}g/kg, but in the same sediment without microbes (autoclaved sediment), the extractable U concentration was only 103 {micro}g/kg. When the autoclaved amended sediment was treated with autoclaved biological apatite, U concentration in the 1 M MgCl{sub 2} extract was {approx}0 {micro}g/kg. Together these tests suggest that microbes may enhance U leaching and reduce phosphate amendment remedial effectiveness.

  19. Interactions among phosphate amendments, microbes and uranium mobility in contaminated sediments

    Energy Technology Data Exchange (ETDEWEB)

    Knox, Anna Sophia [Savannah River National Laboratory, Aiken, SC 29808 (United States)], E-mail: anna.knox@srnl.doe.gov; Brigmon, R.L.; Kaplan, D.I.; Paller, M.H. [Savannah River National Laboratory, Aiken, SC 29808 (United States)

    2008-06-01

    The use of sequestering agents for the transformation of radionuclides in low concentrations in contaminated soils/sediments offers considerable potential for environmental cleanup. This study evaluated the influence of three types of phosphate (rock phosphate, biological phosphate, and calcium phytate) and two microbial amendments (Alcaligenes piechaudii and Pseudomonas putida) on U mobility. All tested phosphate amendments reduced aqueous U concentrations more than 90%, likely due to formation of insoluble phosphate precipitates. The addition of A. piechaudii and P. putida alone were found to reduce U concentrations 63% and 31%, respectively. Uranium removal in phosphate treatments was significantly reduced in the presence of the two microbes. Two sediments were evaluated in experiments on the effects of phosphate amendments on U mobility, one from a stream on the Department of Energy's Savannah River Site near Aiken, SC and the other from the Hanford Site, a Department of Energy facility in Washington state. Increased microbial activity in the treated sediment led to a reduction in phosphate effectiveness. The average U concentration in 1 M MgCl{sub 2} extract from U contaminated sediment was 437 {mu}g/kg, but in the same sediment without microbes (autoclaved), the extractable U concentration was only 103 {mu}g/kg. The U concentration in the 1 M MgCl{sub 2} extract was {approx} 0 {mu}g/kg in autoclaved amended sediment treated with autoclaved biological apatite. These results suggest that microbes may reduce phosphate amendment remedial effectiveness.

  20. Effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus)

    Science.gov (United States)

    Jiang, Yan; Wang, Yingeng; Mai, Kangsen; Zhang, Zheng; Liao, Meijie; Rong, Xiaojun

    2015-10-01

    The effects of different microbes on fermenting feed for sea cucumber ( Apostichopus japonicus) were compared to select the optimal fermentation strain in this study. Saccharomgces cerevisae, Candida utilis, Bacillus subtilis and Geotrichum candidum were independently added into the experimental compound feed, while only saline was mixed with the control feed. The fermentation treatments were inoculated with 10% seed solution under the condition of 25°C and 70% water content, which lasted for 5 days to elucidate the optimal microbe strain for fermenting effect. Physicochemical indexes and sensorial characteristics were measured per day during the fermentation. The indexes included dry matter recovery (DMR), crude protein (CP), the percentage of amino acid nitrogen to total nitrogen (AA-N/tN), the percentage of ammonia nitrogen to total nitrogen (NH3-N/tN), and the ratio of fermentation strains and vibrios to the total microbes, color, smell and viscosity. The results showed that DMR, CP and AA-N/tN of the S. cerevisae group reached the highest level on day 3, but the ratio of fermentation strain was second to C. utilis group. In addition, its NH3-N/tN and the ratio of vibrios were maintained at low levels, and the sensory evaluation score including smell, color and viscosity was the highest in S. cerevisae group on day 3. Therefore, S. cerevisae could be the optimal strain for the feed fermentation for sea cucumber. This research developed a new production method of fermentation feed for sea cucumber.

