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Sample records for addition microbial pathways

  1. Septic tank additive impacts on microbial populations.

    PubMed

    Pradhan, S; Hoover, M T; Clark, G H; Gumpertz, M; Wollum, A G; Cobb, C; Strock, J

    2008-01-01

    Environmental health specialists, other onsite wastewater professionals, scientists, and homeowners have questioned the effectiveness of septic tank additives. This paper describes an independent, third-party, field scale, research study of the effects of three liquid bacterial septic tank additives and a control (no additive) on septic tank microbial populations. Microbial populations were measured quarterly in a field study for 12 months in 48 full-size, functioning septic tanks. Bacterial populations in the 48 septic tanks were statistically analyzed with a mixed linear model. Additive effects were assessed for three septic tank maintenance levels (low, intermediate, and high). Dunnett's t-test for tank bacteria (alpha = .05) indicated that none of the treatments were significantly different, overall, from the control at the statistical level tested. In addition, the additives had no significant effects on septic tank bacterial populations at any of the septic tank maintenance levels. Additional controlled, field-based research iswarranted, however, to address additional additives and experimental conditions.

  2. Microbial biosurfactants as additives for food industries.

    PubMed

    Campos, Jenyffer Medeiros; Stamford, Tânia Lúcia Montenegro; Sarubbo, Leonie Asfora; de Luna, Juliana Moura; Rufino, Raquel Diniz; Banat, Ibrahim M

    2013-01-01

    Microbial biosurfactants with high ability to reduce surface and interfacial surface tension and conferring important properties such as emulsification, detergency, solubilization, lubrication and phase dispersion have a wide range of potential applications in many industries. Significant interest in these compounds has been demonstrated by environmental, bioremediation, oil, petroleum, food, beverage, cosmetic and pharmaceutical industries attracted by their low toxicity, biodegradability and sustainable production technologies. Despite having significant potentials associated with emulsion formation, stabilization, antiadhesive and antimicrobial activities, significantly less output and applications have been reported in food industry. This has been exacerbated by uneconomical or uncompetitive costing issues for their production when compared to plant or chemical counterparts. In this review, biosurfactants properties, present uses and potential future applications as food additives acting as thickening, emulsifying, dispersing or stabilising agents in addition to the use of sustainable economic processes utilising agro-industrial wastes as alternative substrates for their production are discussed.

  3. Rust preventive oil additives based on microbial fats

    SciTech Connect

    Salenko, V.I.; Fedorov, V.V.; Kazantsev, Yu.E.

    1983-03-01

    This article investigates the composition and lubricating properties of microbial fats obtained from microorganisms grown on various hydrocarbon substrates (n-paraffins, alcohols, natural gas, petroleum distillates, etc.). Focuses on the protective functions of the 4 main fractions (unsaponifiables, free fatty acids, glycerides, and phospholipids) which comprise the microbial fat from a yeast grown on purified liquid n-paraffins. Concludes that neutralized microbial fats can be used as preservative additives; that the principal components of the microbial fats have the properties necessary for oil-soluble corrosion inhibitors; that the phospholipids of the microbial fat can fulfill the functions of not only preservative additives, but also highly effective operational/ preservative additives; and that fats of microbial origin can be used in the development of multipurpose polyfunctional additives.

  4. Nutrient Addition Dramatically Accelerates Microbial Community Succession

    PubMed Central

    Knelman, Joseph E.; Schmidt, Steven K.; Lynch, Ryan C.; Darcy, John L.; Castle, Sarah C.; Cleveland, Cory C.; Nemergut, Diana R.

    2014-01-01

    The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients – important drivers of plant succession – affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession. PMID:25050551

  5. Biochar addition impacts soil microbial community in tropical soils

    NASA Astrophysics Data System (ADS)

    Paz-Ferreiro, Jorge; Fu, Shenglei; Méndez, Ana; Gascó, Gabriel

    2014-05-01

    Studies on the effect of biochar on soil microbial activity and community structure in tropical areas are scarce. In this study we report the effect of several types of biochar (sewage sludge biochar, paper mill waste biochar, miscanthus biochar and pinewood biochar) in the soil microbial community of two tropical soils, an Acrisol and an Oxisol. In addition we study the effect of the presence or absence of earthworms in soil microbial community. Soil microbial community was more strongly affected by biochar than by the presence or absence of macrofauna.

  6. Expanding the product profile of a microbial alkane biosynthetic pathway.

    PubMed

    Harger, Matthew; Zheng, Lei; Moon, Austin; Ager, Casey; An, Ju Hye; Choe, Chris; Lai, Yi-Ling; Mo, Benjamin; Zong, David; Smith, Matthew D; Egbert, Robert G; Mills, Jeremy H; Baker, David; Pultz, Ingrid Swanson; Siegel, Justin B

    2013-01-18

    Microbially produced alkanes are a new class of biofuels that closely match the chemical composition of petroleum-based fuels. Alkanes can be generated from the fatty acid biosynthetic pathway by the reduction of acyl-ACPs followed by decarbonylation of the resulting aldehydes. A current limitation of this pathway is the restricted product profile, which consists of n-alkanes of 13, 15, and 17 carbons in length. To expand the product profile, we incorporated a new part, FabH2 from Bacillus subtilis , an enzyme known to have a broader specificity profile for fatty acid initiation than the native FabH of Escherichia coli . When provided with the appropriate substrate, the addition of FabH2 resulted in an altered alkane product profile in which significant levels of n-alkanes of 14 and 16 carbons in length are produced. The production of even chain length alkanes represents initial steps toward the expansion of this recently discovered microbial alkane production pathway to synthesize complex fuels. This work was conceived and performed as part of the 2011 University of Washington international Genetically Engineered Machines (iGEM) project.

  7. Pathways of microbial metabolism of parathion.

    PubMed

    Munnecke, D M; Hsieh, D P

    1976-01-01

    A mixed bacterial culture, consisting of a minimum of nine isolates, was adapted to growth on technical parathion (PAR) as a sole carbon and energy source. The primary oxidative pathway for PAR metabolism involved an initial hydrolysis to yield diethylthiophosphoric acid and p-nitrophenol. A secondary oxidative pathway involved the oxidation of PAR to paraoxon and then hydrolysis to yield p-nitrophenol and diethylphosphoric acid. Under low oxgen conditions PAR was reduced via a third pathway to p-aminoparathion and subsequently hydrolyzed to p-aminophenol and diethylthiophosphoric acid. PAR hydrolase, an enzyme produced by an isolate from the mixed culture, rapidly hydrolyzed PAR and paraoxon (6.0 mumol/mg per min). This enzyme was inducible and stable at room temperature and retained 100% of its activity when heated for 55 C for 10 min.

  8. Microbial Community Responses to Glycine Addition in Kansas Prairie Soils

    NASA Astrophysics Data System (ADS)

    Bottos, E.; Roy Chowdhury, T.; White, R. A., III; Brislawn, C.; Fansler, S.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.

    2015-12-01

    Advances in sequencing technologies are rapidly expanding our abilities to unravel aspects of microbial community structure and function in complex systems like soil; however, characterizing the highly diverse communities is problematic, due primarily to challenges in data analysis. To tackle this problem, we aimed to constrain the microbial diversity in a soil by enriching for particular functional groups within a community through addition of "trigger substrates". Such trigger substrates, characterized by low molecular weight, readily soluble and diffusible in soil solution, representative of soil organic matter derivatives, would also be rapidly degradable. A relatively small energy investment to maintain the cell in a state of metabolic alertness for such substrates would be a better evolutionary strategy and presumably select for a cohort of microorganisms with the energetics and cellular machinery for utilization and growth. We chose glycine, a free amino acid (AA) known to have short turnover times (in the range of hours) in soil. As such, AAs are a good source of nitrogen and easily degradable, and can serve as building blocks for microbial proteins and other biomass components. We hypothesized that the addition of glycine as a trigger substrate will decrease microbial diversity and evenness, as taxa capable of metabolizing it are enriched in relation to those that are not. We tested this hypothesis by incubating three Kansas native prairie soils with glycine for 24 hours at 21 degree Celsius, and measured community level responses by 16S rRNA gene sequencing, metagenomics, and metatranscriptomics. Preliminary evaluation of 16S rRNA gene sequences revealed minor changes in bacterial community composition in response to glycine addition. We will also present data on functional gene abundance and expression. The results of these analyses will be useful in designing sequencing strategies aimed at dissecting and deciphering complex microbial communities.

  9. A Microbial Feed Additive Abates Intestinal Inflammation in Atlantic Salmon

    PubMed Central

    Vasanth, Ghana; Kiron, Viswanath; Kulkarni, Amod; Dahle, Dalia; Lokesh, Jep; Kitani, Yoichiro

    2015-01-01

    The efficacy of a microbial feed additive (Bactocell®) in countering intestinal inflammation in Atlantic salmon was examined in this study. Fish were fed either the additive-coated feed (probiotic) or feed without it (control). After an initial 3-week feeding, an inflammatory condition was induced by anally intubating all the fish with oxazolone. The fish were offered the feeds for 3 more weeks. Distal intestine from the groups was obtained at 4 h, 24 h, and 3 weeks, after oxazolone treatment. Inflammatory responses were prominent in both groups at 24 h, documented by changes in intestinal micromorphology, expression of inflammation-related genes, and intestinal proteome. The control group was characterized by edema, widening of intestinal villi and lamina propria, infiltration of granulocytes and lymphocytes, and higher expression of genes related to inflammatory responses, mul1b, il1b, tnfa, ifng, compared to the probiotic group or other time points of the control group. Further, the protein expression in the probiotic group at 24 h after inducing inflammation revealed five differentially regulated proteins – Calr, Psma5, Trp1, Ctsb, and Naga. At 3 weeks after intubation, the inflammatory responses subsided in the probiotic group. The findings provide evidence that the microbial additive contributes to intestinal homeostasis in Atlantic salmon. PMID:26347738

  10. Kinetic analysis of microbial respiratory response to substrate addition

    NASA Astrophysics Data System (ADS)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Yuyukina, Tatayna; Kuzyakov, Yakov

    2010-05-01

    Heterotrophic component of CO2 emitted from soil is mainly due to the respiratory activity of soil microorganisms. Field measurements of microbial respiration can be used for estimation of C-budget in soil, while laboratory estimation of respiration kinetics allows the elucidation of mechanisms of soil C sequestration. Physiological approaches based on 1) time-dependent or 2) substrate-dependent respiratory response of soil microorganisms decomposing the organic substrates allow to relate the functional properties of soil microbial community with decomposition rates of soil organic matter. We used a novel methodology combining (i) microbial growth kinetics and (ii) enzymes affinity to the substrate to show the shift in functional properties of the soil microbial community after amendments with substrates of contrasting availability. We combined the application of 14C labeled glucose as easily available C source to soil with natural isotope labeling of old and young soil SOM. The possible contribution of two processes: isotopic fractionation and preferential substrate utilization to the shifts in δ13C during SOM decomposition in soil after C3-C4 vegetation change was evaluated. Specific growth rate (µ) of soil microorganisms was estimated by fitting the parameters of the equation v(t) = A + B * exp(µ*t), to the measured CO2 evolution rate (v(t)) after glucose addition, and where A is the initial rate of non-growth respiration, B - initial rate of the growing fraction of total respiration. Maximal mineralization rate (Vmax), substrate affinity of microbial enzymes (Ks) and substrate availability (Sn) were determined by Michaelis-Menten kinetics. To study the effect of plant originated C on δ13C signature of SOM we compared the changes in isotopic composition of different C pools in C3 soil under grassland with C3-C4 soil where C4 plant Miscanthus giganteus was grown for 12 years on the plot after grassland. The shift in 13δ C caused by planting of M. giganteus

  11. Soil microbial responses to nitrogen addition in arid ecosystems

    SciTech Connect

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-08-14

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. With most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration

  12. Soil microbial responses to nitrogen addition in arid ecosystems

    DOE PAGES

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-08-14

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces betweenmore » plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. With most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. The large effect sizes at low N

  13. Soil microbial responses to nitrogen addition in arid ecosystems.

    PubMed

    Sinsabaugh, Robert L; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R; Martinez, Noelle; Sandquist, Darren

    2015-01-01

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha(-1) y(-1) from March 2012 to March 2013. In March 2013, biocrust (0-0.5 cm) and bulk soils (0-10 cm) were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. By most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha(-1) y(-1) and 159 kg ha(-1), respectively, for biomass, and 70 kg ha(-1) y(-1) and 114 kg ha(-1), respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. However, large effect sizes at low N

  14. Soil microbial responses to nitrogen addition in arid ecosystems

    PubMed Central

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-01-01

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. By most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. However, large effect sizes at low N addition

  15. Dispersed oil disrupts microbial pathways in pelagic food webs.

    PubMed

    Ortmann, Alice C; Anders, Jennifer; Shelton, Naomi; Gong, Limin; Moss, Anthony G; Condon, Robert H

    2012-01-01

    Most of the studies of microbial processes in response to the Deepwater Horizon oil spill focused on the deep water plume, and not on the surface communities. The effects of the crude oil and the application of dispersants on the coastal microbial food web in the northern Gulf of Mexico have not been well characterized even though these regions support much of the fisheries production in the Gulf. A mesocosm experiment was carried out to determine how the microbial community off the coast of Alabama may have responded to the influx of surface oil and dispersants. While the addition of glucose or oil alone resulted in an increase in the biomass of ciliates, suggesting transfer of carbon to higher trophic levels was likely; a different effect was seen in the presence of dispersant. The addition of dispersant or dispersed oil resulted in an increase in the biomass of heterotrophic prokaryotes, but a significant inhibition of ciliates, suggesting a reduction in grazing and decrease in transfer of carbon to higher trophic levels. Similar patterns were observed in two separate experiments with different starting nutrient regimes and microbial communities suggesting that the addition of dispersant and dispersed oil to the northern Gulf of Mexico waters in 2010 may have reduced the flow of carbon to higher trophic levels, leading to a decrease in the production of zooplankton and fish on the Alabama shelf. PMID:22860136

  16. Dispersed oil disrupts microbial pathways in pelagic food webs.

    PubMed

    Ortmann, Alice C; Anders, Jennifer; Shelton, Naomi; Gong, Limin; Moss, Anthony G; Condon, Robert H

    2012-01-01

    Most of the studies of microbial processes in response to the Deepwater Horizon oil spill focused on the deep water plume, and not on the surface communities. The effects of the crude oil and the application of dispersants on the coastal microbial food web in the northern Gulf of Mexico have not been well characterized even though these regions support much of the fisheries production in the Gulf. A mesocosm experiment was carried out to determine how the microbial community off the coast of Alabama may have responded to the influx of surface oil and dispersants. While the addition of glucose or oil alone resulted in an increase in the biomass of ciliates, suggesting transfer of carbon to higher trophic levels was likely; a different effect was seen in the presence of dispersant. The addition of dispersant or dispersed oil resulted in an increase in the biomass of heterotrophic prokaryotes, but a significant inhibition of ciliates, suggesting a reduction in grazing and decrease in transfer of carbon to higher trophic levels. Similar patterns were observed in two separate experiments with different starting nutrient regimes and microbial communities suggesting that the addition of dispersant and dispersed oil to the northern Gulf of Mexico waters in 2010 may have reduced the flow of carbon to higher trophic levels, leading to a decrease in the production of zooplankton and fish on the Alabama shelf.

  17. Dispersed Oil Disrupts Microbial Pathways in Pelagic Food Webs

    PubMed Central

    Ortmann, Alice C.; Anders, Jennifer; Shelton, Naomi; Gong, Limin; Moss, Anthony G.; Condon, Robert H.

    2012-01-01

    Most of the studies of microbial processes in response to the Deepwater Horizon oil spill focused on the deep water plume, and not on the surface communities. The effects of the crude oil and the application of dispersants on the coastal microbial food web in the northern Gulf of Mexico have not been well characterized even though these regions support much of the fisheries production in the Gulf. A mesocosm experiment was carried out to determine how the microbial community off the coast of Alabama may have responded to the influx of surface oil and dispersants. While the addition of glucose or oil alone resulted in an increase in the biomass of ciliates, suggesting transfer of carbon to higher trophic levels was likely; a different effect was seen in the presence of dispersant. The addition of dispersant or dispersed oil resulted in an increase in the biomass of heterotrophic prokaryotes, but a significant inhibition of ciliates, suggesting a reduction in grazing and decrease in transfer of carbon to higher trophic levels. Similar patterns were observed in two separate experiments with different starting nutrient regimes and microbial communities suggesting that the addition of dispersant and dispersed oil to the northern Gulf of Mexico waters in 2010 may have reduced the flow of carbon to higher trophic levels, leading to a decrease in the production of zooplankton and fish on the Alabama shelf. PMID:22860136

  18. Soil microbial responses to forest floor litter manipulation and nitrogen addition in a mixed-wood forest of northern China

    PubMed Central

    Sun, Xiao-Lu; Zhao, Jing; You, Ye-Ming; Jianxin Sun, Osbert

    2016-01-01

    Changes in litterfall dynamics and soil properties due to anthropogenic or natural perturbations have important implications to soil carbon (C) and nutrient cycling via microbial pathway. Here we determine soil microbial responses to contrasting types of litter inputs (leaf vs. fine woody litter) and nitrogen (N) deposition by conducting a multi-year litter manipulation and N addition experiment in a mixed-wood forest. We found significantly higher soil organic C, total N, microbial biomass C (MBC) and N (MBN), microbial activity (MR), and activities of four soil extracellular enzymes, including β-glucosidase (BG), N-acetyl-β-glucosaminidase (NAG), phenol oxidase (PO), and peroxidase (PER), as well as greater total bacteria biomass and relative abundance of gram-negative bacteria (G-) community, in top soils of plots with presence of leaf litter than of those without litter or with presence of only fine woody litter. No apparent additive or interactive effects of N addition were observed in this study. The occurrence of more labile leaf litter stimulated G-, which may facilitate microbial community growth and soil C stabilization as inferred by findings in literature. A continued treatment with contrasting types of litter inputs is likely to result in divergence in soil microbial community structure and function. PMID:26762490

  19. Microbial chemical factories: recent advances in pathway engineering for synthesis of value added chemicals.

    PubMed

    Dhamankar, Himanshu; Prather, Kristala L J

    2011-08-01

    The dwindling nature of petroleum and other fossil reserves has provided impetus towards microbial synthesis of fuels and value added chemicals from biomass-derived sugars as a renewable resource. Microbes have naturally evolved enzymes and pathways that can convert biomass into hundreds of unique chemical structures, a property that can be effectively exploited for their engineering into Microbial Chemical Factories (MCFs). De novo pathway engineering facilitates expansion of the repertoire of microbially synthesized compounds beyond natural products. In this review, we visit some recent successes in such novel pathway engineering and optimization, with particular emphasis on the selection and engineering of pathway enzymes and balancing of their accessory cofactors.

  20. Stimulation of methane generation from nonproductive coal by addition of nutrients or a microbial consortium

    USGS Publications Warehouse

    Jones, Elizabeth J.P.; Voytek, Mary A.; Corum, Margo D.; Orem, William H.

    2010-01-01

    Biogenic formation of methane from coal is of great interest as an underexploited source of clean energy. The goal of some coal bed producers is to extend coal bed methane productivity and to utilize hydrocarbon wastes such as coal slurry to generate new methane. However, the process and factors controlling the process, and thus ways to stimulate it, are poorly understood. Subbituminous coal from a nonproductive well in south Texas was stimulated to produce methane in microcosms when the native population was supplemented with nutrients (biostimulation) or when nutrients and a consortium of bacteria and methanogens enriched from wetland sediment were added (bioaugmentation). The native population enriched by nutrient addition included Pseudomonas spp., Veillonellaceae, and Methanosarcina barkeri. The bioaugmented microcosm generated methane more rapidly and to a higher concentration than the biostimulated microcosm. Dissolved organics, including long-chain fatty acids, single-ring aromatics, and long-chain alkanes accumulated in the first 39 days of the bioaugmented microcosm and were then degraded, accompanied by generation of methane. The bioaugmented microcosm was dominated by Geobacter sp., and most of the methane generation was associated with growth of Methanosaeta concilii. The ability of the bioaugmentation culture to produce methane from coal intermediates was confirmed in incubations of culture with representative organic compounds. This study indicates that methane production could be stimulated at the nonproductive field site and that low microbial biomass may be limiting in situ methane generation. In addition, the microcosm study suggests that the pathway for generating methane from coal involves complex microbial partnerships.

  1. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

    SciTech Connect

    Cusack, Daniela F.; Silver, Whendee; Torn, Margaret S.; Burton, Sarah D.; Firestone, Mary

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

  2. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

    PubMed

    Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

  3. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

    PubMed

    Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types. PMID:21608471

  4. Stimulation of Methane Generation from Nonproductive Coal by Addition of Nutrients or a Microbial Consortium▿

    PubMed Central

    Jones, Elizabeth J. P.; Voytek, Mary A.; Corum, Margo D.; Orem, William H.

    2010-01-01

    Biogenic formation of methane from coal is of great interest as an underexploited source of clean energy. The goal of some coal bed producers is to extend coal bed methane productivity and to utilize hydrocarbon wastes such as coal slurry to generate new methane. However, the process and factors controlling the process, and thus ways to stimulate it, are poorly understood. Subbituminous coal from a nonproductive well in south Texas was stimulated to produce methane in microcosms when the native population was supplemented with nutrients (biostimulation) or when nutrients and a consortium of bacteria and methanogens enriched from wetland sediment were added (bioaugmentation). The native population enriched by nutrient addition included Pseudomonas spp., Veillonellaceae, and Methanosarcina barkeri. The bioaugmented microcosm generated methane more rapidly and to a higher concentration than the biostimulated microcosm. Dissolved organics, including long-chain fatty acids, single-ring aromatics, and long-chain alkanes accumulated in the first 39 days of the bioaugmented microcosm and were then degraded, accompanied by generation of methane. The bioaugmented microcosm was dominated by Geobacter sp., and most of the methane generation was associated with growth of Methanosaeta concilii. The ability of the bioaugmentation culture to produce methane from coal intermediates was confirmed in incubations of culture with representative organic compounds. This study indicates that methane production could be stimulated at the nonproductive field site and that low microbial biomass may be limiting in situ methane generation. In addition, the microcosm study suggests that the pathway for generating methane from coal involves complex microbial partnerships. PMID:20817801

  5. Final report - Microbial pathways for the reduction of mercury in saturated subsurface sediments

    SciTech Connect

    Tamar barkay; Lily Young; Gerben Zylstra

    2009-08-25

    Mercury is a component of mixed wastes that have contaminated vast areas of the deep subsurface as a result of nuclear weapon and energy production. While this mercury is mostly bound to soil constituents episodes of groundwater contamination are known in some cases resulting in potable water super saturated with Hg(0). Microbial processes that reduce Hg(II) to the elemental form Hg(0) in the saturated subsurface sediments may contribute to this problem. When we started the project, only one microbial pathway for the reduction of Hg(II), the one mediated by the mer operon in mercury resistant bacteria was known. As we had previously demonstrated that the mer mediated process occurred in highly contaminated environments (Schaefer et al., 2004), and mercury concentrations in the subsurface were reported to be low (Krabbenhoft and Babiarz, 1992), we hypothesized that other microbial processes might be active in reducing Hg(II) to Hg(0) in saturated subsurface environments. The specific goals of our projects were: (1) Investigating the potential for Hg(II) reduction under varying electron accepting conditions in subsurface sediments and relating these potential to mer gene distribution; and (2) Examining the physiological and biochemical characteristics of the interactions of anaerobic bacteria with mercury. The results are briefly summarized with references to published papers and manuscripts in preparation where details about our research can be found. Additional information may be found in copies of our published manuscripts and conference proceedings, and our yearly reports that were submitted through the RIMS system.