  1. Microbial conversion of food wastes for biofertilizer production with thermophilic lipolytic microbes

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, Shu-Hsien; Yang, Shang-Shyng [Institute of Microbiology and Biochemistry, National Taiwan University, Taipei 10617, (Taiwan); Liu, Ching-Piao [Department of Biological Science and Technology, Meiho Institute of Technology, Pingtung 91201, (Taiwan)

    2007-05-15

    Food waste is approximately one quarter of the total garbage in Taiwan. To investigate the feasibility of microbial conversion of food waste to multiple functional biofertilizer, food waste was mixed with bulking materials, inoculated with thermophilic and lipolytic microbes and incubated at 50{sup o}C in a mechanical composter. Microbial inoculation enhanced the degradation of food wastes, increased the total nitrogen and the germination rate of alfalfa seed, shortened the maturity period and improved the quality of biofertilizer. In food waste inoculated with thermophilic and lipolytic Brevibacillus borstelensis SH168 for 28 days, total nitrogen increased from 2.01% to 2.10%, ash increased from 24.94% to 29.21%, crude fat decreased from 4.88% to 1.34% and the C/N ratio decreased from 18.02 to 17.65. Each gram of final product had a higher population of thermophilic microbes than mesophilic microbes. Microbial conversion of food waste to biofertilizer is a feasible and potential technology in the future to maintain the natural resources and to reduce the impact on environmental quality. (author)

  2. Changes of cellular fatty acids of soil Actinobacteria producing antibiotics

    OpenAIRE

    LIPENSKÁ, Ivana

    2010-01-01

    Changes of cellular fatty acids in membrane of Actinobacteria. Changes of fatty acids are significant biomarkers of changing conditions of surroundings. This can also indicate production of antibiotics along with production of atypical fatty acids.

  3. Nitrogen uptake during one year in subarctic plant functional groups and in microbes after long-term warming and fertilization

    DEFF Research Database (Denmark)

    Sørensen, Pernille Lærkedal; Michelsen, Anders; Jonasson, Sven Evert

    2008-01-01

    For the first time in an arctic long-term warming and fertilization experiment, the short-term (days) and longer-term (month and year) nitrogen (N) uptake and allocation in plants, microbes, and soil pools were studied, with 15N-labeling of an organic nitrogen form, glycine. The long-term warming...... and fertilization had no marked effect on soil inorganic N content, but both dissolved organic N (DON) and plant biomass did increase after fertilization. Soil microbes initially immobilized most of the added 15N, but in the following months, they lost two-thirds, while label concentration in plants increased....... After a year, however, the 15N recovered in microbes was still 10-fold higher than that in the plant biomass, showing the high importance of soil microbes in nutrient retention in arctic ecosystems, irrespective of the impact of long-term warming or fertilization. The effects of the treatments...

  4. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

    Science.gov (United States)

    Meena, Kamlesh K.; Sorty, Ajay M.; Bitla, Utkarsh M.; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P.; Prabha, Ratna; Sahu, Pramod K.; Gupta, Vijai K.; Singh, Harikesh B.; Krishanani, Kishor K.; Minhas, Paramjit S.

    2017-01-01

    Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding

  5. Plants + soil/wetland microbes: Food crop systems that also clean air and water

    Science.gov (United States)

    Nelson, Mark; Wolverton, B. C.

    2011-02-01

    The limitations that will govern bioregenerative life support applications in space, especially volume and weight, make multi-purpose systems advantageous. This paper outlines two systems which utilize plants and associated microbial communities of root or growth medium to both produce food crops and clean air and water. Underlying these approaches are the large numbers and metabolic diversity of microbes associated with roots and found in either soil or other suitable growth media. Biogeochemical cycles have microbial links and the ability of microbes to metabolize virtually all trace gases, whether of technogenic or biogenic origin, has long been established. Wetland plants and the rootzone microbes of wetland soils/media also been extensively researched for their ability to purify wastewaters of a great number of potential water pollutants, from nutrients like N and P, to heavy metals and a range of complex industrial pollutants. There is a growing body of research on the ability of higher plants to purify air and water. Associated benefits of these approaches is that by utilizing natural ecological processes, the cleansing of air and water can be done with little or no energy inputs. Soil and rootzone microorganisms respond to changing pollutant types by an increase of the types of organisms with the capacity to use these compounds. Thus living systems have an adaptive capacity as long as the starting populations are sufficiently diverse. Tightly sealed environments, from office buildings to spacecraft, can have hundreds or even thousands of potential air pollutants, depending on the materials and equipment enclosed. Human waste products carry a plethora of microbes which are readily used in the process of converting its organic load to forms that can be utilized by green plants. Having endogenous means of responding to changing air and water quality conditions represents safety factors as these systems operate without the need for human intervention. We review

  6. Divergent utilization patterns of grass fructan, inulin, and other nonfiber carbohydrates by ruminal microbes.

    Science.gov (United States)

    Hall, M B; Weimer, P J

    2016-01-01

    Fructans are an important nonfiber carbohydrate in cool season grasses. Their fermentation by ruminal microbes is not well described, though such information is needed to understand their nutritional value to ruminants. Our objective was to compare kinetics and product formation of orchardgrass fructan (phlein; PHL) to other nonfiber carbohydrates when fermented in vitro with mixed or pure culture ruminal microbes. Studies were carried out as randomized complete block designs. All rates given are first-order rate constants. With mixed ruminal microbes, rate of substrate disappearance tended to be greater for glucose (GLC) than for PHL and chicory fructan (inulin; INU), which tended to differ from each other (0.74, 0.62, and 0.33 h(-1), respectively). Disappearance of GLC had almost no lag time (0.04 h), whereas the fructans had lags of 1.4h. The maximum microbial N accumulation, a proxy for cell growth, tended to be 20% greater for PHL and INU than for GLC. The N accumulation rate for GLC (1.31h(-1)) was greater than for PHL (0.75 h(-1)) and INU (0.26 h(-1)), which also differed. More microbial glycogen (+57%) was accumulated from GLC than from PHL, though accumulation rates did not differ (1.95 and 1.44 h(-1), respectively); little glycogen accumulated from INU. Rates of organic acid formation were 0.80, 0.28, and 0.80 h(-1) for GLC, INU, and PHL, respectively, with PHL tending to be greater than INU. Lactic acid production was more than 7-fold greater for GLC than for the fructans. The ratio of microbial cell carbon to organic acid carbon tended to be greater for PHL (0.90) and INU (0.86) than for GLC (0.69), indicating a greater yield of cell mass per amount of substrate fermented with fructans. Reduced microbial yield for GLC may relate to the greater glycogen production that requires ATP, and lactate production that yields less ATP; together, these processes could have reduced ATP available for cell growth. Acetate molar proportion was less for GLC than for

  7. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.

    Science.gov (United States)

    Meena, Kamlesh K; Sorty, Ajay M; Bitla, Utkarsh M; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P; Prabha, Ratna; Sahu, Pramod K; Gupta, Vijai K; Singh, Harikesh B; Krishanani, Kishor K; Minhas, Paramjit S

    2017-01-01

    Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding

  8. Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Costliow, Zachary A; Degnan, Patrick H

    2017-01-01

    Thiamine (vitamin B1) is an essential cofactor for all organisms. Humans primarily acquire thiamine through their diet, and thiamine deficiencies have adverse neurological effects. However, the role gut microbes play in modulating thiamine availability is poorly understood, and little is known about how thiamine impacts the stability of microbial gut communities. To investigate thiamine's role in the gut, we utilized the model gut microbe Bacteroides thetaiotaomicron. Transcriptome sequencing (RNA-seq) revealed a global downregulation of thiamine and amino acid biosynthesis, glycolysis, and purine metabolism when thiamine was present. Using genetic mutants with thiamine biosynthesis and transport locus mutations, we determined both systems were critical for growth in thiamine-deficient medium. The defect in the double transport mutant suggests an uncharacterized feedback mechanism between thiamine transport and biosynthesis in B. thetaiotaomicron. Mutant phenotypes were recapitulated during pairwise competitions, reinforcing the importance of encoding versatile thiamine acquisition mechanisms when thiamine concentrations are variable. In addition, liquid chromatography-mass spectrometry (LC-MS) analyses corroborate that exogenous thiamine levels affect the internal thiamine pool of B. thetaiotaomicron. Furthermore, we computationally examined the ability of other gut microbes to acquire thiamine and identified lineage-specific differences in thiamine acquisition strategies. Among the Bacteroidetes, the capacities for both thiamine transport and biosynthesis are common. Together, these data show that thiamine acquisition mechanisms used by B. thetaiotaomicron not only are critical for its physiology and fitness but also provide the opportunity to model how other gut microbes may respond to the shifting availability of thiamine in the gut. IMPORTANCE Variation in the ability of gut microbes to transport, synthesize, and compete for vitamin B1 (thiamine) is

  9. Study of Thiosemicarbazone Derivative of Essential Fatty Acid

    OpenAIRE

    2014-01-01

    Essential fatty acids results in numerous health benefits. Only two fatty acids are known to be essential for human alpha-linolenic acid (an omega-3 fatty acid) and linoleic acid (an omega-6 fatty acid).The importance of omega-3 fatty acids for physical well-being has been recognised for several decades . Omega-3 fatty acids have anti-inflammatory, antithrombotic, antiarrhythmic and hypolipidaemic effects. Cannabis sativa (Hemp) is an angiosperm belonging to the cannabaceae family and cannabi...