  6. Engineering and comparison of non-natural pathways for microbial phenol production.

    PubMed

    Thompson, Brian; Machas, Michael; Nielsen, David R

    2016-08-01

    The non-renewable petrochemical phenol is used as a precursor to produce numerous fine and commodity chemicals, including various pharmaceuticals and phenolic resins. Microbial phenol biosynthesis has previously been established, stemming from endogenous tyrosine via tyrosine phenol lyase (TPL). TPL, however, suffers from feedback inhibition and equilibrium limitations, both of which contribute to reduced flux through the overall pathway. To address these limitations, two novel and non-natural phenol biosynthesis pathways, both stemming instead from chorismate, were constructed and comparatively evaluated. The first proceeds to phenol in one heterologous step via the intermediate p-hydroxybenzoic acid, while the second involves two heterologous steps and the associated intermediates isochorismate and salicylate. Maximum phenol titers achieved via these two alternative pathways reached as high as 377 ± 14 and 259 ± 31 mg/L in batch shake flask cultures, respectively. In contrast, under analogous conditions, phenol production via the established TPL-dependent route reached 377 ± 23 mg/L, which approaches the maximum achievable output reported to date under batch conditions. Additional strain development and optimization of relevant culture conditions with respect to each individual pathway is ultimately expected to result in further improved phenol production. Biotechnol. Bioeng. 2016;113: 1745-1754. © 2016 Wiley Periodicals, Inc. PMID:26804162

  7. Using Stable Isotopes to Trace Microbial Hydrogen Production Pathways

    NASA Astrophysics Data System (ADS)

    Moran, J.; Hill, E.; Bartholomew, R.; Yang, H.; Shi, L.; Ostrom, N. E.; Gandhi, H.; Hegg, E.; Kreuzer, H.

    2010-12-01

    Biological H2 production by hydrogenase enzymes (H2ases) plays an important role in anaerobic microbial metabolism and community structure. Despite considerable progress in elucidating H2 metabolism, the regulation of and flux through key H2 production pathways remain largely undefined. Our goal is to improve understanding of biological H2 production by using H isotope ratios to dissect proton fluxes through different H2ase enzymes and from different substrates. We hypothesized that the isotope ratio of H2 produced by various hydrogenases (H2ase) would differ, and that the H isotope ratios would allow us to define the contribution of different enzymes when more than one is present in vivo. We chose Shewanella oneidensis (S.o.) MR-1, a facultative anaerobe capable of transferring electrons to a variety of terminal acceptors, including protons, as a model system for in vivo studies. S. o. encodes one [FeFe]- and one [NiFe]-H2ase. We purified three [FeFe]-H2ases (S.o., Clostridium pasteurianum, and Chlamydomonas reinhardtii) and two [NiFe]-H2ases (S. o. and Desulfovibrio fructosovorans) to test the isotope fractionation associated with activity by each enzyme in vitro. For in vivo analysis we used wild-type S.o. as well as electron transfer-deficient and H2ase-deficient strains. We employed batch cultures using lactate as an electron donor and O2 as an initial electron acceptor (with H2 production after O2 consumption). The five H2ases we tested all had a unique isotope fractionation. Measurements of H2 produced in vivo showed distinct periods of H2 production having isotope signatures consistent with in vitro results. Isotope data as well as studies of H2 production by mutants in the genes encoding either the [NiFe]-H2ase or the [FeFe]-H2ase, respectively, show that the [NiFe]- and [FeFe]- H2ases became active at different times. The [NiFe]-H2ase both produces and consumes H2 before the [FeFe]-H2ase becomes active. RNA analysis is consistent with up regulation of

  8. Effects of biological pit additives on microbial ecology of stored pig manure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of biological pit additives on microbial ecology in stored pig manure were investigated using a dynamic manure storage system, which allowed for continual addition of swine feces and urine. After 13 weeks of manure collection and storage, four treatments were added to tanks (900 L capaci...

  9. Phosphate addition and plant species alters microbial community structure in acidic upland grassland soil.

    PubMed

    Rooney, Deirdre C; Clipson, Nicholas J W

    2009-01-01

    Agricultural improvement (addition of fertilizers, liming) of seminatural acidic grasslands across Ireland and the UK has resulted in significant shifts in floristic composition, soil chemistry, and microbial community structure. Although several factors have been proposed as responsible for driving shifts in microbial communities, the exact causes of such changes are not well defined. Phosphate was added to grassland microcosms to investigate the effect on fungal and bacterial communities. Plant species typical of unimproved grasslands (Agrostis capillaris, Festuca ovina) and agriculturally improved grasslands (Lolium perenne) were grown, and phosphate was added 25 days after seed germination, with harvesting after a further 50 days. Phosphate addition significantly increased root biomass (p < 0.001) and shoot biomass (p < 0.05), soil pH (by 0.1 U), and microbial activity (by 5.33 mg triphenylformazan [TPF] g(-1) soil; p < 0.001). A slight decrease (by 0.257 mg biomass-C g(-1) soil; p < 0.05) in microbial biomass after phosphate addition was found. The presence of plant species significantly decreased soil pH (p < 0.05; by up to 0.2 U) and increased microbial activity (by up to 6.02 mg TPF g(-1) soil) but had no significant effect on microbial biomass. Microbial communities were profiled using automated ribosomal intergenic spacer analysis. Multidimensional scaling plots and canonical correspondence analysis revealed that phosphate addition and its interactions with upland grassland plant species resulted in considerable changes in the fungal and bacterial communities of upland soil. The fungal community structure was significantly affected by both phosphate (R = 0.948) and plant species (R = 0.857), and the bacterial community structure was also significantly affected by phosphate (R = 0.758) and plant species (R = 0.753). Differences in microbial community structure following P addition were also revealed by similarity percentage analysis. These data suggest

  10. Microbial oils as food additives: recent approaches for improving microbial oil production and its polyunsaturated fatty acid content.

    PubMed

    Bellou, Stamatia; Triantaphyllidou, Irene-Eva; Aggeli, Dimitra; Elazzazy, Ahmed Mohammed; Baeshen, Mohammed Nabih; Aggelis, George

    2016-02-01

    In this short review, we summarize the latest research in the production of polyunsaturated microbial oils that are of interest in food technology. The current research targets the productivity of oleaginous microorganisms, as well as the biosynthesis of particular polyunsaturated fatty acids (PUFAs). The most important efforts target the efficiency of the oleaginous machinery, via overexpression of key-enzymes involved in lipid biosynthesis, as well as the minimization of lipid degradation, by repressing genes involved in the β-oxidation pathway. The production of specific PUFAs is approached by homologous or heterologous expression of specific desaturases and elongases involved in PUFA biosynthesis in oleaginous microorganisms. New perspectives, such as the production of triacylglycerols of specific structure and the employment of adaptive experimental evolution for creating robust oleaginous strains able to produce PUFAs are also discussed.

  11. Pathway engineering strategies for production of beneficial carotenoids in microbial hosts.

    PubMed

    Ye, Victor M; Bhatia, Sujata K

    2012-08-01

    Carotenoids, such as lycopene, β-carotene, zeaxanthin, canthaxanthin and astaxanthin have many benefits for human health. In addition to the functional role of carotenoids as vitamin A precursors, adequate consumption of carotenoids prevents the development of a variety of serious diseases. Biosynthesis of carotenoids is a complex process and it starts with the common isoprene precursors. Condensation of these precursors and subsequent modifications, by introducing hydroxyl- and keto-groups, leads to the generation of diversified carotenoid structures. To improve carotenoid production, metabolic engineering has been explored in bacteria, yeast, and algae. The success of the pathway engineering effort depends on the host metabolism, specific enzymes used, the enzyme expression levels, and the strategies employed. Despite the difficulty of pathway engineering for carotenoid production, great progress has been made over the past decade. We review metabolic engineering approaches used in a variety of microbial hosts for carotenoid biosynthesis. These advances will greatly expedite our efforts to bring the health benefits of carotenoids and other nutritional compounds to our diet. PMID:22488437

  12. Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis

    PubMed Central

    Xia, Yu; Wang, Yubo; Fang, Herbert H. P.; Jin, Tao; Zhong, Huanzi; Zhang, Tong

    2014-01-01

    The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified. The novel information obtained herein revealed interesting patterns and provides an initial transcriptional insight into the thermophilic cellulose methanization process. Synergistic beta-sugar consumption by Thermotogales is crucial for cellulose hydrolysis in the thermophilic cellulose-degrading consortium because the primary cellulose degraders Clostridiales showed metabolic incompetence in subsequent beta-sugar pathways. Additionally, comparable transcription of putative Sus-like polysaccharide utilization loci (PULs) was observed in an unclassified order of Bacteroidetes suggesting the importance of PULs mechanism for polysaccharides breakdown in thermophilic systems. Despite the abundance of acetate as a fermentation product, the acetate-utilizing Methanosarcinales were less prevalent by 60% than the hydrogenotrophic Methanobacteriales. Whereas the aceticlastic methanogenesis pathway was markedly more active in terms of transcriptional activities in key genes, indicating that the less dominant Methanosarcinales are more active than their hydrogenotrophic counterparts in methane metabolism. These findings suggest that the minority of aceticlastic methanogens are not necessarily associated with repressed metabolism, in a pattern that was commonly observed in the cellulose-based methanization consortium, and thus challenge the causal likelihood proposed by previous studies. PMID:25330991

  13. RESPONSE OF SOIL MICROBIAL BIOMASS AND COMMUNITY COMPOSITION TO CHRONIC NITROGEN ADDITIONS AT HARVARD FOREST

    EPA Science Inventory

    Soil microbial communities may respond to anthropogenic increases in ecosystem nitrogen (N) availability, and their response may ultimately feedback on ecosystem carbon and N dynamics. We examined the long-term effects of chronic N additions on soil microbes by measuring soil mi...

  14. Thermodynamic network model for predicting effects of substrate addition and other perturbations on subsurface microbial communities

    SciTech Connect

    Jack Istok; Melora Park; James McKinley; Chongxuan Liu; Lee Krumholz; Anne Spain; Aaron Peacock; Brett Baldwin

    2007-04-19

    The overall goal of this project is to develop and test a thermodynamic network model for predicting the effects of substrate additions and environmental perturbations on microbial growth, community composition and system geochemistry. The hypothesis is that a thermodynamic analysis of the energy-yielding growth reactions performed by defined groups of microorganisms can be used to make quantitative and testable predictions of the change in microbial community composition that will occur when a substrate is added to the subsurface or when environmental conditions change.

  15. Substrates and pathway of electricity generation in a nitrification-based microbial fuel cell.

    PubMed

    Chen, Hui; Zheng, Ping; Zhang, Jiqiang; Xie, Zuofu; Ji, Junyuan; Ghulam, Abbas

    2014-06-01

    Nitrification-based microbial fuel cell (N-MFC) is a novel inorganic microbial fuel cell based on nitrification in the anode compartment. So far, little information is available on the substrates and pathway of N-MFC. The results of this study indicated that apart from the primary nitrification substrate (ammonium), the intermediates (hydroxylamine and nitrite) could also serve as anodic fuel to generate current, and the end product nitrate showed an inhibitory effect on electricity generation. Based on the research, a pathway of electricity generation was proposed for N-MFC: ammonium was oxidized first to nitrite by ammonia-oxidizing bacteria (AOB), then the nitrite in anolyte and the potassium permanganate in catholyte constituted a chemical cell to generate current. In other words, the electricity generation in N-MFC was not only supported by microbial reaction as we expected, but both biological and electrochemical reactions contributed.

  16. Evolution of tryptophan biosynthetic pathway in microbial genomes: a comparative genetic study.

    PubMed

    Priya, V K; Sarkar, Susmita; Sinha, Somdatta

    2014-03-01

    Biosynthetic pathway evolution needs to consider the evolution of a group of genes that code for enzymes catalysing the multiple chemical reaction steps leading to the final end product. Tryptophan biosynthetic pathway has five chemical reaction steps that are highly conserved in diverse microbial genomes, though the genes of the pathway enzymes show considerable variations in arrangements, operon structure (gene fusion and splitting) and regulation. We use a combined bioinformatic and statistical analyses approach to address the question if the pathway genes from different microbial genomes, belonging to a wide range of groups, show similar evolutionary relationships within and between them. Our analyses involved detailed study of gene organization (fusion/splitting events), base composition, relative synonymous codon usage pattern of the genes, gene expressivity, amino acid usage, etc. to assess inter- and intra-genic variations, between and within the pathway genes, in diverse group of microorganisms. We describe these genetic and genomic variations in the tryptophan pathway genes in different microorganisms to show the similarities across organisms, and compare the same genes across different organisms to find the possible variability arising possibly due to horizontal gene transfers. Such studies form the basis for moving from single gene evolution to pathway evolutionary studies that are important steps towards understanding the systems biology of intracellular pathways. PMID:24592292

  17. Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

    PubMed Central

    Chapman, Samantha K.; Newman, Gregory S.; Hart, Stephen C.; Schweitzer, Jennifer A.; Koch, George W.

    2013-01-01

    To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate. PMID:23658639

  18. Terrestrial exposure of oilfield flowline additives diminish soil structural stability and remediative microbial function.

    PubMed

    George, S J; Sherbone, J; Hinz, C; Tibbett, M

    2011-10-01

    Onshore oil production pipelines are major installations in the petroleum industry, stretching many thousands of kilometres worldwide which also contain flowline additives. The current study focuses on the effect of the flowline additives on soil physico-chemical and biological properties and quantified the impact using resilience and resistance indices. Our findings are the first to highlight deleterious effect of flowline additives by altering some fundamental soil properties, including a complete loss of structural integrity of the impacted soil and a reduced capacity to degrade hydrocarbons mainly due to: (i) phosphonate salts (in scale inhibitor) prevented accumulation of scale in pipelines but also disrupted soil physical structure; (ii) glutaraldehyde (in biocides) which repressed microbial activity in the pipeline and reduced hydrocarbon degradation in soil upon environmental exposure; (iii) the combinatory effects of these two chemicals synergistically caused severe soil structural collapse and disruption of microbial degradation of petroleum hydrocarbons.

  19. 78 FR 41703 - Regulation of Fuels and Fuel Additives: Additional Qualifying Renewable Fuel Pathways Under the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-11

    ... renewable fuels they produce through approved fuel pathways. See 75 FR 14670 (March 26, 2010); 75 FR 26026 (May 10, 2010); 75 FR 37733 (June 30, 2010); 75 FR 59622 (September 28, 2010); 75 FR 76790 (December 9, 2010); 75 FR 79964 (December 21, 2010); 77 FR 1320 (January 9, 2012); 77 FR 74592 (December 17,...

  20. Regulation of Soil Microbial Carbon-use Efficiency by Soil Moisture, Substrate Addition, and Incubation Time

    NASA Astrophysics Data System (ADS)

    Stark, J.

    2015-12-01

    Microbial carbon-use efficiency (CUE) is a key variable in biogeochemical cycling that regulates soil C sequestration, greenhouse gas emissions, and retention of inorganic nutrients. Microbial CUE is the fraction of C converted to biomass rather than respired as CO2. Biogeochemical models have been shown to be highly sensitive to variation in CUE; however, we currently have a poor understanding of how CUE responds to environmental variables such as soil moisture and nutrient limitations. We examined the effect of soil moisture and C supply on CUE in soil from a western hemlock / sitka spruce forest in Oregon, USA, using a novel technique which supplies 13C and 15N substrates through the gas phase so that water addition is not necessary. Soil samples (28 g oven-dry equiv. wt) at two water potentials (-0.03 and -3.55 MPa) were exposed to 13C-acetic acid vapor for either 6 or 30 sec to provide two different concentrations of acetate to soil microbial communities. The soils were also injected with small amounts of 15NH3 gas to allow quantification of microbial N assimilation rates and to provide an alternate method of calculating CUE. Rates of 13CO2 respiration were measured continuously during a 48-h incubation using cavity ring-down spectroscopy. Soil samples were extracted at seven time intervals (0, 0.5, 1.5, 4.5, 12, 24, and 48 h) in 0.5 M K2SO4 and analyzed for DO13C, microbial 13C, DO15N, inorganic 15N, and microbial 15N to calculate how gross rates of C and N assimilation and microbial CUE change with incubation time. As expected, microbial C and N assimilation rates and CUE increased with soil moisture and the quantity of acetate added; however, C:N assimilated was higher at lower soil moisture, suggesting that either C-storage compounds were being created, or that fungal communities were responsible for a greater proportion of the assimilation in drier soils. Assimilation rates and CUE also changed with incubation time, demonstrating that estimates of CUE

  1. Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes.

    PubMed

    Terrado, Ramon; Monier, Adam; Edgar, Robyn; Lovejoy, Connie

    2015-06-01

    In an effort to better understand the diversity of genes coding for nitrogen (N) uptake and assimilation pathways among microalgae, we analyzed the transcriptomes of five phylogenetically diverse single celled algae originally isolated from the same high arctic marine region. The five photosynthetic flagellates (a pelagophyte, dictyochophyte, chrysoph-yte, cryptophyte and haptophyte) were grown on standard media and media with only urea or nitrate as a nitrogen source; cells were harvested during late exponential growth. Based on homolog protein sequences, transcriptomes of each alga were interrogated to retrieve genes potentially associated with nitrogen uptake and utilization pathways. We further investigated the phylogeny of poorly characterized genes and gene families that were identified. While the phylogeny of the active urea transporter (DUR3) was taxonomically coherent, those for the urea transporter superfamily, putative nitrilases and amidases indicated complex evolutionary histories, and preliminary evidence for horizontal gene transfers. All five algae expressed genes for ammonium assimilation and all but the chrysophyte expressed genes involved in nitrate utilization and the urea cycle. Among the four algae with nitrate transporter transcripts, we detected lower expression levels in three of these (the dictyochophyte, pelagophyte, and cryptophyte) grown in the urea only medium compared with cultures from the nitrate only media. The diversity of N pathway genes in the five algae, and their ability to grow using urea as a nitrogen source, suggest that these flagellates are able to use a variety of organic nitrogen sources, which would be an advantage in an inorganic nitrogen - limited environment, such as the Arctic Ocean. PMID:26986665

  2. Metabolic engineering of microbial pathways for advanced biofuels production.

    PubMed

    Zhang, Fuzhong; Rodriguez, Sarah; Keasling, Jay D

    2011-12-01

    Production of biofuels from renewable resources such as cellulosic biomass provides a source of liquid transportation fuel to replace petroleum-based fuels. This endeavor requires the conversion of cellulosic biomass into simple sugars, and the conversion of simple sugars into biofuels. Recently, microorganisms have been engineered to convert simple sugars into several types of biofuels, such as alcohols, fatty acid alkyl esters, alkanes, and terpenes, with high titers and yields. Here, we review recently engineered biosynthetic pathways from the well-characterized microorganisms Escherichia coli and Saccharomyces cerevisiae for the production of several advanced biofuels.

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

    PubMed

    Treu, Laura; Campanaro, Stefano; Kougias, Panagiotis G; Zhu, Xinyu; Angelidaki, Irini

    2016-06-01

    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 to Clostridiales, Rykenellaceae, and in species of the genera Halothermothrix and Anaerobaculum. Additionally, an interesting transcriptional activation of the chemotaxis genes was evidenced in seven species belonging to Clostridia, Halothermothrix, and Tepidanaerobacter. Surprisingly, methanogens revealed a very versatile behavior different from each other, even among similar species of the Methanoculleus genus, while a strong increase of the expression level in Methanosarcina sp. was evidenced after oleate addition.

  4. Metabolic shifts in hypersaline microbial mats upon addition of organic substrates.

    PubMed

    Grötzschel, Stefan; Abed, Raeid M M; de Beer, Dirk

    2002-11-01

    The responses of hypersaline microbial mats to the addition of acetate, glycolate or glucose were investigated using oxygen, pH and sulphide microsensors. Changes in community structure were investigated with molecular techniques. Acetate addition inhibited respiration in the photic zone, stimulated respiration in the aphotic zone and had no effect on gross photosynthesis. Glycolate addition strongly increased both respiration and gross photosynthesis in the photic zone. Thus, glycolate and acetate were probably consumed in those regions of the mat where these substrates are usually formed. Moreover, photosynthesis was only stimulated by increased respiration and concomitant CO2 production in the photic zone which indicates that the photosynthetic and respiratory populations must be present in close proximity to each other. Glucose addition had an unexpected negative effect on the microbial population, strongly inhibiting both respiration and gross photosynthesis within hours. After four days, oxygen profiles in the light were equal to those measured in the dark. After replacing the water phase with unamended water, photosynthesis and respiration recovered within a week. None of the physiological changes were accompanied by detectable shifts in the cyanobacterial or the overall microbial community. The mechanism of inhibition of photosynthesis by glucose requires further investigation. PMID:12460276

  5. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  6. [Electricity generation of surplus sludge microbial fuel cells enhanced by additional enzyme].

    PubMed

    Yang, Hui; Liu, Zhi-Hu; Li, Xiao-Ming; Yang, Qi; Fang, Li; Huang, Hua-Jun; Zeng, Guang-Ming; Li, Shuo

    2012-01-01

    In this paper the feasibility of enhanced electricity generation of microbial fuel cell fed surplus sludge by additional enzymes (neutral protease and alpha-amylase) was discussed. The effect of dosage of additional enzyme on characteristics of electricity generation of the surplus sludge microbial fuel cell (SSMFC) and the reduction of surplus sludge were investigated. The results indicated that the maximum output power destiny of the group of experiment was higher than that of control under the same condition. Moreover, the maximum output power density, coulomb efficiency, efficiency of reducing TCOD, efficiency of reducing TSS and efficiency of reducing VSS reached up to 507 W x m(-2) (700 mW x m(-2)), 3.98% (5.11%), 88.31% (94.09%), 83.18% (98.02%) and 89.03% (98.80%) respectively for protease (alpha-amylase) at the dosage of 10 mg x g(-1). This study demonstrated that additional enzyme greatly enhanced the electricity generation of MFC with simultaneous accomplishments of sludge treatment, providing a novel approach for the practical application of microbial fuel cell.

  7. Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition

    PubMed Central

    Li, Yue; Liu, Yinghui; Wu, Shanmei; Niu, Lei; Tian, Yuqiang

    2015-01-01

    The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle, and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m−2 yr−1 for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m−2 yr−1, but autotrophic respiration (Ra) was highest with 8 to 16 g N m−2 yr−1. Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components, and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration. PMID:26678303

  8. Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition.

    PubMed

    Li, Yue; Liu, Yinghui; Wu, Shanmei; Niu, Lei; Tian, Yuqiang

    2015-12-18

    The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle, and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m(-2) yr(-1) for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m(-2) yr(-1), but autotrophic respiration (Ra) was highest with 8 to 16 g N m(-2) yr(-1). Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components, and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration.

  9. Microbial properties explain temporal variation in soil respiration in a grassland subjected to nitrogen addition

    NASA Astrophysics Data System (ADS)

    Li, Yue; Liu, Yinghui; Wu, Shanmei; Niu, Lei; Tian, Yuqiang

    2015-12-01

    The role of soil microbial variables in shaping the temporal variability of soil respiration has been well acknowledged but is poorly understood, particularly under elevated nitrogen (N) deposition conditions. We measured soil respiration along with soil microbial properties during the early, middle, and late growing seasons in temperate grassland plots that had been treated with N additions of 0, 2, 4, 8, 16, or 32 g N m-2 yr-1 for 10 years. Representing the averages over three observation periods, total (Rs) and heterotrophic (Rh) respiration were highest with 4 g N m-2 yr-1, but autotrophic respiration (Ra) was highest with 8 to 16 g N m-2 yr-1. Also, the responses of Rh and Ra were unsynchronized considering the periods separately. N addition had no significant impact on the temperature sensitivity (Q10) for Rs but inhibited the Q10 for Rh. Significant interactions between observation period and N level occurred in soil respiration components, and the temporal variations in soil respiration components were mostly associated with changes in microbial biomass carbon (MBC) and phospholipid fatty acids (PLFAs). Further observation on soil organic carbon and root biomass is needed to reveal the long-term effect of N deposition on soil C sequestration.

  10. Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates.