  10. CKD and nonalcoholic fatty liver disease.

    Science.gov (United States)

    Targher, Giovanni; Chonchol, Michel B; Byrne, Christopher D

    2014-10-01

    The possible link between nonalcoholic fatty liver disease and chronic kidney disease (CKD) recently has attracted considerable scientific interest. Accumulating clinical evidence indicates that the presence and severity of nonalcoholic fatty liver disease is associated significantly with CKD (defined as decreased estimated glomerular filtration rate and/or proteinuria) and that nonalcoholic fatty liver disease predicts the development and progression of CKD, independently of traditional cardiorenal risk factors. Experimental evidence also suggests that nonalcoholic fatty liver disease itself may exacerbate systemic and hepatic insulin resistance, cause atherogenic dyslipidemia, and release a variety of proinflammatory, procoagulant, pro-oxidant, and profibrogenic mediators that play important roles in the development and progression of CKD. However, despite the growing evidence linking nonalcoholic fatty liver disease with CKD, it has not been definitively established whether a causal association exists. The clinical implication for these findings is that patients with nonalcoholic fatty liver disease may benefit from more intensive surveillance or early treatment interventions to decrease the risk of CKD. In this review, we discuss the evidence linking nonalcoholic fatty liver disease with CKD and the putative mechanisms by which nonalcoholic fatty liver disease contributes to kidney damage. We also briefly discuss current treatment options for this increasingly prevalent disease that is likely to have an important future impact on the global burden of disease.

  11. Phylogenomic reconstruction of archaeal fatty acid metabolism

    Science.gov (United States)

    Dibrova, Daria V.; Galperin, Michael Y.; Mulkidjanian, Armen Y.

    2014-01-01

    While certain archaea appear to synthesize and/or metabolize fatty acids, the respective pathways still remain obscure. By analyzing the genomic distribution of the key lipid-related enzymes, we were able to identify the likely components of the archaeal pathway of fatty acid metabolism, namely, a combination of the enzymes of bacterial-type β-oxidation of fatty acids (acyl-CoA-dehydrogenase, enoyl-CoA hydratase, and 3-hydroxyacyl-CoA dehydrogenase) with paralogs of the archaeal acetyl-CoA C-acetyltransferase, an enzyme of the mevalonate biosynthesis pathway. These three β-oxidation enzymes working in the reverse direction could potentially catalyze biosynthesis of fatty acids, with paralogs of acetyl-CoA C-acetyltransferase performing addition of C2 fragments. The presence in archaea of the genes for energy-transducing membrane enzyme complexes, such as cytochrome bc complex, cytochrome c oxidase, and diverse rhodopsins, was found to correlate with the presence of the proposed system of fatty acid biosynthesis. We speculate that because these membrane complexes functionally depend on fatty acid chains, their genes could have been acquired via lateral gene transfer from bacteria only by those archaea that already possessed a system of fatty acid biosynthesis. The proposed pathway of archaeal fatty acid metabolism operates in extreme conditions and therefore might be of interest in the context of biofuel production and other industrial applications. PMID:24818264

  12. Polyunsaturated fatty acids for multiple sclerosis treatment

    Directory of Open Access Journals (Sweden)

    Monserrat Kong-González

    2015-01-01

    Full Text Available INTRODUCTION Fatty acids have an important role in structure and function of the nervous system. Recently, epidemiologic studies on neurodegenerative disorders have evaluated the usefulness of polyunsaturated fatty acids on multiple sclerosis. OBJECTIVE To examine recent studies, clinical trials, and reviews on the therapeutic effect of polyunsaturated fatty acids in multiple sclerosis. METHODS We conducted a search in MEDLINE/PubMed and Cochrane Library with the terms "fatty acids", "omega-3" and "omega-6" in combination with "multiple sclerosis". Articles were selected according to their relevance on the topic. RESULTS Epidemiologic studies have shown benefits of dietary supplementation with polyunsaturated fatty acids -especially omega-3- in relation to inflammatory, autoimmune and neurodegenerative disorders. In contrast, the studies do not show a beneficial effect of polyunsaturated fatty acids in multiple sclerosis. However, there are limitations related to design and sample issues in these studies CONCLUSIONS There is some evidence of a protective effect of polyunsaturated fatty acids on the risk of multiple sclerosis. Despite this, to date controlled trials have not produced definite results on the benefits of supplementation with polyunsaturated fatty acids in patients with multiple sclerosis. Any potential benefit will have to be confirmed in the long term.

  13. Effect of fatty acids on leukocyte function

    Directory of Open Access Journals (Sweden)

    Pompéia C.

    2000-01-01

    Full Text Available Fatty acids have various effects on immune and inflammatory responses, acting as intracellular and intercellular mediators. Polyunsaturated fatty acids (PUFAs of the omega-3 family have overall suppressive effects, inhibiting lymphocyte proliferation, antibody and cytokine production, adhesion molecule expression, natural killer cell activity and triggering cell death. The omega-6 PUFAs have both inhibitory and stimulatory effects. The most studied of these is arachidonic acid that can be oxidized to eicosanoids, such as prostaglandins, leukotrienes and thromboxanes, all of which are potent mediators of inflammation. Nevertheless, it has been found that many of the effects of PUFA on immune and inflammatory responses are not dependent on eicosanoid generation. Fatty acids have also been found to modulate phagocytosis, reactive oxygen species production, cytokine production and leukocyte migration, also interfering with antigen presentation by macrophages. The importance of fatty acids in immune function has been corroborated by many clinical trials in which patients show improvement when submitted to fatty acid supplementation. Several mechanisms have been proposed to explain fatty acid modulation of immune response, such as changes in membrane fluidity and signal transduction pathways, regulation of gene transcription, protein acylation, and calcium release. In this review, evidence is presented to support the proposition that changes in cell metabolism also play an important role in the effect of fatty acids on leukocyte functioning, as fatty acids regulate glucose and glutamine metabolism and mitochondrial depolarization.

  14. Dioxygenation of polyunsaturated fatty acids in fungi

    NARCIS (Netherlands)

    Wadman, M.W.

    2007-01-01

    Polyunsaturated fatty acids play a central role in all biological systems. They are constituents of the plasma membrane and serve as precursors to signaling molecules generated in response to external events. The conversion of polyunsaturated fatty acids into signaling molecules starts by the hydrol

  15. Nickel inhibits mitochondrial fatty acid oxidation.

    Science.gov (United States)

    Uppala, Radha; McKinney, Richard W; Brant, Kelly A; Fabisiak, James P; Goetzman, Eric S

    2015-08-07

    Nickel exposure is associated with changes in cellular energy metabolism which may contribute to its carcinogenic properties. Here, we demonstrate that nickel strongly represses mitochondrial fatty acid oxidation-the pathway by which fatty acids are catabolized for energy-in both primary human lung fibroblasts and mouse embryonic fibroblasts. At the concentrations used, nickel suppresses fatty acid oxidation without globally suppressing mitochondrial function as evidenced by increased glucose oxidation to CO2. Pre-treatment with l-carnitine, previously shown to prevent nickel-induced mitochondrial dysfunction in neuroblastoma cells, did not prevent the inhibition of fatty acid oxidation. The effect of nickel on fatty acid oxidation occurred only with prolonged exposure (>5 h), suggesting that direct inhibition of the active sites of metabolic enzymes is not the mechanism of action. Nickel is a known hypoxia-mimetic that activates hypoxia inducible factor-1α (HIF1α). Nickel-induced inhibition of fatty acid oxidation was blunted in HIF1α knockout fibroblasts, implicating HIF1α as one contributor to the mechanism. Additionally, nickel down-regulated the protein levels of the key fatty acid oxidation enzyme very long-chain acyl-CoA dehydrogenase (VLCAD) in a dose-dependent fashion. In conclusion, inhibition of fatty acid oxidation by nickel, concurrent with increased glucose metabolism, represents a form of metabolic reprogramming that may contribute to nickel-induced carcinogenesis.

  16. Historical perspectives on fatty acid chemistry

    Science.gov (United States)

    Fatty acids are basic renewable chemical building blocks that can be used as intermediates for a multitude of products. Today the global value of fatty acids exceeds 18 billion dollars and is expected to increase to nearly 26 billion over the period from 2014-2019. From it auspicious beginnings, the...

  17. Mechanisms of gene regulation by fatty acids

    NARCIS (Netherlands)

    Georgiadi, A.; Kersten, A.H.