    PubMed

    Hu, Hang-Wei; Chen, Deli; He, Ji-Zheng

    2015-09-01

    The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions. PMID:25934121

  11. Sensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways.

    PubMed

    Cress, Brady F; Trantas, Emmanouil A; Ververidis, Filippos; Linhardt, Robert J; Koffas, Mattheos Ag

    2015-12-01

    Natural metabolic pathways are dynamically regulated at the transcriptional, translational, and protein levels. Despite this, traditional pathway engineering has relied on static control strategies to engender changes in metabolism, most likely due to ease of implementation and perceived predictability of design outcome. Increasingly in recent years, however, metabolic engineers have drawn inspiration from natural systems and have begun to harness dynamically controlled regulatory machinery to improve design of engineered microorganisms for production of specialty and commodity chemicals. Here, we review recent enabling technologies for engineering static control over pathway expression levels, and we discuss state-of-the-art dynamic control strategies that have yielded improved outcomes in the field of microbial metabolic engineering. Furthermore, we emphasize design of a novel class of genetically encoded controllers that will facilitate automatic, transient tuning of synthetic and endogenous pathways.

  12. New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

    PubMed Central

    Sierra-García, Isabel Natalia; Correa Alvarez, Javier; Pantaroto de Vasconcellos, Suzan; Pereira de Souza, Anete; dos Santos Neto, Eugenio Vaz; de Oliveira, Valéria Maia

    2014-01-01

    Current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. Metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. Using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communities in oil reservoirs. Here, we describe novel functional metabolic pathways involved in the biodegradation of aromatic compounds in a metagenomic library obtained from an oil reservoir. Although many of the deduced proteins shared homology with known enzymes of different well-described aerobic and anaerobic catabolic pathways, the metagenomic fragments did not contain the complete clusters known to be involved in hydrocarbon degradation. Instead, the metagenomic fragments comprised genes belonging to different pathways, showing novel gene arrangements. These results reinforce the potential of the metagenomic approach for the identification and elucidation of new genes and pathways in poorly studied environments and contribute to a broader perspective on the hydrocarbon degradation processes in petroleum reservoirs. PMID:24587220

  13. Effects of Nutrient Addition on Belowground Stoichiometry and Microbial Activity in an Ombrotrophic Bog

    NASA Astrophysics Data System (ADS)

    Pinsonneault, A. J.; Moore, T. R.; Roulet, N. T.

    2015-12-01

    Ombrotrophic bogs are both nutrient-poor systems and important carbon (C) sinks yet there remains a dearth of information on the stoichiometry of C, nitrogen (N), phosphorus (P), and potassium (K), an important determinant of substrate quality for microorganisms, in these systems. In this study, we quantified the C, N, P, and K concentrations and stoichiometric ratios of both soil organic matter (SOM) and dissolved organic matter (DOM) as well as microbial extracellular enzyme activity from 0 - 10cm depth in a long-term fertilization experiment at Mer Bleue bog, Ontario, Canada. Though trends in C:N, C:P, and C:K between SOM and DOM seem to follow one another, preliminary results indicate that the stoichiometric ratios of DOM were at least an order of magnitude smaller than those of DOM suggesting that nutrient fertilization impacts the quality of DOM as a microbial substrate to a greater degree than SOM. C:N decreased with greater nitrogen addition but C:P and C:K increased; the magnitude of that increase being smaller in NPK treatments relative to N-only treatments suggesting co-limitation by P and/or K. This is further supported by the increase in activity of both the C-cycling enzyme, β-D-glucosidase (bdG), and the P-cycling enzyme, phosphatase (Phos), with greater nitrogen addition; particularly in NPK-treatments for bdG and N-only treatments for Phos. The activity of the N-cycling enzyme, N-acetyl-β-D-glucosaminidase, and the C-cycling enzyme, phenol oxidase, with greater N-addition suggests a decreased need to breakdown organic nitrogen to meet microbial N-requirements in the former and N-inhibition in the latter consistent with findings in the literature. Taken together, these results suggest that higher levels of nutrients impact both microbial substrate quality as well as the activity of microbial enzymes that are key in the decomposition process which may ultimately decrease the ability of peatlands to sequester carbon.

  14. Enhanced Microbial Pathways for Methane Production from Oil Shale

    SciTech Connect

    Paul Fallgren

    2009-02-15

    Methane from oil shale can potentially provide a significant contribution to natural gas industry, and it may be possible to increase and continue methane production by artificially enhancing methanogenic activity through the addition of various substrate and nutrient treatments. Western Research Institute in conjunction with Pick & Shovel Inc. and the U.S. Department of Energy conducted microcosm and scaled-up reactor studies to investigate the feasibility and optimization of biogenic methane production from oil shale. The microcosm study involving crushed oil shale showed the highest yield of methane was produced from oil shale pretreated with a basic solution and treated with nutrients. Incubation at 30 C, which is the estimated temperature in the subsurface where the oil shale originated, caused and increase in methane production. The methane production eventually decreased when pH of the system was above 9.00. In the scaled-up reactor study, pretreatment of the oil shale with a basic solution, nutrient enhancements, incubation at 30 C, and maintaining pH at circumneutral levels yielded the highest rate of biogenic methane production. From this study, the annual biogenic methane production rate was determined to be as high as 6042 cu. ft/ton oil shale.

  15. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies.

    PubMed

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M; Wells, George F

    2012-01-01

    Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial

  16. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    PubMed Central

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  17. Plant and microbial responses to nitrogen and phosphorus addition across an elevational gradient in subarctic tundra.

    PubMed

    Sundqvist, Maja K; Liu, Zhanfeng; Giesler, Reiner; Wardle, David A

    2014-07-01

    Temperature and nutrients are major limiting factors in subarctic tundra. Experimental manipulation of nutrient availability along elevational gradients (and thus temperature) can improve our understanding of ecological responses to climate change. However, no study to date has explored impacts of nutrient addition along a tundra elevational gradient, or across contrasting vegetation types along any elevational gradient. We set up a full factorial nitrogen (N) and phosphorus (P) fertilization experiment in each of two vegetation types (heath and meadow) at 500 m, 800 m, and 1000 m elevation in northern Swedish tundra. We predicted that plant and microbial communities in heath or at lower elevations would be more responsive to N addition while communities in meadow or at higher elevations would be more responsive to P addition, and that fertilizer effects would vary more with elevation for the heath than for the meadow. Although our results provided little support for these predictions, the relationship between nutrient limitation and elevation differed between vegetation types. Most plant and microbial properties were responsive to N and/or P fertilization, but responses often varied with elevation and/or vegetation type. For instance, vegetation density significantly increased with N + P fertilization relative to the other fertilizer treatments, and this increase was greatest at the lowest elevation for the heath but at the highest elevation for the meadow. Arbuscular mycorrhizae decreased with P fertilization at 500 m for the meadow, but with all fertilizer treatments in both vegetation types at 800 m. Fungal to bacterial ratios were enhanced by N+ P fertilization for the two highest elevations in the meadow only. Additionally, microbial responses to fertilization were primarily direct rather than indirect via plant responses, pointing to a decoupled response of plant and microbial communities to nutrient addition and elevation. Because our study shows how two

  18. Bioactive Compost - A Value Added Compost with Microbial Inoculants and Organic Additives

    NASA Astrophysics Data System (ADS)

    Kavitha, R.; Subramanian, P.

    A study was conducted in the Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, to transform the normal compost into bioactive compost through the addition of various substrates, which has multiple benefits to the crop system. The key players in this transformation process were Azotobacter, Pseudomonas, Phosphobacteria, composted poultry litter, rock phosphate and diluted spent wash. This enrichment process has increased the nutritive value of compost. The highest nitrogen content (1.75%) and phosphorus content (1.16%) was observed in the treatment T5 (compost enriched with composted poultry litter, spent wash, microbial inoculants and rock phosphate). The beneficial microorganism viz., Azotobacter, Pseudomonas and Phosphobacteria population were higher in the treatment T5 where all the inputs (composted poultry litter, microbial consortium, rock phosphate and spent wash) were added to the compost. The plant growth promoters viz., IAA and GA content was more in the treatment applied with spent wash and microbial inoculum. Beneficial microorganisms, composted poultry litter, rock phosphate and diluted spent wash contributes maximum level of nutrients and growth promoters to the compost with small expenses.

  19. Effect of Additions on Ensiling and Microbial Community of Senesced Wheat Straw

    SciTech Connect

    David N. Thompson; Joni M. Barnes; Tracy P. Houghton

    2005-04-01

    Crop residues collected during or after grain harvest are available once per year and must be stored for extended periods. The combination of air, high moisture, and high microbial loads leads to shrinkage during storage and risk of spontaneous ignition. Ensiling is a wet preservation method that could be used to store these residues stably. To economically adapt ensiling to biomass that is harvested after it has senesced, the need for nutrient, moisture, and microbial additions must be determined. We tested the ensiling of senesced wheat straw in sealed columns for 83 d. The straw was inoculated with Lactobacillus plantarum and amended with several levels of water and free sugars. The ability to stabilize the straw polysaccharides was strongly influenced by both moisture and free sugars. Without the addition of sugar, the pH increased from 5.2 to as much as 9.1, depending on moisture level, and losses of 22% of the cellulose and 21% of the hemicellulose were observed. By contrast, when sufficient sugars were added and interstitial water was maintained, a final pH of 4.0 was attainable, with correspondingly low (<5%) losses of cellulose and hemicellulose. The results show that ensiling should be considered a promising method for stable storage of wet biorefinery feedstocks.

  20. Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway

    PubMed Central

    Martínez-Lavanchy, P. M.; Chen, Z.; Lünsmann, V.; Marin-Cevada, V.; Vilchez-Vargas, R.; Pieper, D. H.; Reiche, N.; Kappelmeyer, U.; Imparato, V.; Junca, H.; Nijenhuis, I.; Müller, J. A.; Kuschk, P.

    2015-01-01

    In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs. PMID:26150458

  1. Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway.

    PubMed

    Martínez-Lavanchy, P M; Chen, Z; Lünsmann, V; Marin-Cevada, V; Vilchez-Vargas, R; Pieper, D H; Reiche, N; Kappelmeyer, U; Imparato, V; Junca, H; Nijenhuis, I; Müller, J A; Kuschk, P; Heipieper, H J

    2015-09-01

    In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.

  2. Enhancing solubility of deoxyxylulose phosphate pathway enzymes for microbial isoprenoid production

    PubMed Central

    2012-01-01

    Background Recombinant proteins are routinely overexpressed in metabolic engineering. It is well known that some over-expressed heterologous recombinant enzymes are insoluble with little or no enzymatic activity. This study examined the solubility of over-expressed homologous enzymes of the deoxyxylulose phosphate pathway (DXP) and the impact of inclusion body formation on metabolic engineering of microbes. Results Four enzymes of this pathway (DXS, ISPG, ISPH and ISPA), but not all, were highly insoluble, regardless of the expression systems used. Insoluble dxs (the committed enzyme of DXP pathway) was found to be inactive. Expressions of fusion tags did not significantly improve the solubility of dxs. However, hypertonic media containing sorbitol, an osmolyte, successfully doubled the solubility of dxs, with the concomitant improvement in microbial production of the metabolite, DXP. Similarly, sorbitol significantly improved the production of soluble and functional ERG12, the committed enzyme in the mevalonate pathway. Conclusion This study demonstrated the unanticipated findings that some over-expressed homologous enzymes of the DXP pathway were highly insoluble, forming inclusion bodies, which affected metabolite formation. Sorbitol was found to increase both the solubility and function of some of these over-expressed enzymes, a strategy to increase the production of secondary metabolites. PMID:23148661

  3. Investigation of the microbial community in a microbiological additive used in a manure composting process.

    PubMed

    Wakase, Shiho; Sasaki, Hiraku; Itoh, Kikuji; Otawa, Kenichi; Kitazume, Osamu; Nonaka, Jun; Satoh, Masaaki; Sasaki, Takako; Nakai, Yutaka

    2008-05-01

    The objectives of this study were to investigate the fate of microorganisms by using cultivation methods as well as DNA analyses in a commercial microbiological additive (MA) in the course of the composting. Almost all the predominant species in the microbial succession during composting process determined by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) were in disagreement with those determined by the clone library method. None of the microbial species in the composting stages corresponded to the microorganisms identified in the MA either by the cultivation method or DNA analysis. The results in regard to predominant microorganisms of the MA detected from the liquid medium by the PCR-DGGE did not correspond with those detected from the MA itself and composting processes. Although no evidence was found that predominant species in the MA itself dominate in the composting process, predominant species diversity in the MA itself was markedly changed after culturing at different thermophilic temperatures. These results suggested that cultivable microorganisms in the MA did not become predominant in the composting process: however, some microorganisms that are detected from the MA itself by the DNA analysis may act effectively in the composting process.

  4. Microbial community response to addition of polylactate compounds to stimulate hexavalent chromium reduction in groundwater.

    PubMed

    Brodie, Eoin L; Joyner, Dominique C; Faybishenko, Boris; Conrad, Mark E; Rios-Velazquez, Carlos; Malave, Josue; Martinez, Ramon; Mork, Benjamin; Willett, Anna; Koenigsberg, Steven; Herman, Donald J; Firestone, Mary K; Hazen, Terry C

    2011-10-01

    To evaluate the efficacy of bioimmobilization of Cr(VI) in groundwater at the Department of Energy Hanford site, we conducted a series of microcosm experiments using a range of commercial electron donors with varying degrees of lactate polymerization (polylactate). These experiments were conducted using Hanford Formation sediments (coarse sand and gravel) immersed in Hanford groundwater, which were amended with Cr(VI) and several types of lactate-based electron donors (Hydrogen Release Compound, HRC; primer-HRC, pHRC; extended release HRC) and the polylactate-cysteine form (Metal Remediation Compound, MRC). The results showed that polylactate compounds stimulated an increase in bacterial biomass and activity to a greater extent than sodium lactate when applied at equivalent carbon concentrations. At the same time, concentrations of headspace hydrogen and methane increased and correlated with changes in the microbial community structure. Enrichment of Pseudomonas spp. occurred with all lactate additions, and enrichment of sulfate-reducing Desulfosporosinus spp. occurred with almost complete sulfate reduction. The results of these experiments demonstrate that amendment with the pHRC and MRC forms result in effective removal of Cr(VI) from solution most likely by both direct (enzymatic) and indirect (microbially generated reductant) mechanisms.

  5. Investigations of potential microbial methanogenic and carbon monoxide utilization pathways in ultra-basic reducing springs associated with present-day continental serpentinization: the Tablelands, NL, CAN

    PubMed Central

    Morrill, Penny L.; Brazelton, William J.; Kohl, Lukas; Rietze, Amanda; Miles, Sarah M.; Kavanagh, Heidi; Schrenk, Matthew O.; Ziegler, Susan E.; Lang, Susan Q.

    2014-01-01

    Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface environment with H2 and CH4 present. Very little, however, is known about the carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms that live in this ultra-basic environment. The potential for microbial methanogenesis with bicarbonate, formate, acetate, and propionate precursors and carbon monoxide (CO) utilization pathways were tested in laboratory experiments by adding substrates to water and sediment from the Tablelands, NL, CAD, a site of present-day continental serpentinization. Microbial methanogenesis was not observed after bicarbonate, formate, acetate, or propionate addition. CO was consumed in the live experiments but not in the killed controls and the residual CO in the live experiments became enriched in 13C. The average isotopic enrichment factor resulting from this microbial utilization of CO was estimated to be 11.2 ± 0.2‰. Phospholipid fatty acid concentrations and δ13C values suggest limited incorporation of carbon from CO into microbial lipids. This indicates that in our experiments, CO was used primarily as an energy source, but not for biomass growth. Environmental DNA sequencing of spring fluids collected at the same time as the addition experiments yielded a large proportion of Hydrogenophaga-related sequences, which is consistent with previous metagenomic data indicating the potential for these taxa to utilize CO. PMID:25431571

  6. pH-dependent ammonia removal pathways in microbial fuel cell system.

    PubMed

    Kim, Taeyoung; An, Junyeong; Lee, Hyeryeong; Jang, Jae Kyung; Chang, In Seop

    2016-09-01

    In this work, ammonia removal paths in microbial fuel cells (MFCs) under different initial pH conditions (pH 7.0, 8.0, and 8.6) were investigated. At a neutral pH condition (pH 7.0), MFC used an electrical energy of 27.4% and removed 23.3% of total ammonia by electrochemical pathway for 192h. At the identical pH condition, 36.1% of the total ammonia was also removed by the biological path suspected to be biological ammonia oxidation process (e.g., Anammox). With the initial pH increased, the electrochemical removal efficiency decreased to less than 5.0%, while the biological removal efficiency highly increased to 61.8%. In this study, a neutral pH should be maintained in the anode to utilize MFCs for ammonia recovery via electrochemical pathways from wastewater stream.

  7. pH-dependent ammonia removal pathways in microbial fuel cell system.

    PubMed

    Kim, Taeyoung; An, Junyeong; Lee, Hyeryeong; Jang, Jae Kyung; Chang, In Seop

    2016-09-01

    In this work, ammonia removal paths in microbial fuel cells (MFCs) under different initial pH conditions (pH 7.0, 8.0, and 8.6) were investigated. At a neutral pH condition (pH 7.0), MFC used an electrical energy of 27.4% and removed 23.3% of total ammonia by electrochemical pathway for 192h. At the identical pH condition, 36.1% of the total ammonia was also removed by the biological path suspected to be biological ammonia oxidation process (e.g., Anammox). With the initial pH increased, the electrochemical removal efficiency decreased to less than 5.0%, while the biological removal efficiency highly increased to 61.8%. In this study, a neutral pH should be maintained in the anode to utilize MFCs for ammonia recovery via electrochemical pathways from wastewater stream. PMID:27090407

  8. Deregulation of intestinal anti-microbial defense by the dietary additive, maltodextrin

    PubMed Central

    Nickerson, Kourtney P; Chanin, Rachael; McDonald, Christine

    2015-01-01

    Inflammatory bowel disease (IBD) is a complex, multi-factorial disease thought to arise from an inappropriate immune response to commensal bacteria in a genetically susceptible person that results in chronic, cyclical, intestinal inflammation. Dietary and environmental factors are implicated in the initiation and perpetuation of IBD; however, a singular causative agent has not been identified. As of now, the role of environmental priming or triggers in IBD onset and pathogenesis are not well understood, but these factors appear to synergize with other disease susceptibility factors. In previous work, we determined that the polysaccharide dietary additive, maltodextrin (MDX), impairs cellular anti-bacterial responses and suppresses intestinal anti-microbial defense mechanisms. In this addendum, we review potential mechanisms for dietary deregulation of intestinal homeostasis, postulate how dietary and genetic risk factors may combine to result in disease pathogenesis, and discuss these ideas in the context of recent findings related to dietary interventions for IBD. PMID:25738413

  9. Additive Manufacturing of a Microbial Fuel Cell--A detailed study.

    PubMed

    Calignano, Flaviana; Tommasi, Tonia; Manfredi, Diego; Chiolerio, Alessandro

    2015-01-01

    In contemporary society we observe an everlasting permeation of electron devices, smartphones, portable computing tools. The tiniest living organisms on Earth could become the key to address this challenge: energy generation by bacterial processes from renewable stocks/waste through devices such as microbial fuel cells (MFCs). However, the application of this solution was limited by a moderately low efficiency. We explored the limits, if any, of additive manufacturing (AM) technology to fabricate a fully AM-based powering device, exploiting low density, open porosities able to host the microbes, systems easy to fuel continuously and to run safely. We obtained an optimal energy recovery close to 3 kWh m(-3) per day that can power sensors and low-power appliances, allowing data processing and transmission from remote/harsh environments.

  10. Additive Manufacturing of a Microbial Fuel Cell—A detailed study

    PubMed Central

    Calignano, Flaviana; Tommasi, Tonia; Manfredi, Diego; Chiolerio, Alessandro

    2015-01-01

    In contemporary society we observe an everlasting permeation of electron devices, smartphones, portable computing tools. The tiniest living organisms on Earth could become the key to address this challenge: energy generation by bacterial processes from renewable stocks/waste through devices such as microbial fuel cells (MFCs). However, the application of this solution was limited by a moderately low efficiency. We explored the limits, if any, of additive manufacturing (AM) technology to fabricate a fully AM-based powering device, exploiting low density, open porosities able to host the microbes, systems easy to fuel continuously and to run safely. We obtained an optimal energy recovery close to 3 kWh m−3 per day that can power sensors and low-power appliances, allowing data processing and transmission from remote/harsh environments. PMID:26611142

  11. Additive Manufacturing of a Microbial Fuel Cell—A detailed study

    NASA Astrophysics Data System (ADS)

    Calignano, Flaviana; Tommasi, Tonia; Manfredi, Diego; Chiolerio, Alessandro

    2015-11-01

    In contemporary society we observe an everlasting permeation of electron devices, smartphones, portable computing tools. The tiniest living organisms on Earth could become the key to address this challenge: energy generation by bacterial processes from renewable stocks/waste through devices such as microbial fuel cells (MFCs). However, the application of this solution was limited by a moderately low efficiency. We explored the limits, if any, of additive manufacturing (AM) technology to fabricate a fully AM-based powering device, exploiting low density, open porosities able to host the microbes, systems easy to fuel continuously and to run safely. We obtained an optimal energy recovery close to 3 kWh m-3 per day that can power sensors and low-power appliances, allowing data processing and transmission from remote/harsh environments.

  12. Deregulation of intestinal anti-microbial defense by the dietary additive, maltodextrin.

    PubMed

    Nickerson, Kourtney P; Chanin, Rachael; McDonald, Christine

    2015-01-01

    Inflammatory bowel disease (IBD) is a complex, multi-factorial disease thought to arise from an inappropriate immune response to commensal bacteria in a genetically susceptible person that results in chronic, cyclical, intestinal inflammation. Dietary and environmental factors are implicated in the initiation and perpetuation of IBD; however, a singular causative agent has not been identified. As of now, the role of environmental priming or triggers in IBD onset and pathogenesis are not well understood, but these factors appear to synergize with other disease susceptibility factors. In previous work, we determined that the polysaccharide dietary additive, maltodextrin (MDX), impairs cellular anti-bacterial responses and suppresses intestinal anti-microbial defense mechanisms. In this addendum, we review potential mechanisms for dietary deregulation of intestinal homeostasis, postulate how dietary and genetic risk factors may combine to result in disease pathogenesis, and discuss these ideas in the context of recent findings related to dietary interventions for IBD.

  13. Control of hydrogen sulfide production in oil fields by managing microbial communities through nitrate or nitrite addition

    NASA Astrophysics Data System (ADS)

    Hubert, Casey R. J.

    Nitrate or nitrite injection into oil reservoirs during water flooding has the potential to control biological souring, the production of hydrogen sulfide (H2S) by sulfate-reducing bacteria (SRB). Souring control is essential because sulfide is toxic, sulfide precipitates can plug reservoir formations, souring lowers crude oil value, and SRB induce corrosion. Nitrate and nitrite can stimulate heterotrophic nitrate- or nitrite-reducing bacteria (hNRB) and nitrate- or nitrite-reducing, sulfide oxidizing bacteria (NRSOB). Nitrite also inhibits SRB activity by blocking the sulfate reduction pathway. Continuous up-flow packed-bed bioreactors were inoculated with produced water from the Coleville oil field to establish sulfide-producing biofilms similar to those found in sour reservoirs. Nitrate or nitrite addition to bioreactors indicated that the dose required for hNRB or NR-SOB to control souring depended on the concentration of oil organics. Either mechanism mediates the net removal of oil organics (lactate) with nitrate or nitrite, with lower doses of nitrate required due to its greater oxidative power. Microbial community analysis by reverse sample genome probing (RSGP) revealed that NR-SOB mediated sulfide removal at low nitrate or nitrite concentrations when lactate was still available to SRB and the redox potential was low. At high nitrate doses hNRB oxidized lactate directly, produced nitrite and maintained a high redox potential, thus excluding SRB activity. Facultatively chemolithotrophic Campylobacter sp. strains were isolated from the bioreactors and incorporated into RSGP analyses, revealing their dominance in both NR-SOB- and hNRB-containing communities. The metabolic flexibility of these strains may confer a competitive advantage over obligate chemolithotrophs like Thiomicrospira sp. strain CVO or hNRB that do not have NR-SOB activity like newly isolated Thauera sp. and Rhodobacter sp. strains. A single high dose of nitrite resulted in immediate

  14. Microbial nitrogen removal pathways in integrated vertical-flow constructed wetland systems.

    PubMed

    Hu, Yun; He, Feng; Ma, Lin; Zhang, Yi; Wu, Zhenbin

    2016-05-01

    Microbial nitrogen (N) removal pathways in planted (Canna indica L.) and unplanted integrated vertical-flow constructed wetland systems (IVCWs) were investigated. Results of, molecular biological and isotope pairing experiments showed that nitrifying, anammox, and denitrifying bacteria were distributed in both down-flow and up-flow columns of the IVCWs. Further, the N transforming bacteria in the planted IVCWs were significantly higher than that in the unplanted ones (p<0.05). Moreover, the potential nitrification, anammox, and denitrification rates were highest (18.90, 11.75, and 7.84nmolNg(-1)h(-1), respectively) in the down-flow column of the planted IVCWs. Significant correlations between these potential rates and the absolute abundance of N transformation genes further confirmed the existence of simultaneous nitrification, anammox, and denitrification (SNAD) processes in the IVCWs. The anammox process was the major N removal pathway (55.6-60.0%) in the IVCWs. The results will further our understanding of the microbial N removal mechanisms in IVCWs. PMID:26897412

  15. n-butanol: challenges and solutions for shifting natural metabolic pathways into a viable microbial production.