    2012-01-01

    Consumption of specific dietary fatty acids has been shown to influence risk and progression of several chronic diseases, such as cardiovascular disease, obesity, cancer, and arthritis. In recent years, insights into the mechanisms underlying the biological effects of fatty acids have improved consi

  18. Incorporation of extracellular fatty acids by a fatty acid kinase-dependent pathway in Staphylococcus aureus.

    Science.gov (United States)

    Parsons, Joshua B; Frank, Matthew W; Jackson, Pamela; Subramanian, Chitra; Rock, Charles O

    2014-04-01

    Acyl-CoA and acyl-acyl carrier protein (ACP) synthetases activate exogenous fatty acids for incorporation into phospholipids in Gram-negative bacteria. However, Gram-positive bacteria utilize an acyltransferase pathway for the biogenesis of phosphatidic acid that begins with the acylation of sn-glycerol-3-phosphate by PlsY using an acyl-phosphate (acyl-PO4 ) intermediate. PlsX generates acyl-PO4 from the acyl-ACP end-products of fatty acid synthesis. The plsX gene of Staphylococcus aureus was inactivated and the resulting strain was both a fatty acid auxotroph and required de novo fatty acid synthesis for growth. Exogenous fatty acids were only incorporated into the 1-position and endogenous acyl groups were channeled into the 2-position of the phospholipids in strain PDJ39 (ΔplsX). Extracellular fatty acids were not elongated. Removal of the exogenous fatty acid supplement led to the rapid accumulation of intracellular acyl-ACP and the abrupt cessation of fatty acid synthesis. Extracts from the ΔplsX strain exhibited an ATP-dependent fatty acid kinase activity, and the acyl-PO4 was converted to acyl-ACP when purified PlsX is added. These data reveal the existence of a novel fatty acid kinase pathway for the incorporation of exogenous fatty acids into S. aureus phospholipids.

  19. Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Teixeira, Paulo Goncalves; Ferreira, Raphael; Zhou, Yongjin J.

    2017-01-01

    faa4 Delta strain constitutively expressing a carboxylic acid reductase from Mycobacterium marinum (MmCAR) and an endogenous alcohol dehydrogenase (Adh5) for in vivo production of fatty alcohols from FFAs. We observed production of fatty acids and fatty alcohols with different rates leading to high...... loss of precursors that compromises the process yield. In the present study, we aimed for dynamic expression of the fatty acyl-CoA synthetase gene FAA1 to regulate FFA and acyl-CoA pools in order to improve fatty alcohol production yields. Results: We analyzed the metabolite dynamics of a faa1 Delta...... levels of FFAs not being converted to the final product. To address the issue, we expressed the MmCAR + Adh5 pathway together with a fatty acyl-CoA reductase from Marinobacter aquaeolei to enable fatty alcohol production simultaneously from FFA and acyl-CoA, respectively. Then, we expressed FAA1 under...

  20. Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that 'everything is not everywhere'.

    Science.gov (United States)

    Rout, Marnie E; Callaway, Ragan M

    2012-07-01

    The study of soil biota in the context of exotic plant invasions has led to an explosion in our understanding of the ecological roles of many different groups of microbes that function in roots or at the root-soil interface. Part of this progress has been the emergence of two biogeographic patterns involving invasive plants and soil microbes. First, in their non-native ranges invasive plants commonly interact differently with the same soil microbes than native plants. Second, in their native ranges, plants that are invasive elsewhere commonly interact functionally with soil microbes differently in their home ranges than they do in their non-native ranges. These studies pose a challenge to a long-held paradigm about microbial biogeography - the idea that microbes are not limited by dispersal and are thus free from the basic taxonomic, biogeographical and evolutionary framework that characterizes all other life on Earth. As an analogy, the global distribution of animals that function as carnivores does not negate the fascinating evolutionary biogeographic patterns of carnivores. Other challenges to this notion come from new measurements of genetic differences among microbes across geographic boundaries, which also suggest that meaningful biogeographic patterns exist for microorganisms. We expand this discussion of whether or not 'everything is everywhere' by using the inherently biogeographic context of plant invasions by reviewing the literature on interactions among invasive plants and the microorganisms in the rhizosphere. We find that these interactions can be delineated at multiple scales: from individual plants to continents. Thus the microbes that regulate major aspects of plant biology do not appear to be exempt from the fundamental evolutionary processes of geographical isolation and natural selection. At the important scales of taxonomy, ecotype and ecosystem functions, the fundamental ecology of invaders and soil microbes indicates that everything might