    PubMed

    Branduardi, Paola; Porro, Danilo

    2016-04-01

    The economic upturn of the past 200 years would not have been conceivable without fossil resources such as coal and oil. However, the fossil-based economy increasingly reaches its limits and displays contradictions. Bioeconomy, strategically combining economy and ecology willing to make biobased and sustainable growth possible, is promising to make a significant contribution towards solving these issues. In this context, microbial bioconversions are promising to support partially the increasing need for materials and fuels starting from fresh, preferably waste, biomass. Butanol is a very attractive molecule finding applications both as a chemical platform and as a fuel. Today it principally derives from petroleum, but it also represents the final product of microbial catabolic pathways. Because of the need to maximize yield, titer and productivity to make the production competitive and viable, the challenge is to transform a robustly regulated metabolic network into the principal cellular activity. However, this goal can only be accomplished by a profound understanding of the cellular physiology, survival strategy and sensing/signalling cascades. Here, we shortly review on the natural cellular pathways and circumstances that lead to n-butanol accumulation, its physiological consequences that might not match industrial needs and on possible solutions for circumventing these natural constraints. PMID:27020412

  16. Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing.

    PubMed

    Ye, Lin; Zhang, Tong; Wang, Taitao; Fang, Zhiwei

    2012-12-18

    The objective of this study was to explore microbial community structures, functional profiles, and metabolic pathways in a lab-scale and a full-scale wastewater treatment bioreactors. In order to do this, over 12 gigabases of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were generated with the Illumina HiSeq 2000 platform, using DNA extracted from activated sludge in the two bioreactors. Three kinds of sequences (16S rRNA gene amplicons, 16S rRNA gene sequences obtained from metagenomic sequencing, and predicted proteins) were used to conduct taxonomic assignments. Specially, relative abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed. Compared with quantitative real-time PCR (qPCR), metagenomic sequencing was demonstrated to be a better approach to quantify AOA and AOB in activated sludge samples. It was found that AOB were more abundant than AOA in both reactors. Furthermore, the analysis of the metabolic profiles indicated that the overall patterns of metabolic pathways in the two reactors were quite similar (73.3% of functions shared). However, for some pathways (such as carbohydrate metabolism and membrane transport), the two reactors differed in the number of pathway-specific genes.

  17. Microbially-accelerated consolidation of oil sands tailings. Pathway II: solid phase biogeochemistry

    PubMed Central

    Siddique, Tariq; Kuznetsov, Petr; Kuznetsova, Alsu; Li, Carmen; Young, Rozlyn; Arocena, Joselito M.; Foght, Julia M.

    2014-01-01

    Consolidation of clay particles in aqueous tailings suspensions is a major obstacle to effective management of oil sands tailings ponds in northern Alberta, Canada. We have observed that microorganisms indigenous to the tailings ponds accelerate consolidation of mature fine tailings (MFT) during active metabolism by using two biogeochemical pathways. In Pathway I, microbes alter porewater chemistry to indirectly increase consolidation of MFT. Here, we describe Pathway II comprising significant, direct and complementary biogeochemical reactions with MFT mineral surfaces. An anaerobic microbial community comprising Bacteria (predominantly Clostridiales, Synergistaceae, and Desulfobulbaceae) and Archaea (Methanolinea/Methanoregula and Methanosaeta) transformed FeIII minerals in MFT to amorphous FeII minerals during methanogenic metabolism of an added organic substrate. Synchrotron analyses suggested that ferrihydrite (5Fe2O3. 9H2O) and goethite (α-FeOOH) were the dominant FeIII minerals in MFT. The formation of amorphous iron sulfide (FeS) and possibly green rust entrapped and masked electronegative clay surfaces in amended MFT. Both Pathways I and II reduced the surface charge potential (repulsive forces) of the clay particles in MFT, which aided aggregation of clays and formation of networks of pores, as visualized using cryo-scanning electron microscopy (SEM). These reactions facilitated the egress of porewater from MFT and increased consolidation of tailings solids. These results have large-scale implications for management and reclamation of oil sands tailings ponds, a burgeoning environmental issue for the public and government regulators. PMID:24711806

  18. Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing.

    PubMed

    Ye, Lin; Zhang, Tong; Wang, Taitao; Fang, Zhiwei

    2012-12-18

    The objective of this study was to explore microbial community structures, functional profiles, and metabolic pathways in a lab-scale and a full-scale wastewater treatment bioreactors. In order to do this, over 12 gigabases of metagenomic sequence data and 600,000 paired-end sequences of bacterial 16S rRNA gene were generated with the Illumina HiSeq 2000 platform, using DNA extracted from activated sludge in the two bioreactors. Three kinds of sequences (16S rRNA gene amplicons, 16S rRNA gene sequences obtained from metagenomic sequencing, and predicted proteins) were used to conduct taxonomic assignments. Specially, relative abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were analyzed. Compared with quantitative real-time PCR (qPCR), metagenomic sequencing was demonstrated to be a better approach to quantify AOA and AOB in activated sludge samples. It was found that AOB were more abundant than AOA in both reactors. Furthermore, the analysis of the metabolic profiles indicated that the overall patterns of metabolic pathways in the two reactors were quite similar (73.3% of functions shared). However, for some pathways (such as carbohydrate metabolism and membrane transport), the two reactors differed in the number of pathway-specific genes. PMID:23151157

  19. Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

    NASA Astrophysics Data System (ADS)

    Dong, W. Y.; Zhang, X. Y.; Liu, X. Y.; Fu, X. L.; Chen, F. S.; Wang, H. M.; Sun, X. M.; Wen, X. F.

    2015-07-01

    Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil

  20. Effect of the addition of rice straw on microbial community in a sewage sludge digester.

    PubMed

    Nakakihara, E; Ikemoto-Yamamoto, R; Honda, R; Ohtsuki, S; Takano, M; Suetsugu, Y; Watanabe, H

    2014-01-01

    Rice straw was added to a sewage sludge digester and its effects on methane production, dewatering characteristics, and microbial communities in the digested sludge were examined by a continuous digestion experiment under mesophilic conditions (35 °C). Stable gas generation was monitored in all digestion experiments. Methane yield from raw sludge, chopped rice straw and softened rice straw were estimated to be 0.27, 0.18 and 0.26 NL/g total solids load, respectively. The capillary suction time of digested sludge was decreased by the addition of rice straw. Archaeal and bacterial communities in the sludge were elucidated by PCR-DGGE (polymerase chain reaction--denaturing gradient gel electrophoresis) targeting 16S rRNA genes. The Shannon index of DGGE profiles indicated that bacterial diversity increased with the addition of softened rice straw. DNA sequences of significant bands of the digested sludge were most closely related to Methanosaeta concilii (97.4% identity) and Methanoculleus bourgensis (100% identity). Meanwhile, those in the co-digested sludge with rice straw were most closely related to Methanosarcina barkeri (98.4% identity) and Methanoculleus bourgensis (99.3% identity). Although both Methanosaeta spp. and Methanosarcina spp. metabolize acetate to methane, Methanosarcina spp. have a competitive advantage at acetate concentrations of >70 mg/L. Results suggested that the quantity of acetate produced during rice straw degradation may change the archaeal community. PMID:25225928

  1. Pathways of nitrobenzene degradation in horizontal subsurface flow constructed wetlands: Effect of intermittent aeration and glucose addition.

    PubMed

    Kirui, Wesley K; Wu, Shubiao; Kizito, Simon; Carvalho, Pedro N; Dong, Renjie

    2016-01-15

    Intermittent aeration and addition of glucose were applied to horizontal subsurface flow constructed wetlands in order to investigate the effect on pathways of nitrobenzene (NB) degradation and interactions with microbial nitrogen and sulphur transformations. The experiment was carried out in three phases A, B and C consisting of different NB loading and glucose dosing. For each phase, the effect of aeration was assessed by intermittently aerating one wetland and leaving one unaerated. Regardless of whether or not the wetland was aerated, at an influent NB concentration of 140 mg/L, both wetlands significantly reduced NB to less than 2 mg/L, a reduction efficiency of 98%. However, once the influent NB concentration was increased to 280 mg/L, the aerated wetland had a higher removal performance 82% compared to that of the unaerated wetland 71%. Addition of glucose further intensified the NB removal to 95% in the aerated wetlands and 92% in the unaerated. Aeration of wetlands enhanced NB degradation, but also resulted in higher NB volatilization of 6 mg m(-2) d(-1). The detected high concentration of sulphide 20-60 mg/L in the unaerated wetland gave a strong indication that NB may act as an electron donor to sulphate-reducing bacteria, but this should be further investigated. Aeration positively improved NB removal in constructed wetlands, but resulted in higher NB volatilization. Glucose addition induced co-metabolism to enhance NB degradation. PMID:26468606

  2. Pathways of nitrobenzene degradation in horizontal subsurface flow constructed wetlands: Effect of intermittent aeration and glucose addition.

    PubMed

    Kirui, Wesley K; Wu, Shubiao; Kizito, Simon; Carvalho, Pedro N; Dong, Renjie

    2016-01-15

    Intermittent aeration and addition of glucose were applied to horizontal subsurface flow constructed wetlands in order to investigate the effect on pathways of nitrobenzene (NB) degradation and interactions with microbial nitrogen and sulphur transformations. The experiment was carried out in three phases A, B and C consisting of different NB loading and glucose dosing. For each phase, the effect of aeration was assessed by intermittently aerating one wetland and leaving one unaerated. Regardless of whether or not the wetland was aerated, at an influent NB concentration of 140 mg/L, both wetlands significantly reduced NB to less than 2 mg/L, a reduction efficiency of 98%. However, once the influent NB concentration was increased to 280 mg/L, the aerated wetland had a higher removal performance 82% compared to that of the unaerated wetland 71%. Addition of glucose further intensified the NB removal to 95% in the aerated wetlands and 92% in the unaerated. Aeration of wetlands enhanced NB degradation, but also resulted in higher NB volatilization of 6 mg m(-2) d(-1). The detected high concentration of sulphide 20-60 mg/L in the unaerated wetland gave a strong indication that NB may act as an electron donor to sulphate-reducing bacteria, but this should be further investigated. Aeration positively improved NB removal in constructed wetlands, but resulted in higher NB volatilization. Glucose addition induced co-metabolism to enhance NB degradation.

  3. Changes in the structure and function of microbial communities in drinking water treatment bioreactors upon addition of phosphorus.

    PubMed

    Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; Raskin, Lutgarde

    2010-11-01

    Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors.

  4. Muscles provide protection during microbial infection by activating innate immune response pathways in Drosophila and zebrafish

    PubMed Central

    Chatterjee, Arunita; Roy, Debasish; Patnaik, Esha

    2016-01-01

    ABSTRACT Muscle contraction brings about movement and locomotion in animals. However, muscles have also been implicated in several atypical physiological processes including immune response. The role of muscles in immunity and the mechanism involved has not yet been deciphered. In this paper, using Drosophila indirect flight muscles (IFMs) as a model, we show that muscles are immune-responsive tissues. Flies with defective IFMs are incapable of mounting a potent humoral immune response. Upon immune challenge, the IFMs produce anti-microbial peptides (AMPs) through the activation of canonical signaling pathways, and these IFM-synthesized AMPs are essential for survival upon infection. The trunk muscles of zebrafish, a vertebrate model system, also possess the capacity to mount an immune response against bacterial infections, thus establishing that immune responsiveness of muscles is evolutionarily conserved. Our results suggest that physiologically fit muscles might boost the innate immune response of an individual. PMID:27101844

  5. Microbial pathways for the mobilization of mercury as Hg(O) in anoxic subsurface environments

    SciTech Connect

    Barkay, Tamar

    2005-06-01

    The goal of our project which was initiated in June 2005 is focused on the presence of merA in microbial communities of anoxic environments and the effect of anaerobic respiratory pathways on MR expression and activities. The following progress has been made to date: PCR primers were designed to span the known phylogenetic range of merA genes of Gram-negative bacteria. In control experiments, these primers successfully amplified a 288 bp region at the 3? end of previously characterized merA genes from Shewanella putrefaciens pMERPH, Acidithiobacillus ferrooxidans, Pseudomonas stutzeri pPB, Tn5041, Pseudomonas sp. K-62, and Serratia marcescens pDU1358.

  6. Nutrient addition effects on tropical dry forests: a mini-review from microbial to ecosystem scales

    NASA Astrophysics Data System (ADS)

    Powers, Jennifer; Becklund, Kristen; Gei, Maria; Iyengar, Siddarth; Meyer, Rebecca; O'Connell, Christine; Schilling, Erik; Smith, Christina; Waring, Bonnie; Werden, Leland

    2015-06-01

    Humans have more than doubled inputs of reactive nitrogen globally and greatly accelerated the biogeochemical cycles of phosphorus and metals. However, the impacts of increased element mobility on tropical ecosystems remain poorly quantified, particularly for the vast tropical dry forest biome. Tropical dry forests are characterized by marked seasonality, relatively little precipitation, and high heterogeneity in plant functional diversity and soil chemistry. For these reasons, increased nutrient deposition may affect tropical dry forests differently than wet tropical or temperate forests. Here we review studies that investigated how nutrient availability affects ecosystem and community processes from the microsite to ecosystem scales in tropical dry forests. The effects of N and P addition on ecosystem carbon cycling and plant and microbial dynamics depend on forest successional stage, soil parent material and rainfall regime. Responses may depend on whether overall productivity is N- versus P-limited, although data to test this hypothesis are limited. These results highlight the many important gaps in our understanding of tropical dry forest responses to global change. Large-scale experiments are required to resolve these uncertainties.

  7. Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

    NASA Astrophysics Data System (ADS)

    Dong, W. Y.; Zhang, X. Y.; Liu, X. Y.; Fu, X. L.; Chen, F. S.; Wang, H. M.; Sun, X. M.; Wen, X. F.

    2015-09-01

    Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the phospholipid fatty acids (PLFAs) abundance especially in the N2P (100 kg ha-1 yr-1 of N +50 kg ha-1 yr-1 of P) treatment; the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK (control). Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. These findings indicate that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation.

  8. Effect of biodiesel addition on microbial community structure in a simulated fuel storage system.

    PubMed

    Restrepo-Flórez, Juan-Manuel; Bassi, Amarjeet; Rehmann, Lars; Thompson, Michael R

    2013-11-01

    Understanding changes in microbial structure due to biodiesel storage is important both for protecting integrity of storage systems and fuel quality management. In this work a simulated storage system was used to study the effect of biodiesel (0%, 25%, 50%, 75% and 100%) on a microbial population, which was followed by community level physiological profiling (CLPP), 16s rDNA analysis and plating in selective media. Results proved that structure and functionality were affected by biodiesel. CLPP showed at least three populations: one corresponding to diesel, one to biodiesel and one to blends of diesel and biodiesel. Analysis of 16s rDNA revealed that microbial composition was different for populations growing in diesel and biodiesel. Genera identified are known for degradation of hydrocarbons and emulsifier production. Maximum growth was obtained in biodiesel; however, microbial counts in standard media were lower for this samples. Acidification of culture media was observed at high biodiesel concentration.

  9. Bactericidal activity of the food color additive Phloxine B against Staphylococcus aureus and other food borne microbial pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The spread of antibiotic resistance among Staphylococcus aureus strains requires the development of new anti S. aureus agents. The objective of this study was evaluating the antimicrobial activity of the food color additive Phloxine B against S. aureus and other food microbial pathogens. Our result ...

  10. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  11. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid.

  12. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

    PubMed Central

    Robbins, Steven J.; Evans, Paul N.; Parks, Donovan H.; Golding, Suzanne D.; Tyson, Gene W.

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  13. Effects of nitrogen and phosphorus additions on soil microbial biomass and community structure in two reforested tropical forests.

    PubMed

    Liu, Lei; Gundersen, Per; Zhang, Wei; Zhang, Tao; Chen, Hao; Mo, Jiangming

    2015-01-01

    Elevated nitrogen (N) deposition may aggravate phosphorus (P) deficiency in forests in the warm humid regions of China. To our knowledge, the interactive effects of long-term N deposition and P availability on soil microorganisms in tropical replanted forests remain unclear. We conducted an N and P manipulation experiment with four treatments: control, N addition (15 g N m(-2)·yr(-1)), P addition (15 g P m(-2)·yr(-1)), and N and P addition (15 + 15 g N and P m(-2)·yr(-1), respectively) in disturbed (planted pine forest with recent harvests of understory vegetation and litter) and rehabilitated (planted with pine, but mixed with broadleaf returning by natural succession) forests in southern China. Nitrogen addition did not significantly affect soil microbial biomass, but significantly decreased the abundance of gram-negative bacteria PLFAs in both forest types. Microbial biomass increased significantly after P addition in the disturbed forest but not in the rehabilitated forest. No interactions between N and P additions on soil microorganisms were observed in either forest type. Our results suggest that microbial growth in replanted forests of southern China may be limited by P rather than by N, and this P limitation may be greater in disturbed forests. PMID:26395406

  14. Effects of nitrogen and phosphorus additions on soil microbial biomass and community structure in two reforested tropical forests.

    PubMed

    Liu, Lei; Gundersen, Per; Zhang, Wei; Zhang, Tao; Chen, Hao; Mo, Jiangming

    2015-09-23

    Elevated nitrogen (N) deposition may aggravate phosphorus (P) deficiency in forests in the warm humid regions of China. To our knowledge, the interactive effects of long-term N deposition and P availability on soil microorganisms in tropical replanted forests remain unclear. We conducted an N and P manipulation experiment with four treatments: control, N addition (15 g N m(-2)·yr(-1)), P addition (15 g P m(-2)·yr(-1)), and N and P addition (15 + 15 g N and P m(-2)·yr(-1), respectively) in disturbed (planted pine forest with recent harvests of understory vegetation and litter) and rehabilitated (planted with pine, but mixed with broadleaf returning by natural succession) forests in southern China. Nitrogen addition did not significantly affect soil microbial biomass, but significantly decreased the abundance of gram-negative bacteria PLFAs in both forest types. Microbial biomass increased significantly after P addition in the disturbed forest but not in the rehabilitated forest. No interactions between N and P additions on soil microorganisms were observed in either forest type. Our results suggest that microbial growth in replanted forests of southern China may be limited by P rather than by N, and this P limitation may be greater in disturbed forests.

  15. Effects of nitrogen and phosphorus additions on soil microbial biomass and community structure in two reforested tropical forests

    PubMed Central

    Liu, Lei; Gundersen, Per; Zhang, Wei; Zhang, Tao; Chen, Hao; Mo, Jiangming

    2015-01-01

    Elevated nitrogen (N) deposition may aggravate phosphorus (P) deficiency in forests in the warm humid regions of China. To our knowledge, the interactive effects of long-term N deposition and P availability on soil microorganisms in tropical replanted forests remain unclear. We conducted an N and P manipulation experiment with four treatments: control, N addition (15 g N m−2·yr−1), P addition (15 g P m−2·yr−1), and N and P addition (15 + 15 g N and P m−2·yr−1, respectively) in disturbed (planted pine forest with recent harvests of understory vegetation and litter) and rehabilitated (planted with pine, but mixed with broadleaf returning by natural succession) forests in southern China. Nitrogen addition did not significantly affect soil microbial biomass, but significantly decreased the abundance of gram-negative bacteria PLFAs in both forest types. Microbial biomass increased significantly after P addition in the disturbed forest but not in the rehabilitated forest. No interactions between N and P additions on soil microorganisms were observed in either forest type. Our results suggest that microbial growth in replanted forests of southern China may be limited by P rather than by N, and this P limitation may be greater in disturbed forests. PMID:26395406

  16. Consistent effects of canopy vs. understory nitrogen addition on the soil exchangeable cations and microbial community in two contrasting forests.

    PubMed

    Shi, Leilei; Zhang, Hongzhi; Liu, Tao; Zhang, Weixin; Shao, Yuanhu; Ha, Denglong; Li, Yuanqiu; Zhang, Chuangmao; Cai, Xi-an; Rao, Xingquan; Lin, Yongbiao; Zhou, Lixia; Zhao, Ping; Ye, Qing; Zou, Xiaoming; Fu, Shenglei

    2016-05-15

    Anthropogenic N deposition has been well documented to cause substantial impacts on the chemical and biological properties of forest soils. In most studies, however, atmospheric N deposition has been simulated by directly adding N to the forest floor. Such studies thus ignored the potentially significant effect of some key processes occurring in forest canopy (i.e., nitrogen retention) and may therefore have incorrectly assessed the effects of N deposition on soils. Here, we conducted an experiment that included both understory addition of N (UAN) and canopy addition of N (CAN) in two contrasting forests (temperate deciduous forest vs. subtropical evergreen forest). The goal was to determine whether the effects on soil exchangeable cations and microbial biomass differed between CAN and UAN. We found that N addition reduced pH, BS (base saturation) and exchangeable Ca and increased exchangeable Al significantly only at the temperate JGS site, and reduced the biomass of most soil microbial groups only at the subtropical SMT site. Except for soil exchangeable Mn, however, effects on soil chemical properties and soil microbial community did not significantly differ between CAN and UAN. Although biotic and abiotic soil characteristics differ significantly and the responses of both soil exchangeable cations and microbial biomass were different between the two study sites, we found no significant interactive effects between study site and N treatment approach on almost all soil properties involved in this study. In addition, N addition rate (25 vs. 50 kg N ha(-1) yr(-1)) did not show different effects on soil properties under both N addition approaches. These findings did not support previous prediction which expected that, by bypassing canopy effects (i.e., canopy retention and foliage fertilization), understory addition of N would overestimate the effects of N deposition on forest soil properties, at least for short time scale.

  17. Consistent effects of canopy vs. understory nitrogen addition on the soil exchangeable cations and microbial community in two contrasting forests.

    PubMed

    Shi, Leilei; Zhang, Hongzhi; Liu, Tao; Zhang, Weixin; Shao, Yuanhu; Ha, Denglong; Li, Yuanqiu; Zhang, Chuangmao; Cai, Xi-an; Rao, Xingquan; Lin, Yongbiao; Zhou, Lixia; Zhao, Ping; Ye, Qing; Zou, Xiaoming; Fu, Shenglei

    2016-05-15

    Anthropogenic N deposition has been well documented to cause substantial impacts on the chemical and biological properties of forest soils. In most studies, however, atmospheric N deposition has been simulated by directly adding N to the forest floor. Such studies thus ignored the potentially significant effect of some key processes occurring in forest canopy (i.e., nitrogen retention) and may therefore have incorrectly assessed the effects of N deposition on soils. Here, we conducted an experiment that included both understory addition of N (UAN) and canopy addition of N (CAN) in two contrasting forests (temperate deciduous forest vs. subtropical evergreen forest). The goal was to determine whether the effects on soil exchangeable cations and microbial biomass differed between CAN and UAN. We found that N addition reduced pH, BS (base saturation) and exchangeable Ca and increased exchangeable Al significantly only at the temperate JGS site, and reduced the biomass of most soil microbial groups only at the subtropical SMT site. Except for soil exchangeable Mn, however, effects on soil chemical properties and soil microbial community did not significantly differ between CAN and UAN. Although biotic and abiotic soil characteristics differ significantly and the responses of both soil exchangeable cations and microbial biomass were different between the two study sites, we found no significant interactive effects between study site and N treatment approach on almost all soil properties involved in this study. In addition, N addition rate (25 vs. 50 kg N ha(-1) yr(-1)) did not show different effects on soil properties under both N addition approaches. These findings did not support previous prediction which expected that, by bypassing canopy effects (i.e., canopy retention and foliage fertilization), understory addition of N would overestimate the effects of N deposition on forest soil properties, at least for short time scale. PMID:26930308

  18. 13C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells

    PubMed Central

    Luo, Shuai; Guo, Weihua; H. Nealson, Kenneth; Feng, Xueyang; He, Zhen

    2016-01-01

    Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and 13C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the 13C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that 13C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms. PMID:26868848

  19. ¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells.

    PubMed

    Luo, Shuai; Guo, Weihua; Nealson, Kenneth H; Feng, Xueyang; He, Zhen

    2016-02-12

    Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and (13)C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the (13)C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that (13)C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.

  20. On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis

    PubMed Central

    Li, Bing; Chun, Hyonho; Zhao, Hongyu

    2014-01-01

    We introduce a nonparametric method for estimating non-gaussian graphical models based on a new statistical relation called additive conditional independence, which is a three-way relation among random vectors that resembles the logical structure of conditional independence. Additive conditional independence allows us to use one-dimensional kernel regardless of the dimension of the graph, which not only avoids the curse of dimensionality but also simplifies computation. It also gives rise to a parallel structure to the gaussian graphical model that replaces the precision matrix by an additive precision operator. The estimators derived from additive conditional independence cover the recently introduced nonparanormal graphical model as a special case, but outperform it when the gaussian copula assumption is violated. We compare the new method with existing ones by simulations and in genetic pathway analysis. PMID:26401064

  1. Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats.

    PubMed

    Gomez-Garcia, Maria R; Davison, Michelle; Blain-Hartnung, Matthew; Grossman, Arthur R; Bhaya, Devaki

    2011-01-01

    Synechococcus sp. represents an ecologically diverse group of cyanobacteria found in numerous environments, including hot-spring microbial mats, where they are spatially distributed along thermal, light and oxygen gradients. These thermophiles engage in photosynthesis and aerobic respiration during the day, but switch to fermentative metabolism and nitrogen fixation at night. The genome of Synechococcus OS-B', isolated from Octopus Spring (Yellowstone National Park) contains a phn gene cluster encoding a phosphonate (Phn) transporter and a C-P lyase. A closely related isolate, Synechococcus OS-A, lacks this cluster, but contains genes encoding putative phosphonatases (Phnases) that appear to be active only in the presence of the Phn substrate. Both isolates grow well on several different Phns as a sole phosphorus (P) source. Interestingly, Synechococcus OS-B' can use the organic carbon backbones of Phns for heterotrophic growth in the dark, whereas in the light this strain releases organic carbon from Phn as ethane or methane (depending on the specific Phn available); Synechococcus OS-A has neither of these capabilities. These differences in metabolic strategies for assimilating the P and C of Phn by two closely related Synechococcus spp. are suggestive of niche-specific constraints in the evolution of nutrient assimilation pathways and syntrophic relationships among the microbial populations of the hot-spring mats. Thus, it is critical to evaluate levels of various P sources, including Phn, in thermally active habitats and the potential importance of these compounds in the biogeochemical cycling of P and C (some Phn compounds also contain N) in diverse terrestrial environments. PMID:20631809

  2. Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

    PubMed Central

    Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

    2014-01-01

    Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

  3. Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

    PubMed

    Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

    2014-01-01

    Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

  4. Microbially-accelerated consolidation of oil sands tailings. Pathway I: changes in porewater chemistry

    PubMed Central

    Siddique, Tariq; Kuznetsov, Petr; Kuznetsova, Alsu; Arkell, Nicholas; Young, Rozlyn; Li, Carmen; Guigard, Selma; Underwood, Eleisha; Foght, Julia M.

    2014-01-01

    Dispersed clay particles in mine tailings and soft sediments remain suspended for decades, hindering consolidation and challenging effective management of these aqueous slurries. Current geotechnical engineering models of self-weight consolidation of tailings do not consider microbial contribution to sediment behavior, however, here we show that microorganisms indigenous to oil sands tailings change the porewater chemistry and accelerate consolidation of oil sands tailings. A companion paper describes the role of microbes in alteration of clay chemistry in tailings. Microbial metabolism in mature fine tailings (MFT) amended with an organic substrate (hydrolyzed canola meal) produced methane (CH4) and carbon dioxide (CO2). Dissolution of biogenic CO2 lowered the pH of amended MFT to pH 6.4 vs. unamended MFT (pH 7.7). About 12% more porewater was recovered from amended than unamended MFT during 2 months of active microbial metabolism, concomitant with consolidation of tailings. The lower pH in amended MFT dissolved carbonate minerals, thereby releasing divalent cations including calcium (Ca2+) and magnesium (Mg2+) and increasing bicarbonate (HCO−3) in porewater. The higher concentrations increased the ionic strength of the porewater, in turn reducing the thickness of the diffuse double layer (DDL) of clay particles by reducing the surface charge potential (repulsive forces) of the clay particles. The combination of these processes accelerated consolidation of oil sands tailings. In addition, ebullition of biogenic gases created transient physical channels for release of porewater. In contrast, saturating the MFT with non-biogenic CO2 had little effect on consolidation. These results have significant implications for management and reclamation of oil sands tailings ponds and broad importance in anaerobic environments such as contaminated harbors and estuaries containing soft sediments rich in clays and organics. PMID:24711805

  5. Microbially-accelerated consolidation of oil sands tailings. Pathway I: changes in porewater chemistry.

    PubMed

    Siddique, Tariq; Kuznetsov, Petr; Kuznetsova, Alsu; Arkell, Nicholas; Young, Rozlyn; Li, Carmen; Guigard, Selma; Underwood, Eleisha; Foght, Julia M

    2014-01-01

    Dispersed clay particles in mine tailings and soft sediments remain suspended for decades, hindering consolidation and challenging effective management of these aqueous slurries. Current geotechnical engineering models of self-weight consolidation of tailings do not consider microbial contribution to sediment behavior, however, here we show that microorganisms indigenous to oil sands tailings change the porewater chemistry and accelerate consolidation of oil sands tailings. A companion paper describes the role of microbes in alteration of clay chemistry in tailings. Microbial metabolism in mature fine tailings (MFT) amended with an organic substrate (hydrolyzed canola meal) produced methane (CH4) and carbon dioxide (CO2). Dissolution of biogenic CO2 lowered the pH of amended MFT to pH 6.4 vs. unamended MFT (pH 7.7). About 12% more porewater was recovered from amended than unamended MFT during 2 months of active microbial metabolism, concomitant with consolidation of tailings. The lower pH in amended MFT dissolved carbonate minerals, thereby releasing divalent cations including calcium (Ca(2+)) and magnesium (Mg(2+)) and increasing bicarbonate (HCO(-) 3) in porewater. The higher concentrations increased the ionic strength of the porewater, in turn reducing the thickness of the diffuse double layer (DDL) of clay particles by reducing the surface charge potential (repulsive forces) of the clay particles. The combination of these processes accelerated consolidation of oil sands tailings. In addition, ebullition of biogenic gases created transient physical channels for release of porewater. In contrast, saturating the MFT with non-biogenic CO2 had little effect on consolidation. These results have significant implications for management and reclamation of oil sands tailings ponds and broad importance in anaerobic environments such as contaminated harbors and estuaries containing soft sediments rich in clays and organics. PMID:24711805

  6. Phosphorus applications improved the soil microbial responses under nitrogen additions in Chinese fir plantations of subtropical China

    NASA Astrophysics Data System (ADS)

    Zhang, Xinyu; Li, Dandan; Yang, Yang; Tang, Yuqian; Wang, Huimin; Chen, Fusheng; Sun, Xiaomin

    2016-04-01

    Nitrogen (N) deposition and low soil phosphorus (P) content aggravate the P limitation in subtropical forest soils. However, the responses of soil microbial communities, enzyme kinetics, and N cycling genes to P additions in subtropical plantations are still not clear. The hypothesis that P application can alleviate the limitation and improve the soil microbial properties was tested by long term field experiment in the Chinese fir plantations in subtropical China. Thirty 20m×20m plots were established in November 2011 and six different treatments were randomly distributed with five replicates. The treatments are control (CK, no N and P application), low N addition (N1: 50 kg N ha-1 yr-1), high N addition (N2: 100 kg N ha-1 yr-1), P addition (P: 50 kg P ha-1 yr-1), low N and P addition (N1P: 50 kg N ha-1 yr-1 and 50 kg P ha-1 yr-1) and high N and P addition (N2P: 100 kg N ha-1 yr-1 and 50 kg P ha-1 yr-1). A suite of responses of soil microorganism across four years (2012-2015) during three seasons (spring, summer and autumn) were measured. Following 4 years of N amendments, fertilized soils were more acidic and had lower soil microbial biomass carbon contents than CK. However, P alleviated the soil acidification and increased the soil microbial biomass carbon contents. Increases in microbial PLFA biomarkers and exoenzyme kinetics in N fertilized plots were observed in the initial year (2013) but reduced since then (2014 and 2015). Whereas P amendments increased the soil PLFA biomarkers and exoenzyme kinetics through the four years except that the acid phosphatase activities declined after 3 years applications. P applications enhanced the soil N cycling by increases the abundances of nitrifiers (ammonia-oxidizing archea) and denitrifiers (nos Z, norG, and nirK). The bacterial and fungal residue carbons (calculated by amino sugar indicators) were higher under NP fertilizations than the other treatments. Our results suggest that P application could improve the soil

  7. A comparison of additional treatment processes to limit particle accumulation and microbial growth during drinking water distribution.

    PubMed

    Liu, G; Lut, M C; Verberk, J Q J C; Van Dijk, J C

    2013-05-15

    Water quality changes, particle accumulation and microbial growth occurring in pilot-scale water distribution systems fed with normally treated and additional treated groundwater were monitored over a period of almost one year. The treatment processes were ranked in the following order: nanofiltration (NF) > (better than) ultrafiltration (UF) > ion exchange (IEX) for limiting particle accumulation. A different order was found for limiting overall microbial growth: NF > IEX > UF. There were strong correlations between particle load and particle accumulation, and between nutrient load and microbial growth. It was concluded that particle accumulation can be controlled by reducing the particle load in water treatment plants; and the microbial growth can be better controlled by limiting organic nutrients rather than removing biomass in water treatment plants. The major focus of this study was on microbial growth. The results demonstrated that growth occurred in all types of treated water, including the phases of bulk water, biofilm and loose deposits. Considering the growth in different phases, similar growth in bulk water was observed for all treatments; NF strongly reduced growth both in loose deposits and in biofilm; UF promoted growth in biofilm, while strongly limiting growth in loose deposits. IEX had good efficiency in between UF and NF, limiting both growths in loose deposits and in biofilm. Significant growth was found in loose deposits, suggesting that loose deposit biomass should be taken into account for growth evaluation and/or prediction. Strong correlations were found between microbial growth and pressure drop in a membrane fouling simulator which proved that a membrane fouling simulator can be a fast growth predictor (within a week). Different results obtained by adenosine triphosphate and flow cytometry cell counts revealed that ATP can accurately describe both suspended and particle-associated biomass, and flow cytometry files of TCC measurements needs

  8. Response of Functional Structure of Soil Microbial Community to Multi-level Nitrogen Additions on the Central Tibetan Plateau

    NASA Astrophysics Data System (ADS)

    Zhang, G.; Yuan, Y.

    2015-12-01

    The use of fossil fuels and fertilizers has increased the amount of biologically reactive nitrogen in the atmosphere over the past century. Tibet is the one of the most threatened regions by nitrogen deposition, thus understanding how its microbial communities function maybe of high importance to predicting microbial responses to nitrogen deposition. Here we describe a short-time nitrogen addition conducted in an alpine steppe ecosystem to investigate the response of functional structure of soil microbial community to multi-level nitrogen addition. Using a GeoChip 4.0, we showed that functional diversities and richness of functional genes were unchanged at low level of nitrogen fertilizer inputs (<20 kg N ha-1 yr-1), but significantly decreased at higher nitrogen fertilizer inputs (>=40 kg N ha-1 yr-1). Detrended correspondence analysis indicated that the functional structure of microbial communities was markedly different across the nitrogen gradients. Most C degradation genes whose abundances significantly increased under elevated N fertilizer were those involved in the degradation of relatively labile C (starch, hemicellulose, cellulose), whereas the abundance of certain genes involved in the degradation of recalcitrant C (i.e. lignin) was largely decreased (such as manganese peroxidase, mnp). The results suggest that the elevated N fertilization rates might significantly accelerate the labile C degradation, but might not spur recalcitrant C degradation. The combined effect of gdh and ureC genes involved in N cycling appeared to shift the balance between ammonia and organic N toward organic N ammonification and hence increased the N mineralization potential. Moreover, Urease directly involved in urea mineralization significantly increased. Lastly, Canonical correspondence analysis showed that soil (TOC+NH4++NO3-+NO2-+pH) and plant (Aboveground plant productivity + Shannon Diversity) variables could explain 38.9% of the variation of soil microbial community

  9. Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate

    PubMed Central

    Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge M.; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2016-01-01

    CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs. PMID:27047478

  10. Formate-Dependent Microbial Conversion of CO2 and the Dominant Pathways of Methanogenesis in Production Water of High-temperature Oil Reservoirs Amended with Bicarbonate.

    PubMed

    Yang, Guang-Chao; Zhou, Lei; Mbadinga, Serge M; Liu, Jin-Feng; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2016-01-01

    CO2 sequestration in deep-subsurface formations including oil reservoirs is a potential measure to reduce the CO2 concentration in the atmosphere. However, the fate of the CO2 and the ecological influences in carbon dioxide capture and storage (CDCS) facilities is not understood clearly. In the current study, the fate of CO2 (in bicarbonate form; 0∼90 mM) with 10 mM of formate as electron donor and carbon source was investigated with high-temperature production water from oilfield in China. The isotope data showed that bicarbonate could be reduced to methane by methanogens and major pathway of methanogenesis could be syntrophic formate oxidation coupled with CO2 reduction and formate methanogenesis under the anaerobic conditions. The bicarbonate addition induced the shift of microbial community. Addition of bicarbonate and formate was associated with a decrease of Methanosarcinales, but promotion of Methanobacteriales in all treatments. Thermodesulfovibrio was the major group in all the samples and Thermacetogenium dominated in the high bicarbonate treatments. The results indicated that CO2 from CDCS could be transformed to methane and the possibility of microbial CO2 conversion for enhanced microbial energy recovery in oil reservoirs. PMID:27047478

  11. Alteration of extracellular enzyme activity and microbial abundance by biochar addition: Implication for carbon sequestration in subtropical mangrove sediment.

    PubMed

    Luo, Ling; Gu, Ji-Dong

    2016-11-01

    Biochar has attracted more and more attention due to its essential role in adsorbing pollutants, improving soil fertility, and modifying greenhouse gas emission. However, the influences of biochar on extracellular enzyme activity and microbial abundance are still lack and debatable. Currently, there is no information about the impact of biochar on the function of mangrove ecosystems. Therefore, we explored the effects of biochar on extracellular enzyme activity and microbial abundance in subtropical mangrove sediment, and further estimated the contribution of biochar to C sequestration. In this study, sediments were amended with 0 (control), 0.5, 1.0 and 2.0% of biochar and incubated at 25 °C for 90 days. After incubation, enzyme activities, microbial abundance and the increased percentage of sediment organic C content were determined. Both increase (phenol oxidase and β-glucosidase) and decrease (peroxidase, N-acetyl-glucosaminidase and acid phosphatase) of enzyme activities were observed in biochar treatments, but only peroxidase activity showed statistical significance (at least p < 0.01) compared to the control. Moreover, the activities of all enzymes tested were significantly related to the content of biochar addition (at least p < 0.05). On the other hand, bacterial and fungal abundance in biochar treatments were remarkably lower than control (p < 0.001), and the significantly negative relationship (p < 0.05) between bacterial abundance and the content of biochar was found. Additionally, the increased percentage of organic C gradually increased with biochar addition rate, which provided evidence for applying biochar to mitigate climate change. Given the importance of microorganisms and enzyme activities in sediment organic matter decomposition, the increased C sequestration might be explained by the large decrease of microbial abundance and enzyme activity after biochar intervention. PMID:27454094

  12. Alteration of extracellular enzyme activity and microbial abundance by biochar addition: Implication for carbon sequestration in subtropical mangrove sediment.

    PubMed

    Luo, Ling; Gu, Ji-Dong

    2016-11-01

    Biochar has attracted more and more attention due to its essential role in adsorbing pollutants, improving soil fertility, and modifying greenhouse gas emission. However, the influences of biochar on extracellular enzyme activity and microbial abundance are still lack and debatable. Currently, there is no information about the impact of biochar on the function of mangrove ecosystems. Therefore, we explored the effects of biochar on extracellular enzyme activity and microbial abundance in subtropical mangrove sediment, and further estimated the contribution of biochar to C sequestration. In this study, sediments were amended with 0 (control), 0.5, 1.0 and 2.0% of biochar and incubated at 25 °C for 90 days. After incubation, enzyme activities, microbial abundance and the increased percentage of sediment organic C content were determined. Both increase (phenol oxidase and β-glucosidase) and decrease (peroxidase, N-acetyl-glucosaminidase and acid phosphatase) of enzyme activities were observed in biochar treatments, but only peroxidase activity showed statistical significance (at least p < 0.01) compared to the control. Moreover, the activities of all enzymes tested were significantly related to the content of biochar addition (at least p < 0.05). On the other hand, bacterial and fungal abundance in biochar treatments were remarkably lower than control (p < 0.001), and the significantly negative relationship (p < 0.05) between bacterial abundance and the content of biochar was found. Additionally, the increased percentage of organic C gradually increased with biochar addition rate, which provided evidence for applying biochar to mitigate climate change. Given the importance of microorganisms and enzyme activities in sediment organic matter decomposition, the increased C sequestration might be explained by the large decrease of microbial abundance and enzyme activity after biochar intervention.

  13. Microbial pathways and palaeoenvironmental conditions involved in the formation of phosphorite grains, Safaga District, Egypt

    NASA Astrophysics Data System (ADS)

    Salama, Walid; El-Kammar, Ahmed; Saunders, Martin; Morsy, Rania; Kong, Charlie

    2015-07-01

    Phosphatic grains of the shallow marine phosphorite deposits of Egypt are classified as either phosphatic bioclasts preserving biological structure (e.g. skeletal fragments such as fish bones and teeth) or phosphatic peloids and intraclasts. This study describes the destructive and constructive microbial pathways represented by bioerosion of bones by endolithic cyanobacteria and accretion of phosphatic peloids by bacteria. The palaeoenvironmental conditions and post-depositional/diagenetic history of these grains have also been considered. Scanning and transmission electron microscopy showed that the phosphatic peloids under transmitted light microscopy are composed mainly of microspheres (0.5 to 2.5 μm) similar in shape and size to coccoid-like bacteria. Chemical mapping showed that these microspheres are composed of carbonate-fluorapatite (CFA) and surrounded by degraded carbonaceous matrix. These grains are suggested to be reworked from pre-existing microbial mats during transgressive-regressive cycles affecting the southern Tethyan Campanian-Maastrichtian shallow continental shelf. The bioerosion of phosphatic bones is characterized by a network of meandering microborings that penetrated inward from the bone surface by endolithic cyanobacteria. The bioerosion of bones resulted in a gradual centripetal digestion and conversion of bones into micritic phosphate peloids. The bioerosion mechanism is probably started in the acidic sheath surrounding cyanobacteria followed by supersaturation of PO4 and reprecipitation of crystalline CFA as electron dense remineralized rims. Electron microprobe microanalyses showed that the remineralized microbored areas are higher in CaO, P2O5, and F and depleted in Cl, relative to unaltered bones. A gradual demineralization of remineralized rims followed by dissolution of cyanobacterial cells is probably occurred during diagenesis and meteoric water alteration leaving behind empty microborings. Bone exposed to meteoric water

  14. Microbial Community Responses to Organophosphate Substrate Additions in Contaminated Subsurface Sediments

    PubMed Central

    Martinez, Robert J.; Wu, Cindy H.; Beazley, Melanie J.; Andersen, Gary L.; Conrad, Mark E.; Hazen, Terry C.; Taillefert, Martial; Sobecky, Patricia A.

    2014-01-01

    Background Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. Methodology/Principal Findings Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO43−) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%–50% and 3%–17% of total detected Archaea and Bacteria, respectively. Conclusions/Significance This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that

  15. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  16. Improved TNT detoxification by starch addition in a nitrogen-fixing Methylophilus-dominant aerobic microbial consortium.

    PubMed

    Khan, Muhammad Imran; Lee, Jaejin; Yoo, Keunje; Kim, Seonghoon; Park, Joonhong

    2015-12-30

    In this study, a novel aerobic microbial consortium for the complete detoxification of 2,4,6-trinitrotoluene (TNT) was developed using starch as a slow-releasing carbon source under nitrogen-fixing conditions. Aerobic TNT biodegradation coupled with microbial growth was effectively stimulated by the co-addition of starch and TNT under nitrogen-fixing conditions. The addition of starch with TNT led to TNT mineralization via ring cleavage without accumulation of any toxic by-products, indicating improved TNT detoxification by the co-addition of starch and TNT. Pyrosequencing targeting the bacterial 16S rRNA gene suggested that Methylophilus and Pseudoxanthomonas population were significantly stimulated by the co-addition of starch and TNT and that the Methylophilus population became predominant in the consortium. Together with our previous study regarding starch-stimulated RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) degradation (Khan et al., J. Hazard. Mater. 287 (2015) 243-251), this work suggests that the co-addition of starch with a target explosive is an effective way to stimulate aerobic explosive degradation under nitrogen-fixing conditions for enhancing explosive detoxification.

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

    PubMed

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

    2016-01-01

    Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample. PMID:27578483

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

    PubMed Central

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

    2016-01-01

    Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample. PMID:27578483

  19. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    DOE PAGES

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; et al

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS).more » Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have implications on atmospheric gas-phase chemistry and the oxidative stability of organic substances.« less

  20. Effects of feeding corn silage inoculated with microbial additives on the ruminal fermentation, microbial protein yield, and growth performance of lambs.

    PubMed

    Basso, F C; Adesogan, A T; Lara, E C; Rabelo, C H S; Berchielli, T T; Teixeira, I A M A; Siqueira, G R; Reis, R A

    2014-12-01

    This study aimed to examine the effects of feeding corn silage inoculated without or with either Lactobacillus buchneri (LB) alone or a combination of LB and Lactobacillus plantarum (LBLP) on the apparent digestibility, ruminal fermentation, microbial protein synthesis, and growth performance of lambs. Thirty Santa Inês×Dorper crossbred intact males lambs weighing 20.4±3.8 kg were blocked by weight into 10 groups. Lambs in each group were randomly assigned to 1 of the following 3 dietary treatments: untreated (Control), LB, and LBLP silage. Lambs were fed experimental diets for 61 d. The apparent digestibility was indirectly estimated from indigestible NDF measured on d 57 to 59. Spot urine samples were collected from all animals on d 59 to estimate microbial protein synthesis. Lambs were slaughtered for carcass evaluation on d 61 when they weighed 32.4±5.2 kg. Six additional ruminally cannulated Santa Inês×Dorper crossbred wethers weighing 40.5±1.8 kg were used to examine dietary effects on ruminal fermentation. Average daily gain was increased when lambs were fed LBLP silage (P<0.05) but not LB silage. The LBLP silage had the highest (P<0.05) lactic acid concentration and both inoculated silages had greater acetic acid concentrations than the Control silage (P<0.05). Inoculation of corn silage increased intakes of DM, OM, CP, NDF, total carbohydrate (CHO), and GE by the lambs but decreased digestibility of DM, OM, CP, total and nonstructural carbohydrates, and concentration of GE and ME. (P<0.05). Nevertheless, lambs fed inoculated silages had greater microbial N supply than those on the Control treatment (P<0.05). The acetate to propionate ratio was lower in ruminal fluid of wethers in LBLP treatment than LB and Control treatment (P<0.05) and ruminal pH tended to be greater in LB lambs than in LBLP and Control wethers (P<0.10). Finally, the inoculation with both bacteria combined enhanced the silage fermentation. The intakes of DM, OM, CP, NDF, and GE

  1. An enhanced anaerobic membrane bioreactor treating bamboo industry wastewater by bamboo charcoal addition: Performance and microbial community analysis.

    PubMed

    Xia, Tian; Gao, Xinyi; Wang, Caiqin; Xu, Xiangyang; Zhu, Liang

    2016-11-01

    In this study, two anaerobic membrane bioreactors (AnMBRs) were operated for 150days to treat bamboo industry wastewater (BIWW), and one of them was enhanced with bamboo charcoal (B-AnMBR). During the steady period, average chemical oxygen demand (COD) removal efficiencies of 94.5±2.9% and 89.1±3.1% were achieved in B-AnMBR and AnMBR, respectively. The addition of bamboo charcoal (BC) increased the amount of biomass and improved the performance of the systems. A higher biogas production and methane yield were also observed in B-AnMBR. Regarding the issue of membrane fouling, BC lowered the soluble microbial product (SMP) content by approximately 62.73mg/L and decreased the membrane resistance, thereby mitigating membrane fouling. Analysis of the microbial communities demonstrated that BC increased the microbial diversity and promoted the activity of Methanosaeta, Methanospirillum, and Methanobacterium, which are dominant in methane production. PMID:27552720

  2. Fertilizer addition lessens the flux of microbial carbon to higher trophic levels in soil food webs of grassland.

    PubMed

    Lemanski, Kathleen; Scheu, Stefan

    2014-10-01

    Roots and root-derived C compounds are increasingly recognised as important resources for soil animal food webs. We used (13)C-labelled glucose as a model C compound representing root exudates to follow the incorporation of root-derived C into the soil animal food web of a temperate grassland over a period of 52 weeks. We investigated variations in glucose C incorporation with fertilizer addition and sward composition, i.e. variations in plant functional groups. The approach allowed the differentiation of trophic chains based on primary decomposers feeding on litter and phytophagous species feeding on roots (i.e. not incorporating glucose C) from those based on secondary decomposers feeding on microorganisms (thereby assimilating glucose C). Each of the studied soil animal species incorporated glucose C, indicating that the majority of grassland soil animal species rely on microorganisms as food resources with microorganisms being fuelled by root exudates. However, incorporation of glucose C into soil animal species varied markedly with species identity, suggesting that detritivorous microarthropods complement each other in channelling microbial C through soil food webs. Fertilizer addition markedly reduced the concentration of glucose C in most soil animal species as well as the absolute transfer of glucose C into oribatid mites as major secondary decomposers. The results suggest that fertilizer addition shifts the basis of the decomposer food web towards the use of unlabelled resources, presumably roots, i.e. towards a herbivore system, thereby lessening the link between microorganisms and microbial grazers and hampering the propagation of microbial C to higher trophic levels.

  3. Effect of Microbial and Chemical Combo Additives on Nutritive Value and Fermentation Characteristic of Whole Crop Barley Silage

    PubMed Central

    Kim, Dong Hyeon; Amanullah, Sardar M.; Lee, Hyuk Jun; Joo, Young Ho; Kim, Sam Churl

    2015-01-01

    This study was conducted to assess the effects of microbial and chemical combo additives on nutritive values, fermentation indices and aerobic stability of whole crop barley silage. Barley forage (Youngyang) was harvested at about 30% dry matter (DM) by treatments, chopped to 5 cm length and treated with distilled water only (CON), Lactobacillus plantarum (INO), propionic acid (PRO) or an equal mixture of INO and PRO (MIX). Barley forages were ensiled in 4 replications for 0, 2, 7, and 100 days. On 100 days of ensiling, MIX silage had higher (p<0.05) in vitro DM digestibility than CON silage, but lower (p<0.05) acid detergent fiber concentration. The pH in all treated silages was lower (p<0.05) than CON silage. The MIX silage had higher (p<0.05) lactate concentration and lactate to acetate ratio than in CON, but lower (p<0.05) yeast count. Aerobic stability in CON, PRO, and MIX silages were higher (p<0.05) than in INO silage. It is concluded that microbial and chemical combo additives using L. plantarum and propionic acid could efficiently improve nutritive values of barley silage in terms of increased in vitro DM digestibility compared to other treatments. In addition, all treatments except CON reduced yeast count which is the initiate microorganism of aerobic spoilage. PMID:26323517

  4. Multiple Pathways Suppress Telomere Addition to DNA Breaks in the Drosophila Germline

    PubMed Central

    Beaucher, Michelle; Zheng, Xiao-Feng; Amariei, Flavia; Rong, Yikang S.

    2012-01-01

    Telomeres protect chromosome ends from being repaired as double-strand breaks (DSBs). Just as DSB repair is suppressed at telomeres, de novo telomere addition is suppressed at the site of DSBs. To identify factors responsible for this suppression, we developed an assay to monitor de novo telomere formation in Drosophila, an organism in which telomeres can be established on chromosome ends with essentially any sequence. Germline expression of the I-SceI endonuclease resulted in precise telomere formation at its cut site with high efficiency. Using this assay, we quantified the frequency of telomere formation in different genetic backgrounds with known or possible defects in DNA damage repair. We showed that disruption of DSB repair factors (Rad51 or DNA ligase IV) or DSB sensing factors (ATRIP or MDC1) resulted in more efficient telomere formation. Interestingly, partial disruption of factors that normally regulate telomere protection (ATM or NBS) also led to higher frequencies of telomere formation, suggesting that these proteins have opposing roles in telomere maintenance vs. establishment. In the ku70 mutant background, telomere establishment was preceded by excessive degradation of DSB ends, which were stabilized upon telomere formation. Most strikingly, the removal of ATRIP caused a dramatic increase in telomeric retrotransposon attachment to broken ends. Our study identifies several pathways thatsuppress telomere addition at DSBs, paving the way for future mechanistic studies. PMID:22446318

  5. A Gut Microbial Metabolite of Linoleic Acid, 10-Hydroxy-cis-12-octadecenoic Acid, Ameliorates Intestinal Epithelial Barrier Impairment Partially via GPR40-MEK-ERK Pathway*

    PubMed Central

    Miyamoto, Junki; Mizukure, Taichi; Park, Si-Bum; Kishino, Shigenobu; Kimura, Ikuo; Hirano, Kanako; Bergamo, Paolo; Rossi, Mauro; Suzuki, Takuya; Arita, Makoto; Ogawa, Jun; Tanabe, Soichi

    2015-01-01

    Gut microbial metabolites of polyunsaturated fatty acids have attracted much attention because of their various physiological properties. Dysfunction of tight junction (TJ) in the intestine contributes to the pathogenesis of many disorders such as inflammatory bowel disease. We evaluated the effects of five novel gut microbial metabolites on tumor necrosis factor (TNF)-α-induced barrier impairment in Caco-2 cells and dextran sulfate sodium-induced colitis in mice. 10-Hydroxy-cis-12-octadecenoic acid (HYA), a gut microbial metabolite of linoleic acid, suppressed TNF-α and dextran sulfate sodium-induced changes in the expression of TJ-related molecules, occludin, zonula occludens-1, and myosin light chain kinase. HYA also suppressed the expression of TNF receptor 2 (TNFR2) mRNA and protein expression in Caco-2 cells and colonic tissue. In addition, HYA suppressed the protein expression of TNFR2 in murine intestinal epithelial cells. Furthermore, HYA significantly up-regulated G protein-coupled receptor (GPR) 40 expression in Caco-2 cells. It also induced [Ca2+]i responses in HEK293 cells expressing human GPR40 with higher sensitivity than linoleic acid, its metabolic precursor. The barrier-recovering effects of HYA were abrogated by a GPR40 antagonist and MEK inhibitor in Caco-2 cells. Conversely, 10-hydroxyoctadacanoic acid, which is a gut microbial metabolite of oleic acid and lacks a carbon-carbon double bond at Δ12 position, did not show these TJ-restoring activities and down-regulated GPR40 expression. Therefore, HYA modulates TNFR2 expression, at least partially, via the GPR40-MEK-ERK pathway and may be useful in the treatment of TJ-related disorders such as inflammatory bowel disease. PMID:25505251

  6. Effects of Microbial Additives on Chemical Composition and Fermentation Characteristics of Barley Silage

    PubMed Central

    Amanullah, S. M.; Kim, D. H.; Lee, H. J.; Joo, Y. H.; Kim, S. B.; Kim, S. C.

    2014-01-01

    This study examined the effects of bacterial inoculants on chemical composition and fermentation indices of barley silage. Barley forage (Youngyang) was harvested at 24% dry matter (DM) and wilted to 47.9% DM. The wilted barley forage was chopped to 3–5 cm length and applied with no inoculant (CON), L. plantarum (1×1010 cfu/g, LP) or Effective Microorganisms (0.5×109 cfu/g, EM). Then the forages were ensiled in four replications for each treatment in 20 L mini silos and stored for 100 days. The contents of crude protein and ether extract were higher in CON silage ensiled for 100-d, while the contents of DM and crude ash were higher in EM silage (p<0.05). The contents of ADF, NDF and hemicellulose as well as the in vitro DM digestibility were not affected by microbial inoculation (p>0.05). The pH, ammonia-N concentration and lactate to acetate ratio were higher (p<0.05) in CON silage, while lactate concentrations were higher (p<0.05) in CON and LP silage. Acetate concentration and lactic acid bacteria was increased (p<0.05) by both inoculants (LP and EM), but propionate concentration and yeast was increased (p<0.05) by EM and LP, respectively. These results indicated that the fermentation quality of barley silage was improved by the application of bacterial inoculants. PMID:25049981

  7. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    SciTech Connect

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Sarathy, S. Mani

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS). Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have

  8. Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members.

    PubMed

    Tan, Boonfei; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia

    2013-10-01

    A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6-C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic-fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO(2) fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction. PMID:24237341

  9. Composting of waste paint sludge containing melamine resin as affected by nutrients and gypsum addition and microbial inoculation.

    PubMed

    Tian, Yongqiang; Chen, Liming; Gao, Lihong; Michel, Frederick C; Wan, Caixia; Li, Yebo; Dick, Warren A

    2012-03-01

    Melamine formaldehyde resins have hard and durable properties and are found in many products, including automobile paints. These resins contain high concentrations of nitrogen and, if properly composted, can yield valuable products. We evaluated the effects of starter compost, nutrients, gypsum and microbial inoculation on composting of paint sludge containing melamine resin. A bench-scale composting experiment was conducted at 55 °C for 91 days and then at 30 °C for an additional 56 days. After 91 days, the composts were inoculated with a mixed population of melamine-degrading microorganisms. Melamine resin degradation after the entire 147 days of composting varied between 73 and 95% for the treatments with inoculation of microorganisms compared to 55-74% for the treatments without inoculation. Degradation was also enhanced by nutrients and gypsum additions. Our results infer that large scale composting of melamine resins in paint sludge is possible.

  10. Composting of waste paint sludge containing melamine resin as affected by nutrients and gypsum addition and microbial inoculation.

    PubMed

    Tian, Yongqiang; Chen, Liming; Gao, Lihong; Michel, Frederick C; Wan, Caixia; Li, Yebo; Dick, Warren A

    2012-03-01

    Melamine formaldehyde resins have hard and durable properties and are found in many products, including automobile paints. These resins contain high concentrations of nitrogen and, if properly composted, can yield valuable products. We evaluated the effects of starter compost, nutrients, gypsum and microbial inoculation on composting of paint sludge containing melamine resin. A bench-scale composting experiment was conducted at 55 °C for 91 days and then at 30 °C for an additional 56 days. After 91 days, the composts were inoculated with a mixed population of melamine-degrading microorganisms. Melamine resin degradation after the entire 147 days of composting varied between 73 and 95% for the treatments with inoculation of microorganisms compared to 55-74% for the treatments without inoculation. Degradation was also enhanced by nutrients and gypsum additions. Our results infer that large scale composting of melamine resins in paint sludge is possible. PMID:22243857

  11. Effects of biochar addition on greenhouse gas emissions and microbial responses in a short-term laboratory experiment.

    PubMed

    Yoo, Gayoung; Kang, Hojeong

    2012-01-01

    Biochar application to soil has drawn much attention as a strategy to sequester atmospheric carbon in soil ecosystems. The applicability of this strategy as a climate change mitigation option is limited by our understanding of the mechanisms responsible for the observed changes in greenhouse gas emissions from soils, microbial responses, and soil fertility changes. We conducted an 8-wk laboratory incubation using soils from PASTURE (silt loam) and RICE PADDY (silt loam) sites with and without two types of biochar (biochar from swine manure [CHAR-M] and from barley stover [CHAR-B]). Responses to addition of the different biochars varied with the soil source. Addition of CHAR-B did not change CO and CH evolution from the PASTURE or the RICE PADDY soils, but there was a decrease in NO emissions from the PASTURE soil. The effects of CHAR-M addition on greenhouse gas emissions were different for the soils. The most substantial change was an increase in NO emissions from the RICE PADDY soil. This result was attributed to a combination of abundant denitrifiers in this soil and increased net nitrogen mineralization. Soil phosphatase and N-acetylglucosaminidase activity in the CHAR-B-treated soils was enhanced compared with the controls for both soils. Fungal biomass was higher in the CHAR-B-treated RICE PADDY soil. From our results, we suggest CHAR-B to be an appropriate amendment for the PASTURE and RICE PADDY soils because it provides increased nitrogen availability and microbial activity with no net increase in greenhouse gas emissions. Application of CHAR-M to RICE PADDY soils could result in excess nitrogen availability, which may increase NO emissions and possible NO leaching problems. Thus, this study confirms that the ability of environmentally sound biochar additions to sequester carbon in soils depends on the characteristics of the receiving soil as well as the nature of the biochar.

  12. Effects of biochar addition on greenhouse gas emissions and microbial responses in a short-term laboratory experiment.

    PubMed

    Yoo, Gayoung; Kang, Hojeong

    2012-01-01

    Biochar application to soil has drawn much attention as a strategy to sequester atmospheric carbon in soil ecosystems. The applicability of this strategy as a climate change mitigation option is limited by our understanding of the mechanisms responsible for the observed changes in greenhouse gas emissions from soils, microbial responses, and soil fertility changes. We conducted an 8-wk laboratory incubation using soils from PASTURE (silt loam) and RICE PADDY (silt loam) sites with and without two types of biochar (biochar from swine manure [CHAR-M] and from barley stover [CHAR-B]). Responses to addition of the different biochars varied with the soil source. Addition of CHAR-B did not change CO and CH evolution from the PASTURE or the RICE PADDY soils, but there was a decrease in NO emissions from the PASTURE soil. The effects of CHAR-M addition on greenhouse gas emissions were different for the soils. The most substantial change was an increase in NO emissions from the RICE PADDY soil. This result was attributed to a combination of abundant denitrifiers in this soil and increased net nitrogen mineralization. Soil phosphatase and N-acetylglucosaminidase activity in the CHAR-B-treated soils was enhanced compared with the controls for both soils. Fungal biomass was higher in the CHAR-B-treated RICE PADDY soil. From our results, we suggest CHAR-B to be an appropriate amendment for the PASTURE and RICE PADDY soils because it provides increased nitrogen availability and microbial activity with no net increase in greenhouse gas emissions. Application of CHAR-M to RICE PADDY soils could result in excess nitrogen availability, which may increase NO emissions and possible NO leaching problems. Thus, this study confirms that the ability of environmentally sound biochar additions to sequester carbon in soils depends on the characteristics of the receiving soil as well as the nature of the biochar. PMID:22751062

  13. Evaluation of Virus and Microbial Purification in Wastewater Soil Absorption Systems Using Multicomponent Surrogate and Tracer Addition

    NASA Astrophysics Data System (ADS)

    Van Cuyk, S.; Siegrist, R. L.

    2001-05-01

    Wastewater soil absorption systems (WSAS) have the potential to achieve high treatment efficiencies, yet the understanding and predictability of performance with respect to removal of viruses and other pathogens remains limited. As part of a long-term program of research to elucidate the fundamental relationships between performance and WSAS process designs and environmental conditions, research has been completed to evaluate virus and microbial purification using multicomponent surrogate and tracer addition. The primary goal of this research was to quantify the removal of virus and bacteria in land-based treatment systems through the use of microbial surrogates and conservative tracers during controlled experiments with 3-D lysimeters in the laboratory and testing of mature WSAS under field conditions. The surrogates and tracers employed to date have included two viruses (MS-2 and PRD-1 bacteriophages), one bacterium (ice-nucleating active (INA) Pseudomonas) and one conservative tracer (bromide). In addition, efforts have been made to determine the relationship between virus and fecal coliforms in soil samples below a WSAS, and the correlation between E.coli concentrations measured in the percolating soil solution as compared to those estimated from analysis of soil solids samples. The results of the research completed to date have revealed that episodic breakthrough of virus and bacteria does occur in WSAS, particularly during early operation, but that a 3-log removal of virus and near complete removal of fecal coliform bacteria can reasonably be expected in WSAS with 60 to 90 cm of sandy medium. Additionally, results from the research indicate that fecal coliforms may be indicative of virus in soil media directly beneath WSAS receiving STE and the concentrations of fecal coliforms in percolating soil solution may be conservatively estimated from analysis of soil solids. Further laboratory and field research is continuing.

  14. Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?

    NASA Astrophysics Data System (ADS)

    Scoma, Alberto; Barbato, Marta; Hernandez-Sanabria, Emma; Mapelli, Francesca; Daffonchio, Daniele; Borin, Sara; Boon, Nico

    2016-03-01

    Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO43‑ uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential.

  15. Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?

    PubMed

    Scoma, Alberto; Barbato, Marta; Hernandez-Sanabria, Emma; Mapelli, Francesca; Daffonchio, Daniele; Borin, Sara; Boon, Nico

    2016-03-29

    Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO4(3-) uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential.

  16. Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?

    PubMed Central

    Scoma, Alberto; Barbato, Marta; Hernandez-Sanabria, Emma; Mapelli, Francesca; Daffonchio, Daniele; Borin, Sara; Boon, Nico

    2016-01-01

    Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO43− uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential. PMID:27020120

  17. Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?

    PubMed

    Scoma, Alberto; Barbato, Marta; Hernandez-Sanabria, Emma; Mapelli, Francesca; Daffonchio, Daniele; Borin, Sara; Boon, Nico

    2016-01-01

    Oil spills represent an overwhelming carbon input to the marine environment that immediately impacts the sea surface ecosystem. Microbial communities degrading the oil fraction that eventually sinks to the seafloor must also deal with hydrostatic pressure, which linearly increases with depth. Piezosensitive hydrocarbonoclastic bacteria are ideal candidates to elucidate impaired pathways following oil spills at low depth. In the present paper, we tested two strains of the ubiquitous Alcanivorax genus, namely A. jadensis KS_339 and A. dieselolei KS_293, which is known to rapidly grow after oil spills. Strains were subjected to atmospheric and mild pressure (0.1, 5 and 10 MPa, corresponding to a depth of 0, 500 and 1000 m, respectively) providing n-dodecane as sole carbon source. Pressures equal to 5 and 10 MPa significantly lowered growth yields of both strains. However, in strain KS_293 grown at 10 MPa CO2 production per cell was not affected, cell integrity was preserved and PO4(3-) uptake increased. Analysis of its transcriptome revealed that 95% of its genes were downregulated. Increased transcription involved protein synthesis, energy generation and respiration pathways. Interplay between these factors may play a key role in shaping the structure of microbial communities developed after oil spills at low depth and limit their bioremediation potential. PMID:27020120

  18. Effect of addition of Versagel on microbial, chemical, and physical properties of low-fat yogurt.

    PubMed

    Ramchandran, L; Shah, N P

    2008-09-01

    The objective of this study was to examine the effect of Versagel on the growth and proteolytic activity of Streptococcus thermophilus 1275 and Lactobacillus delbrueckii ssp. bulgaricus 1368 and angiotensin-I converting enzyme inhibitory activity of the peptides generated thereby as well as on the physical properties of low-fat yogurt during a storage period of 28 d at 4 degrees C. Three different types of low-fat yogurts, YV0, YV1, and YV2, were prepared using Versagel as a fat replacer. The fermentation time of the low-fat yogurts containing Versagel was less than that of the control yogurt (YV0). The starter cultures maintained their viability (8.68 to 8.81 log CFU/g of S. thermophilus and 8.51 to 8.81 log CFU/g of L. delbrueckii ssp. bulgaricus) in all the yogurts throughout the storage period. There was some decrease in the pH of the yogurts during storage and an increase in the concentration of lactic acid. However, the proteolytic and ACE-inhibitory potential of the starter cultures was suppressed in the presence of Versagel. On the other hand, the addition of Versagel had a positive impact on the physical properties of the low-fat yogurt, namely, spontaneous whey separation, firmness, and pseudoplastic properties.

  19. Constraining pathways of microbial mediation for carbonate concretions of the Miocene Monterey Formation using carbonate-associated sulfate

    NASA Astrophysics Data System (ADS)

    Loyd, Sean J.; Berelson, William M.; Lyons, Timothy W.; Hammond, Douglas E.; Corsetti, Frank A.

    2012-02-01

    Carbonate concretions can form as a result of organic matter degradation within sediments. However, the ability to determine specific processes and timing relationships to particular concretions has remained elusive. Previously employed proxies (e.g., carbon and oxygen isotopes) cannot uniquely distinguish among diagenetic alkalinity sources generated by microbial oxidation of organic matter using oxygen, nitrate, metal oxides, and sulfate as electron acceptors, in addition to degradation by thermal decarboxylation. Here, we employ concentrations of carbonate-associated sulfate (CAS) and δ 34S CAS (along with more traditional approaches) to determine the specific nature of concretion authigenesis within the Miocene Monterey Formation. Integrated geochemical analyses reveal that at least three specific organo-diagenetic reaction pathways can be tied to concretion formation and that these reactions are largely sample-site specific. One calcitic concretion from the Phosphatic Shale Member at Naples Beach yields δ 34S CAS values near Miocene seawater sulfate (˜+22‰ VCDT), abundant CAS (ca. 1000 ppm), depleted δ 13C carb (˜-11‰ VPDB), and very low concentrations of Fe (ca. 700 ppm) and Mn (ca. 15 ppm)—characteristics most consistent with shallow formation in association with organic matter degradation by nitrate, iron-oxides and/or minor sulfate reduction. Cemented concretionary layers of the Phosphatic Shale Member at Shell Beach display elevated δ 34S CAS (up to ˜+37‰), CAS concentrations of ˜600 ppm, mildly depleted δ 13C carb (˜-6‰), moderate amounts of Mn (ca. 250 ppm), and relatively low Fe (ca. 1700 ppm), indicative of formation in sediments dominated by sulfate reduction. Finally, concretions within a siliceous host at Montaña de Oro and Naples Beach show minimal CAS concentrations, positive δ 13C values, and the highest concentrations of Fe (ca. 11,300 ppm) and Mn (ca. 440 ppm), consistent with formation in sediments experiencing

  20. Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase.

    PubMed

    Cornish, Adam J; Ginovska, Bojana; Thelen, Adam; da Silva, Julio C S; Soares, Thereza A; Raugei, Simone; Dupuis, Michel; Shaw, Wendy J; Hegg, Eric L

    2016-06-01

    The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a water molecule. A computational analysis of this pathway in the [FeFe]-hydrogenase from Clostridium pasteurianum revealed that the solvent-exposed residue of the pathway (Glu282) forms hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implying that these residues could function in regulating proton transfer. In this study, we show that substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in an ∼3-fold enhancement of H2 production activity when methyl viologen is used as an electron donor, suggesting that Arg286 may help control the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate ∼5-fold, implying that it either acts as a member of the pathway or influences Glu282 to permit proton transfer. Interestingly, quantum mechanics/molecular mechanics and molecular dynamics calculations indicate that Ser320 does not play a structural role or indirectly influence the barrier for proton movement at the entrance of the channel. Rather, it may act as an additional proton acceptor for the pathway or serve in a regulatory role. While further studies are needed to elucidate the role of Ser320, collectively these data provide insights into the complex proton transport process. PMID:27186945

  1. Using Phospholipids and Stable Carbon Isotopes to Assess Microbial Community Structures and Carbon Cycle Pathways in Kamchatka Hot Springs

    NASA Astrophysics Data System (ADS)

    Zhao, W.; Romanek, C. S.; Burgess, E. A.; Wiegel, J.; Mills, G.; Zhang, C. L.

    2006-12-01

    Phospholipid fatty acid (PLFA) and stable carbon isotopes were used to assess the microbial community structures in Kamchatka hot springs. Eighteen mats or surface sediments were collected from hot springs having temperatures of 31 to 91°C and pHs of 4.9 to 8.5. These samples were clearly separated into three groups according to the bacterial PLFA: 1) those dominated by terminally branched odd-numbered fatty acids, 2) those dominated by C18:1 and 3) those dominated by C20:1. With support from other minor PLFA components, group 2 may be used as biomarkers for Chloroflexales or other phototrophic bacteria and group 3 for Aquificales, respectively. Among the sampled hot springs, the Arkashin pool represents the simplest microbial structure with members of Aquificales being the dominant primary producers. On the other hand, the Zavarzin pool may represent the most heterogeneous pool that may include members of Chloroflexales and Aquificales as primary producers. Bacterial 16S rDNA clone libraries confirmed the presence of these microbial groups in the two pools. Results of stable carbon isotope fractionation between CO2 source, bulk biomass and total PLFA showed that primary producers in the Arkashin pool primarily used the reductive tricarboxylic acid (rTCA) cycle (e.g., members of Aquificales); whereas the Zavarzin pool may be a mixture of the 3-hydroxypropionate (3-HP) pathway (e.g. members of Chloroflexales) and the rTCA cycle. Bacterial contribution using the Calvin cycle was not significant and may be less important in Kamchatka hot springs.

  2. Evidence of additional excitation energy transfer pathways in the phycobiliprotein antenna system of Acaryochloris marina.

    PubMed

    Nganou, A C; David, L; Adir, N; Pouhe, D; Deen, M J; Mkandawire, M

    2015-02-01

    To improve the energy conversion efficiency of solar organic cells, the clue may lie in the development of devices inspired by an efficient light harvesting mechanism of some aquatic photosynthetic microorganisms that are adapted to low light intensity. Consequently, we investigated the pathways of excitation energy transfer (EET) from successive light harvesting pigments to the low energy level inside the phycobiliprotein antenna system of Acaryochloris marina, a cyanobacterium, using a time resolved absorption difference spectroscopy with a resolution time of 200 fs. The objective was to understand the actual biochemical process and pathways that determine the EET mechanism. Anisotropy of the EET pathway was calculated from the absorption change trace in order to determine the contribution of excitonic coupling. The results reveal a new electron energy relaxation pathway of 14 ps inside the phycocyanin component, which runs from phycocyanin to the terminal emitter. The bleaching of the 660 nm band suggests a broader absorption of the terminal emitter between 660 nm and 675 nm. Further, there are trimer depolarization kinetics of 450 fs and 500 fs in high and low ionic strength, respectively, which arise from the relaxation of the β84 and α84 in adjacent monomers of phycocyanin. Under conditions of low ionic strength buffer solution, the evolution of the kinetic amplitude during the depolarization of the trimer is suggestive of trimer conservation within the phycocyanin hexamer. The anisotropy values were 0.38 and 0.40 in high and in low ionic strength, respectively, indicating that there is no excitonic delocalization in the high energy level of phycocyanin hexamers.

  3. Distributing a metabolic pathway among a microbial consortium enhances production of natural products

    PubMed Central

    Zhou, Kang; Qiao, Kangjian; Edgar, Steven; Stephanopoulos, Gregory

    2016-01-01

    Metabolic engineering of microorganisms such as Escherichia coli and Saccharomyces cerevisiae to produce high-value natural metabolites is often done through functional reconstitution of long metabolic pathways. Problems arise when parts of pathways require specialized environments or compartments for optimal function. Here we solve this problem through co-culture of engineered organisms, each of which contains the part of the pathway that it is best suited to hosting. In one example, we divided the synthetic pathway for the acetylated diol paclitaxel precursor into two modules, expressed in either S. cerevisiae or E. coli, neither of which can produce the paclitaxel precursor on their own. Stable co-culture in the same bioreactor was achieved by designing a mutualistic relationship between the two species in which a metabolic intermediate produced by E. coli was used and functionalized by yeast. This synthetic consortium produced 33 mg/L oxygenated taxanes, including a monoacetylated dioxygenated taxane. The same method was also used to produce tanshinone precursors and functionalized sesquiterpenes. PMID:25558867

  4. Enhanced photo-fermentative H2 production using Rhodobacter sphaeroides by ethanol addition and analysis of soluble microbial products

    PubMed Central

    2014-01-01

    Background Biological fermentation routes can provide an environmentally friendly way of producing H2 since they use renewable biomass as feedstock and proceed under ambient temperature and pressure. In particular, photo-fermentation has superior properties in terms of achieving high H2 yield through complete degradation of substrates. However, long-term H2 production data with stable performance is limited, and this data is essential for practical applications. In the present work, continuous photo-fermentative H2 production from lactate was attempted using the purple non-sulfur bacterium, Rhodobacter sphaeroides KD131. As a gradual drop in H2 production was observed, we attempted to add ethanol (0.2% v/v) to the medium. Results As continuous operation went on, H2 production was not sustained and showed a negligible H2 yield (< 0.5 mol H2/mol lactateadded) within two weeks. Electron balance analysis showed that the reason for the gradual drop in H2 production was ascribed to the increase in production of soluble microbial products (SMPs). To see the possible effect of ethanol addition, a batch test was first conducted. The presence of ethanol significantly increased the H2 yield from 1.15 to 2.20 mol H2/mol lactateadded, by suppressing the production of SMPs. The analysis of SMPs by size exclusion chromatography showed that, in the later period of fermentation, more than half of the low molecular weight SMPs (< 1 kDa) were consumed and used for H2 production when ethanol had been added, while the concentration of SMPs continuously increased in the absence of ethanol. It was found that the addition of ethanol facilitated the utilization of reducing power, resulting in an increase in the cellular levels of NAD+ and NADP+. In continuous operation, ethanol addition was effective, such that stable H2 production was attained with an H2 yield of 2.5 mol H2/mol lactateadded. Less than 15% of substrate electrons were used for SMP production, whereas 35% were used in

  5. First Evidence of an Important Organic Matter Trophic Pathway between Temperate Corals and Pelagic Microbial Communities.

    PubMed

    Fonvielle, J A; Reynaud, S; Jacquet, S; LeBerre, B; Ferrier-Pages, C

    2015-01-01

    Mucus, i.e., particulate and dissolved organic matter (POM, DOM) released by corals, acts as an important energy carrier in tropical ecosystems, but little is known on its ecological role in temperate environments. This study assessed POM and DOM production by the temperate coral Cladocora caespitosa under different environmental conditions. The subsequent enzymatic degradation, growth of prokaryotes and virus-like particles (VLPs) as well as changes in the structure of the prokaryotic communities were also monitored. C. caespitosa produced an important quantity of mucus, which varied according to the environmental conditions (from 37.8 to 67.75 nmol carbon h-1 cm-2), but remained higher or comparable to productions observed in tropical corals. It has an important nutritional value, as highlighted by the high content in dissolved nitrogen (50% to 90% of the organic matter released). Organic matter was rapidly degraded by prokaryotes' enzymatic activities, and due to its nitrogen content, aminopeptidase activity was 500 fold higher than the α-glucosidase activity. Prokaryotes, as well as VLPs, presented a rapid growth in the mucus, with prokaryote production rates as high as 0.31 μg h-1 L-1. Changes in bacterial and archaeal communities were observed in the ageing mucus and between mucus and the water column, suggesting a clear impact of mucus on microorganism diversity. Overall, our results show that the organic matter released by temperate corals, such as C. caespitosa, which can form reef structures in the Mediterranean Sea, stimulates microbial activity and thereby functions as a significant carbon and nitrogen supplier to the microbial loop. PMID:26466126

  6. Atmospheric transport and deposition, an additional input pathway for triazine herbicides to surface waters

    SciTech Connect

    Muir, D.C.G.; Rawn, D.F.

    1996-10-01

    Although surface runoff from treated fields is regarded as the major route of entry of triazine herbicides to surface waters, other pathways such as deposition via precipitation, gas absorption and dryfall may also be important. Triazine herbicides have been detected in precipitation but there has been only a very limited amount of work on gas phase and aerosols. To examine the importance of atmospheric inputs concentrations of atrazine, cyanazine and terbuthylazine in gas phase/aerosols, precipitation, and surface waters were determined (along with other herbicides) using selected ion GC-MS. Atrazine was detected at low ng/L concentrations in surface waters (<0.04-5.3 ng/L) and precipitation (0.1-53 ng/L), and at 0.02-0.1 ng/m{sup 3} in air. Cyanazine and terbuthylazine were detected in air and infrequently in water. Highest atrazine concentrations in air were found during June each year on both gas phase and particles. Concentrations of atrazine in surface waters at both locations increased during June, even in the absence of precipitation or overland flow, presumably due to inputs from dryfall and to gas areas and boreal forest lakes due to transport and deposition. Ecological risk assessment of triazines, especially for pristine aquatic environments should include consideration of this atmospheric pathway.

  7. [Engineering of the xylose metabolic pathway for microbial production of bio-based chemicals].

    PubMed

    Liu, Weixi; Fu, Jing; Zhang, Bo; Chen, Tao

    2013-08-01

    As the rapid development of economy necessitates a large number of oil, the contradiction between energy supply and demand is further exacerbated by the dwindling reserves of petroleum resource. Therefore, the research of the renewable cellulosic biomass resources is gaining unprecedented momentum. Because xylose is the second most abundant monosaccharide after glucose in lignocellulose hydrolyzes, high-efficiency bioconversion of xylose becomes one of the vital factors that affect the industrial prospects of lignocellulose application. According to the research progresses in recent years, this review summarized the advances in bioconversion of xylose, which included identification and redesign of the xylose metabolic pathway, engineering the xylose transport pathway and bio-based chemicals production. In order to solve the energy crisis and environmental pollution issues, the development of advanced bio-fuel technology, especially engineering the microbe able to metabolize xylose and produce ethanol by synthetic biology, is environmentally benign and sustainable. PMID:24364352

  8. Microbial effectors target multiple steps in the salicylic acid production and signaling pathway

    PubMed Central

    Tanaka, Shigeyuki; Han, Xiaowei; Kahmann, Regine

    2015-01-01

    Microbes attempting to colonize plants are recognized through the plant immune surveillance system. This leads to a complex array of global as well as specific defense responses, which are often associated with plant cell death and subsequent arrest of the invader. The responses also entail complex changes in phytohormone signaling pathways. Among these, salicylic acid (SA) signaling is an important pathway because of its ability to trigger plant cell death. As biotrophic and hemibiotrophic pathogens need to invade living plant tissue to cause disease, they have evolved efficient strategies to downregulate SA signaling by virulence effectors, which can be proteins or secondary metabolites. Here we review the strategies prokaryotic pathogens have developed to target SA biosynthesis and signaling, and contrast this with recent insights into how plant pathogenic eukaryotic fungi and oomycetes accomplish the same goal. PMID:26042138

  9. Trimethylamine and Organic Matter Additions Reverse Substrate Limitation Effects on the δ13C Values of Methane Produced in Hypersaline Microbial Mats

    PubMed Central

    Nicholson, Brooke E.; Beaudoin, Claire S.; Detweiler, Angela M.; Bebout, Brad M.

    2014-01-01

    Methane production has been observed in a number of hypersaline environments, and it is generally thought that this methane is produced through the use of noncompetitive substrates, such as the methylamines, dimethylsulfide and methanol. Stable isotope measurements of the produced methane have also suggested that the methanogens are operating under conditions of substrate limitation. Here, substrate limitation in gypsum-hosted endoevaporite and soft-mat hypersaline environments was investigated by the addition of trimethylamine, a noncompetitive substrate for methanogenesis, and dried microbial mat, a source of natural organic matter. The δ13C values of the methane produced after amendments were compared to those in unamended control vials. At all hypersaline sites investigated, the δ13C values of the methane produced in the amended vials were statistically lower (by 10 to 71‰) than the unamended controls, supporting the hypothesis of substrate limitation at these sites. When substrates were added to the incubation vials, the methanogens within the vials fractionated carbon isotopes to a greater degree, resulting in the production of more 13C-depleted methane. Trimethylamine-amended samples produced lower methane δ13C values than the mat-amended samples. This difference in the δ13C values between the two types of amendments could be due to differences in isotope fractionation associated with the dominant methane production pathway (or substrate used) within the vials, with trimethylamine being the main substrate used in the trimethylamine-amended vials. It is hypothesized that increased natural organic matter in the mat-amended vials would increase fermentation rates, leading to higher H2 concentrations and increased CO2/H2 methanogenesis. PMID:25239903

  10. The Effects of Trimethylamine and Organic Matter Additions on the Stable Carbon Isotopic Composition of Methane Produced in Hypersaline Microbial Mat Environments

    NASA Astrophysics Data System (ADS)

    Kelley, C. A.; Nicholson, B. E.; Beaudoin, C. S.; Detweiler, A. M.; Bebout, B.

    2014-12-01

    Methane production has been observed in a number of hypersaline environments, and it is generally thought that this methane is produced through the use of non-competitive substrates, such as the methylamines, methanol and dimethylsulfide. The stable carbon isotopic composition of the produced methane has suggested that the methanogens are operating under conditions of substrate limitation. We investigated substrate limitation in gypsum-hosted endoevaporite and soft mat hypersaline environments by the additions of trimethylamine, a non-competitive substrate for methanogenesis, and dried microbial mat, a source of natural organic matter. The δ13C values of the methane produced after amendments were compared to those in unamended control vials. At all hypersaline sites investigated, the δ13C values of the methane produced in the amended vials were statistically lower (by 10 to 71 ‰) than the unamended controls, supporting the hypothesis of substrate limitation at these sites. When substrates were added to the incubation vials, the methanogens within the vials fractionated carbon isotopes to a greater degree, resulting in the production of more 13C-depleted methane. Trimethylamine-amended samples produced lower methane δ13C values than the mat-amended samples. This difference in the δ13C values between the two types of amendments could be due to differences in isotope fractionation associated with the dominant methane production pathway (or substrate used) within the vials, with trimethylamine being the main substrate used in the trimethylamine-amended vials. We hypothesize that increased natural organic matter in the mat-amended vials would increase fermentation rates, leading to higher H2 concentrations and increased CO2/H2 methanogenesis.

  11. Microbial degradation of fluorinated drugs: biochemical pathways, impacts on the environment and potential applications.

    PubMed

    Murphy, Cormac D

    2016-03-01

    Since the discovery over 60 years ago of fluorocortisone's biological properties (9-α-Fluoro derivatives of cortisone and hydrocortisone; Fried J and Sabo EF, J Am Chem Soc 76: 1455-1456, 1954), the number of fluorinated drugs has steadily increased. With the improvement in synthetic methodologies, this trend is likely to continue and will lead to the introduction of new fluorinated substituents into pharmaceutical compounds. Although the biotransformation of organofluorine compounds by microorganisms has been well studied, specific investigations on fluorinated drugs are relatively few, despite the increase in the number and variety of fluorinated drugs that are available. The strength of the carbon-fluorine bond conveys stability to fluorinated drugs; thus, they are likely to be recalcitrant in the environment or may be partially metabolized to a more toxic metabolite. This review examines the research done on microbial biotransformation and biodegradation of fluorinated drugs and highlights the importance of understanding how microorganisms interact with this class of compound from environmental, clinical and biotechnological perspectives.

  12. Genomic organisation, activity and distribution analysis of the microbial putrescine oxidase degradation pathway.

    PubMed

    Foster, Alexander; Barnes, Nicole; Speight, Robert; Keane, Mark A

    2013-10-01

    The catalytic action of putrescine specific amine oxidases acting in tandem with 4-aminobutyraldehyde dehydrogenase is explored as a degradative pathway in Rhodococcus opacus. By limiting the nitrogen source, increased catalytic activity was induced leading to a coordinated response in the oxidative deamination of putrescine to 4-aminobutyraldehyde and subsequent dehydrogenation to 4-aminobutyrate. Isolating the dehydrogenase by ion exchange chromatography and gel filtration revealed that the enzyme acts principally on linear aliphatic aldehydes possessing an amino moiety. Michaelis-Menten kinetic analysis delivered a Michaelis constant (K(M)=0.014 mM) and maximum rate (Vmax=11.2 μmol/min/mg) for the conversion of 4-aminobutyraldehyde to 4-aminobutyrate. The dehydrogenase identified by MALDI-TOF mass spectrometric analysis (E value=0.031, 23% coverage) belongs to a functionally related genomic cluster that includes the amine oxidase, suggesting their association in a directed cell response. Key regulatory, stress and transport encoding genes have been identified, along with candidate dehydrogenases and transaminases for the further conversion of 4-aminobutyrate to succinate. Genomic analysis has revealed highly similar metabolic gene clustering among members of Actinobacteria, providing insight into putrescine degradation notably among Micrococcaceae, Rhodococci and Corynebacterium by a pathway that was previously uncharacterised in bacteria. PMID:23906496

  13. Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses

    PubMed Central

    Azarbad, Hamed; van Gestel, Cornelis A. M.; Niklińska, Maria; Laskowski, Ryszard; Röling, Wilfred F. M.; van Straalen, Nico M.

    2016-01-01

    Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the “costs” of adaptation to metals affect the responses of metal-tolerant communities to other stress factors (“stress-on-stress”). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors. PMID:27314330

  14. Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition.

    PubMed

    Kohler, J; Caravaca, F; Azcón, R; Díaz, G; Roldán, A

    2016-03-15

    The recovery of species composition and functions of soil microbial community of degraded lands is crucial in order to guarantee the long-term self-sustainability of the ecosystems. A field experiment was carried out to test the influence of combining fermented sugar beet residue (SBR) addition and inoculation with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae on the plant growth parameters and microbial community composition and function in the rhizosphere of two autochthonous plant species (Dorycnium pentaphyllum L. and Asteriscus maritimus L.) growing in a semiarid soil contaminated by heavy metals. We analysed the phospholipid fatty acids (PLFAs), neutral lipids fatty acids (NLFAs) and enzyme activities to study the soil microbial community composition and function, respectively. The combined treatment was not effective for increasing plant growth. The SBR promoted the growth of both plant species, whilst the AM fungus was effective only for D. pentaphyllum. The effect of the treatments on plant growth was linked to shifts in the rhizosphere microbial community composition and function. The highest increase in dehydrogenase and β-glucosidase activities was recorded in SBR-amended soil. The SBR increased the abundance of marker PLFAs for saprophytic fungi, Gram+ and Gram- bacteria and actinobacteria, whereas the AM fungus enhanced the abundance of AM fungi-related NLFA and marker PLFAs for Gram- bacteria. Measurement of the soil microbial community composition and function was useful to assess the success of phytomanagement technologies in a semiarid, contaminated soil.

  15. Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing "Stress-on-Stress" Responses.

    PubMed

    Azarbad, Hamed; van Gestel, Cornelis A M; Niklińska, Maria; Laskowski, Ryszard; Röling, Wilfred F M; van Straalen, Nico M

    2016-01-01

    Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the "costs" of adaptation to metals affect the responses of metal-tolerant communities to other stress factors ("stress-on-stress"). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors. PMID:27314330

  16. Theoretical study of the oxidation mechanisms of naphthalene initiated by hydroxyl radicals: the OH-addition pathway.

    PubMed

    Shiroudi, Abolfazl; Deleuze, Michael S; Canneaux, Sébastien

    2014-07-01

    The oxidation mechanisms of naphthalene by OH radicals under inert (He) conditions have been studied using density functional theory along with various exchange-correlation functionals. Comparison has been made with benchmark CBS-QB3 theoretical results. Kinetic rate constants were correspondingly estimated by means of transition state theory and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Comparison with experiment confirms that, on the OH-addition reaction pathway leading to 1-naphthol, the first bimolecular reaction step has an effective negative activation energy around -1.5 kcal mol(-1), whereas this step is characterized by an activation energy around 1 kcal mol(-1) on the OH-addition reaction pathway leading to 2-naphthol. Effective rate constants have been calculated according to a steady state analysis upon a two-step model reaction mechanism. In line with experiment, the correspondingly obtained branching ratios indicate that, at temperatures lower than 410 K, the most abundant product resulting from the oxidation of naphthalene by OH radicals must be 1-naphthol. The regioselectivity of the OH(•)-addition onto naphthalene decreases with increasing temperatures and decreasing pressures. Because of slightly positive or even negative activation energies, the RRKM calculations demonstrate that the transition state approximation breaks down at ambient pressure (1 bar) for the first bimolecular reaction steps. Overwhelmingly high pressures, larger than 10(5) bar, would be required for restoring to some extent (within ∼5% accuracy) the validity of this approximation for all the reaction channels that are involved in the OH-addition pathway. Analysis of the computed structures, bond orders, and free energy profiles demonstrate that all reaction steps involved in the oxidation of naphthalene by OH radicals satisfy Leffler-Hammond's principle. Nucleus independent chemical shift indices and natural bond orbital analysis also show that the computed

  17. p53 and ATF4 mediate distinct and additive pathways to skeletal muscle atrophy during limb immobilization.

    PubMed

    Fox, Daniel K; Ebert, Scott M; Bongers, Kale S; Dyle, Michael C; Bullard, Steven A; Dierdorff, Jason M; Kunkel, Steven D; Adams, Christopher M

    2014-08-01

    Immobilization causes skeletal muscle atrophy via complex signaling pathways that are not well understood. To better understand these pathways, we investigated the roles of p53 and ATF4, two transcription factors that mediate adaptations to a variety of cellular stresses. Using mouse models, we demonstrate that 3 days of muscle immobilization induces muscle atrophy and increases expression of p53 and ATF4. Furthermore, muscle fibers lacking p53 or ATF4 are partially resistant to immobilization-induced muscle atrophy, and forced expression of p53 or ATF4 induces muscle fiber atrophy in the absence of immobilization. Importantly, however, p53 and ATF4 do not require each other to promote atrophy, and coexpression of p53 and ATF4 induces more atrophy than either transcription factor alone. Moreover, muscle fibers lacking both p53 and ATF4 are more resistant to immobilization-induced atrophy than fibers lacking only p53 or ATF4. Interestingly, the independent and additive nature of the p53 and ATF4 pathways allows for combinatorial control of at least one downstream effector, p21. Using genome-wide mRNA expression arrays, we identified p21 mRNA as a skeletal muscle transcript that is highly induced in immobilized muscle via the combined actions of p53 and ATF4. Additionally, in mouse muscle, p21 induces atrophy in a manner that does not require immobilization, p53 or ATF4, and p21 is required for atrophy induced by immobilization, p53, and ATF4. Collectively, these results identify p53 and ATF4 as essential and complementary mediators of immobilization-induced muscle atrophy and discover p21 as a critical downstream effector of the p53 and ATF4 pathways.

  18. Carbon stabilization and microbial growth in acidic mine soils after addition of different amendments for soil reclamation

    NASA Astrophysics Data System (ADS)

    Zornoza, Raúl; Acosta, Jose; Ángeles Muñoz, María; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

    2016-04-01

    The extreme soil conditions in metalliferous mine soils have a negative influence on soil biological activity and therefore on soil carbon estabilization. Therefore, amendments are used to increase organic carbon content and activate microbial communities. In order to elucidate some of the factors controlling soil organic carbon stabilization in reclaimed acidic mine soils and its interrelationship with microbial growth and community structure, we performed an incubation experiment with four amendments: pig slurry (PS), pig manure (PM) and biochar (BC), applied with and without marble waste (MW; CaCO3). Results showed that PM and BC (alone or together with MW) contributed to an important increment in recalcitrant organic C, C/N ratio and aggregate stability. Bacterial and fungal growths were highly dependent on pH and labile organic C. PS supported the highest microbial growth; applied alone it stimulated fungal growth, and applied with MW it stimulated bacterial growth. BC promoted the lowest microbial growth, especially for fungi, with no significant increase in fungal biomass. MW+BC increased bacterial growth up to values similar to PM and MW+PM, suggesting that part of the biochar was degraded, at least in short-term mainly by bacteria rather than fungi. PM, MW+PS and MW+PM supported the highest microbial biomass and a similar community structure, related with the presence of high organic C and high pH, with immobilization of metals and increased soil quality. BC contributed to improved soil structure, increased recalcitrant organic C, and decreased metal mobility, with low stimulation of microbial growth.

  19. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage.

    PubMed

    Grindberg, Rashel V; Ishoey, Thomas; Brinza, Dumitru; Esquenazi, Eduardo; Coates, R Cameron; Liu, Wei-ting; Gerwick, Lena; Dorrestein, Pieter C; Pevzner, Pavel; Lasken, Roger; Gerwick, William H

    2011-04-12

    Filamentous marine cyanobacteria are extraordinarily rich sources of structurally novel, biomedically relevant natural products. To understand their biosynthetic origins as well as produce increased supplies and analog molecules, access to the clustered biosynthetic genes that encode for the assembly enzymes is necessary. Complicating these efforts is the universal presence of heterotrophic bacteria in the cell wall and sheath material of cyanobacteria obtained from the environment and those grown in uni-cyanobacterial culture. Moreover, the high similarity in genetic elements across disparate secondary metabolite biosynthetic pathways renders imprecise current gene cluster targeting strategies and contributes sequence complexity resulting in partial genome coverage. Thus, it was necessary to use a dual-method approach of single-cell genomic sequencing based on multiple displacement amplification (MDA) and metagenomic library screening. Here, we report the identification of the putative apratoxin. A biosynthetic gene cluster, a potent cancer cell cytotoxin with promise for medicinal applications. The roughly 58 kb biosynthetic gene cluster is composed of 12 open reading frames and has a type I modular mixed polyketide synthase/nonribosomal peptide synthetase (PKS/NRPS) organization and features loading and off-loading domain architecture never previously described. Moreover, this work represents the first successful isolation of a complete biosynthetic gene cluster from Lyngbya bouillonii, a tropical marine cyanobacterium renowned for its production of diverse bioactive secondary metabolites.

  20. Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

    PubMed

    Du, Qingzhang; Tian, Jiaxing; Yang, Xiaohui; Pan, Wei; Xu, Baohua; Li, Bailian; Ingvarsson, Pär K; Zhang, Deqiang

    2015-02-01

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

  1. Microbial ecology and performance of ammonia oxidizing bacteria (AOB) in biological processes treating petrochemical wastewater with high strength of ammonia: effect of Na(2)CO(3) addition.

    PubMed

    Whang, L M; Yang, K H; Yang, Y F; Han, Y L; Chen, Y J; Cheng, S S

    2009-01-01

    This study evaluated nitrification performance and microbial ecology of AOB in a full-scale biological process, powder activated carbon treatment (PACT), and a pilot-scale biological process, moving bed biofilm reactor (MBBR), treating wastewater collected from a petrochemical industry park. The petrochemical influent wastewater characteristics showed a relative low carbon to nitrogen ratio around 1 with average COD and ammonia concentrations of 310 mg/L and 325 mg-N/L, respectively. The average nitrification efficiency of the full-scale PACT process was around 11% during this study. For the pilot-scale MBBR, the average nitrification efficiency was 24% during the Run I operation mode, which provided a slightly better performance in nitrification than that of the PACT process. During the Run II operation, the pH control mode was switched from addition of NaOH to Na(2)CO(3), leading to a significant improvement in nitrification efficiency of 51%. In addition to a dramatic change in nitrification performance, the microbial ecology of AOB, monitored with the terminal restriction fragment length polymorphism (T-RFLP) molecular methodology, was found to be different between Runs I and II. The amoA-based TRFLP results indicated that Nitrosomonas europaea lineage was the dominant AOB population during Run I operation, while Nitrosospira-like AOB was dominant during Run II operation. To confirm the effects of Na(2)CO(3) addition on the nitrification performance and AOB microbial ecology observed in the MBBR process, batch experiments were conducted. The results suggest that addition of Na(2)CO(3) as a pH control strategy can improve nitrification performance and also influence AOB microbial ecology as well. Although the exact mechanisms are not clear at this time, the results showing the effects of adding different buffering chemicals such as NaOH or Na(2)CO(3) on AOB populations have never been demonstrated until this study. PMID:19182331

  2. Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

    NASA Astrophysics Data System (ADS)

    Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

    2012-12-01

    The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

  3. Evaluation of the effect of an additional fertilizer on the dynamics of microbial community and the decomposition of organic matter in soil

    NASA Astrophysics Data System (ADS)

    Fabiola, B.; Olivier, M.; Houdusse, F.; Fuentes, M.; Garcia, M. J. M.; Lévêque, J.; Yvin, J. C.; Maron, P. A.; Lemenager, D.

    2012-04-01

    Organic matter (OM) influences many of the soil functions and occupies a central position in the global carbon cycle. At the scale of the agro-ecosystem, primary productivity is dependent on the recycling of soil organic matter (SOM) by the action of decomposers (mainly bacteria and fungi), which mineralize organic compounds, releasing the nutrients needed for plant growth. At a global scale, the recycling of the SOM determines the carbon flux between soil and atmosphere, with major consequences in terms of environmental quality. In this context, the management of SOM stocks in agro-ecosystems is a major issue from which depend the maintenance of the productivity and sustainability of agricultural practices. The use of additional fertilizer appears to be a promising way to achieve such management. These products have been proven effectives in many field trials. However, their mode of action, particularly in terms of impact on soil microbial component, is still nearly unknown. In this context, this study aims to test the influence of an additional fertilizer on (i) soil microbial communities (total biomass, density of bacteria and fungi), and (ii) soil functioning in terms of dynamics of organic matter. It is based on experiments in soil microcosms which follow in parallel the kinetics of mineralization of different organic carbon compartments (endogenous compartment: soil organic matter; exogenous compartment: wheat residue provided) and the dynamics of microbial communities after the addition of wheat residues in soil. Two different soils were used to evaluate the influence of soil physicochemical characteristics on the effect induced by the addition in terms of fertilization. The first results show a significant effect of the input of additional fertilizer on the dynamics of soil organic matter. They also show that soil pH as well as the dose at which the additional fertilizer is applied are important for modulating the observed effect. Characterization of

  4. Well-to-Wheels analysis of landfill gas-based pathways and their addition to the GREET model.

    SciTech Connect

    Mintz, M.; Han, J.; Wang, M.; Saricks, C.; Energy Systems

    2010-06-30

    Today, approximately 300 million standard cubic ft/day (mmscfd) of natural gas and 1600 MW of electricity are produced from the decomposition of organic waste at 519 U.S. landfills (EPA 2010a). Since landfill gas (LFG) is a renewable resource, this energy is considered renewable. When used as a vehicle fuel, compressed natural gas (CNG) produced from LFG consumes up to 185,000 Btu of fossil fuel and generates from 1.5 to 18.4 kg of carbon dioxide-equivalent (CO{sub 2}e) emissions per million Btu of fuel on a 'well-to-wheel' (WTW) basis. This compares with approximately 1.1 million Btu and 78.2 kg of CO{sub 2}e per million Btu for CNG from fossil natural gas and 1.2 million Btu and 97.5 kg of CO{sub 2}e per million Btu for petroleum gasoline. Because of the additional energy required for liquefaction, LFG-based liquefied natural gas (LNG) requires more fossil fuel (222,000-227,000 Btu/million Btu WTW) and generates more GHG emissions (approximately 22 kg CO{sub 2}e /MM Btu WTW) if grid electricity is used for the liquefaction process. However, if some of the LFG is used to generate electricity for gas cleanup and liquefaction (or compression, in the case of CNG), vehicle fuel produced from LFG can have no fossil fuel input and only minimal GHG emissions (1.5-7.7 kg CO{sub 2}e /MM Btu) on a WTW basis. Thus, LFG-based natural gas can be one of the lowest GHG-emitting fuels for light- or heavy-duty vehicles. This report discusses the size and scope of biomethane resources from landfills and the pathways by which those resources can be turned into and utilized as vehicle fuel. It includes characterizations of the LFG stream and the processes used to convert low-Btu LFG into high-Btu renewable natural gas (RNG); documents the conversion efficiencies and losses of those processes, the choice of processes modeled in GREET, and other assumptions used to construct GREET pathways; and presents GREET results by pathway stage. GREET estimates of well-to-pump (WTP), pump

  5. Monitoring Subsurface Microbial Biomass, Community Composition and Physiological Status during Biological Uranium Reduction with Acetate Addition using Lipid Analysis, DNA Arrays and q-PCR

    NASA Astrophysics Data System (ADS)

    Peacock, A. D.; Long, P. E.; N'Guessan, L.; Williams, K. H.; Chandler, D.

    2011-12-01

    Our objectives for this effort were to investigate microbial community dynamics during each of the distinct terminal electron accepting phases that occur during long-term acetate addition for the immobilization of Uranium. Groundwater was collected from four wells (one up gradient and three down gradient) at three different depths and at four different times (pre-acetate injection, peak iron reduction, iron/sulfate reduction transition and during heavy sulfate reduction). Phospholipid fatty acid analysis (PLFA) results from ground water showed that microbial biomass was highest during Iron reduction and then lower during the transition from Iron reduction to Sulfate reduction and lowest during Sulfate reduction. Microbial community composition parameters as measured by PLFA showed distinct differences with terminal electron accepting status. Monounsaturated PLFA that have been shown to correspond with Gram-negative bacteria and Geobacteracea increased markedly with Iron reduction and then decreased with the onset of sulfate reduction. Bacterial physiological stress levels as measured by PLFA fluctuated with terminal electron acceptor status. Low bacterial stress levels coincided with pre-donor addition and Iron reduction but were much higher during Iron to Sulfate transition and during Sulfate reduction. Microarray results showed the expected progression of microbial signatures from Iron to Sulfate -reducers with changes in acetate amendment and in situ field conditions. The microarray response for Geobacter was highly correlated with qPCR for the same target gene (R2 = 0.84). Probes targeting Desulfobacter and Desulfitobacterium were the most reactive during the Iron to Sulfate transition and into Sulfate reduction, with a consistent Desulfotomaculum signature throughout the field experiment and a general decrease in Geobacter signal to noise ratios during the onset of Sulfate reducing conditions. Nitrate reducers represented by Dechloromonas and Dechlorosoma

  6. Changing Feeding Regimes To Demonstrate Flexible Biogas Production: Effects on Process Performance, Microbial Community Structure, and Methanogenesis Pathways.

    PubMed

    Mulat, Daniel Girma; Jacobi, H Fabian; Feilberg, Anders; Adamsen, Anders Peter S; Richnow, Hans-Hermann; Nikolausz, Marcell

    2015-10-23

    Flexible biogas production that adapts biogas output to energy demand can be regulated by changing feeding regimes. In this study, the effect of changes in feeding intervals on process performance, microbial community structure, and the methanogenesis pathway was investigated. Three different feeding regimes (once daily, every second day, and every 2 h) at the same organic loading rate were studied in continuously stirred tank reactors treating distiller's dried grains with solubles. A larger amount of biogas was produced after feeding in the reactors fed less frequently (once per day and every second day), whereas the amount remained constant in the reactor fed more frequently (every 2 h), indicating the suitability of the former for the flexible production of biogas. Compared to the conventional more frequent feeding regimes, a methane yield that was up to 14% higher and an improved stability of the process against organic overloading were achieved by employing less frequent feeding regimes. The community structures of bacteria and methanogenic archaea were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA and mcrA genes, respectively. The results showed that the composition of the bacterial community varied under the different feeding regimes, and the observed T-RFLP patterns were best explained by the differences in the total ammonia nitrogen concentrations, H2 levels, and pH values. However, the methanogenic community remained stable under all feeding regimes, with the dominance of the Methanosarcina genus followed by that of the Methanobacterium genus. Stable isotope analysis showed that the average amount of methane produced during each feeding event by acetoclastic and hydrogenotrophic methanogenesis was not influenced by the three different feeding regimes.

  7. Changing Feeding Regimes To Demonstrate Flexible Biogas Production: Effects on Process Performance, Microbial Community Structure, and Methanogenesis Pathways

    PubMed Central

    Mulat, Daniel Girma; Jacobi, H. Fabian; Feilberg, Anders; Adamsen, Anders Peter S.; Richnow, Hans-Hermann

    2015-01-01

    Flexible biogas production that adapts biogas output to energy demand can be regulated by changing feeding regimes. In this study, the effect of changes in feeding intervals on process performance, microbial community structure, and the methanogenesis pathway was investigated. Three different feeding regimes (once daily, every second day, and every 2 h) at the same organic loading rate were studied in continuously stirred tank reactors treating distiller's dried grains with solubles. A larger amount of biogas was produced after feeding in the reactors fed less frequently (once per day and every second day), whereas the amount remained constant in the reactor fed more frequently (every 2 h), indicating the suitability of the former for the flexible production of biogas. Compared to the conventional more frequent feeding regimes, a methane yield that was up to 14% higher and an improved stability of the process against organic overloading were achieved by employing less frequent feeding regimes. The community structures of bacteria and methanogenic archaea were monitored by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA and mcrA genes, respectively. The results showed that the composition of the bacterial community varied under the different feeding regimes, and the observed T-RFLP patterns were best explained by the differences in the total ammonia nitrogen concentrations, H2 levels, and pH values. However, the methanogenic community remained stable under all feeding regimes, with the dominance of the Methanosarcina genus followed by that of the Methanobacterium genus. Stable isotope analysis showed that the average amount of methane produced during each feeding event by acetoclastic and hydrogenotrophic methanogenesis was not influenced by the three different feeding regimes. PMID:26497462

  8. Short-term enhancement effect of nitrogen addition on microbial degradation and plant uptake of polybrominated diphenyl ethers (PBDEs) in contaminated mangrove soil.

    PubMed

    Chen, Juan; Zhou, Hai Chao; Wang, Chao; Zhu, Chun Quan; Tam, Nora Fung-Yee

    2015-12-30

    Effects of nitrogen (N) addition on the microbial degradation and uptake of a mixture of BDE-47 and -209 by Aegiceras corniculatum, a typical mangrove plant species were investigated. At the end of 3-month experiment, a significant dissipation of BDE-47 was observed in the planted soil, and this dissipation, particularly in rhizosphere soil, was significantly accelerated by the frequent addition of N in the form of ammonium chloride. The removal percentage of BDE-47 in the rhizosphere soil without N addition was 47.3% and increased to 58.2% with N. However, the unplanted soil only removed less than 25% BDE-47, irrespective to N supply. The N addition in planted treatments significantly increased soil N content, urease and dehydrogenase activities, and the abundances of total bacteria and dehalogenating bacteria, leading to more microbial degradation of BDE-47. The N addition also enhanced the root uptake and translocation of PBDEs to above-ground tissues of A. corniculatum. These results suggested that N addition could enhance the phytoremediation of BDE-47-contaminated soil within a short period of time. Different from BDE-47, BDE-209 in all contaminated soils was difficult to be removed due to its persistence and low bioavailability.

  9. Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

    PubMed

    Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

    2014-01-01

    The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of

  10. Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

    PubMed Central

    Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

    2014-01-01

    The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of

  11. Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain

    PubMed

    Pennanen; Fritze; Vanhala; Kiikkila; Neuvonen; Baath

    1998-06-01

    Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.

  12. Automated microbial metabolism laboratory. [design of advanced labeled release experiment based on single addition of soil and multiple sequential additions of media into test chambers

    NASA Technical Reports Server (NTRS)

    1974-01-01

    The design and rationale of an advanced labeled release experiment based on single addition of soil and multiple sequential additions of media into each of four test chambers are outlined. The feasibility for multiple addition tests was established and various details of the methodology were studied. The four chamber battery of tests include: (1) determination of the effect of various atmospheric gases and selection of that gas which produces an optimum response; (2) determination of the effect of incubation temperature and selection of the optimum temperature for performing Martian biochemical tests; (3) sterile soil is dosed with a battery of C-14 labeled substrates and subjected to experimental temperature range; and (4) determination of the possible inhibitory effects of water on Martian organisms is performed initially by dosing with 0.01 ml and 0.5 ml of medium, respectively. A series of specifically labeled substrates are then added to obtain patterns in metabolic 14CO2 (C-14)O2 evolution.

  13. Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism.

    PubMed

    Tripathy, Swetaleena; Padhi, Soumesh Kumar; Mohanty, Sriprakash; Samanta, Mrinal; Maiti, Nikhil Kumar

    2016-07-01

    Alkaline sulfur hot springs notable for their specialized and complex ecosystem powered by geothermal energy are abundantly rich in different chemotrophic and phototrophic thermophilic microorganisms. Survival and adaptation of these organisms in the extreme environment is specifically related to energy metabolism. To gain a better understanding of survival mechanism of the organisms in these ecosystems, we determined the different gene encoding enzymes associated with anaerobic pathways of energy metabolism by applying the metatranscriptomics approach. The analysis of the microbial population of hot sulfur spring revealed the presence of both aerobic and anaerobic organisms indicating dual mode of lifestyle of the community members. Proteobacteria (28.1 %) was the most dominant community. A total of 988 reads were associated with energy metabolism, out of which 33.7 % of the reads were assigned to nitrogen, sulfur, and methane metabolism based on KEGG classification. The major lineages of hot spring communities were linked with the anaerobic pathways. Different gene encoding enzymes (hao, nir, nar, cysH, cysI, acs) showed the involvement of microbial members in nitrification, denitrification, dissimilatory sulfate reduction, and methane generation. This study enhances our understanding of important gene encoding enzymes involved in energy metabolism, required for the survival and adaptation of microbial communities in the hot spring.

  14. Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism.

    PubMed

    Tripathy, Swetaleena; Padhi, Soumesh Kumar; Mohanty, Sriprakash; Samanta, Mrinal; Maiti, Nikhil Kumar

    2016-07-01

    Alkaline sulfur hot springs notable for their specialized and complex ecosystem powered by geothermal energy are abundantly rich in different chemotrophic and phototrophic thermophilic microorganisms. Survival and adaptation of these organisms in the extreme environment is specifically related to energy metabolism. To gain a better understanding of survival mechanism of the organisms in these ecosystems, we determined the different gene encoding enzymes associated with anaerobic pathways of energy metabolism by applying the metatranscriptomics approach. The analysis of the microbial population of hot sulfur spring revealed the presence of both aerobic and anaerobic organisms indicating dual mode of lifestyle of the community members. Proteobacteria (28.1 %) was the most dominant community. A total of 988 reads were associated with energy metabolism, out of which 33.7 % of the reads were assigned to nitrogen, sulfur, and methane metabolism based on KEGG classification. The major lineages of hot spring communities were linked with the anaerobic pathways. Different gene encoding enzymes (hao, nir, nar, cysH, cysI, acs) showed the involvement of microbial members in nitrification, denitrification, dissimilatory sulfate reduction, and methane generation. This study enhances our understanding of important gene encoding enzymes involved in energy metabolism, required for the survival and adaptation of microbial communities in the hot spring. PMID:27290724

  15. Microbial biotransformation as a tool for drug development based on natural products from mevalonic acid pathway: A review

    PubMed Central

    Hegazy, Mohamed-Elamir F.; Mohamed, Tarik A.; ElShamy, Abdelsamed I.; Mohamed, Abou-El-Hamd H.; Mahalel, Usama A.; Reda, Eman H.; Shaheen, Alaa M.; Tawfik, Wafaa A.; Shahat, Abdelaaty A.; Shams, Khalid A.; Abdel-Azim, Nahla S.; Hammouda, Fayza M.

    2014-01-01

    Natural products are structurally and biologically interesting metabolites, but they have been isolated in minute amounts. The syntheses of such natural products help in obtaining them in bulk amounts. The recognition of microbial biotransformation as important manufacturing tool has increased in chemical and pharmaceutical industries. In recent years, microbial transformation is increasing significantly from limited interest into highly active area in green chemistry including preparation of pharmaceutical products. This is the first review published on the usage of microbial biocatalysts for some natural product classes and natural product drugs. PMID:25685541

  16. Analyses of microbial community within a composter operated using household garbage with special reference to the addition of soybean oil.

    PubMed

    Aoshima, M; Pedro, M S; Haruta, S; Ding, L; Fukada, T; Kigawa, A; Kodama, T; Ishii, M; Igarashi, Y

    2001-01-01

    A commercially available composter was operated using fixed composition of garbage with or without the addition of soybean oil. The composter was operated without adding seed microorganisms or bulking materials. Microflora within the composter were analyzed by denaturing gradient gel electrophoresis (DGGE) in the case of oil addition, or by 16/18 S rRNA gene sequencing of the isolated microorganisms in the case of no oil addition. The results showed that, irrespective of the addition of oil, the bacteria identified were all gram positive, and that lactobacilli seemed to be the key microorganisms. Based on the results, suitable microflora for use in a household composter are discussed.

  17. [Effects of grape seed addition in swine manure-wheat straw composting on the compost microbial community and carbon and nitrogen contents].

    PubMed

    Huang, Yi-Mei; Liu, Xue-Ling; Jiang, Ji-Shao; Huang, Hua; Liu, Dong

    2012-08-01

    Taking substrates swine manure and wheat straw (fresh mass ratio 10.5:1) as the control (PMW), a composting experiment was conducted in a self-made aerated static composting bin to study the effects of adding 8% grape seed (treatment PMW + G) on the succession of microbial community and the transformation of carbon and nitrogen in the substrates during the composting. Seven samples were collected from each treatment, according to the temperature of the compost during the 30 d composting period. The microbial population and physiological groups were determined, and the NH4(+)-N, NO3(-)-N, organic N, and organic C concentrations in the compost were measured. Grape seed addition induced a slight increase of bacterial count and a significant increase of actinomycetes count, but decreased the fungal count significantly. Grape seed addition also decreased the ratio of bacteria to actinomycetes and the counts of ammonifiers and denitrifiers, but increased the counts of nitrifiers, N-fixing bacteria, and cellulose-decomposing microorganisms. The contents of NH4(+)-N and organic C decreased, while that of NO3(-)-N increased obviously. The NO3(-)-N content in the compost was positively correlated with the actinomycetes count. During composting, the compost temperature in treatment PMW + G increased more rapidly, and remained steady in thermophilic phase, while the water content changed little, which provided a stable and higher population of actinomycetes and nitrifiers in thermophilic phase, being beneficial to the increase of compost nitrate N.

  18. Establishment of cellulolytic bacteria and development of fermentative activities in the rumen of gnotobiotically-reared lambs receiving the microbial additive Saccharomyces cerevisiae CNCM I-1077.

    PubMed

    Chaucheyras-Durand, F; Fonty, G

    2001-01-01

    We studied the effects of a yeast additive used in ruminant nutrition on the establishment of cellulolytic bacteria, on plant cell wall degradation and on digestive functions in the rumen of gnotobiotically-reared lambs. Cellulolytic bacteria inoculated to the lambs tended to become established earlier in the presence of Saccharomyces cerevisiae CNCM I-1077 (SC). In addition, their population was maintained at a higher level, when the physico-chemical conditions of the biotope were altered. In these lambs, specific activities of fibrolytic enzymes were greater, and in sacco degradation of wheat straw tended to increase. In the presence of SC there was a decrease in ruminal ammonia concentration and a higher volatile fatty acid (VFA) concentration when lambs were 20 to 50 days old. These data suggest that this yeast strain may stimulate the development of cellulolytic microflora and enhance microbial activity in the rumen of young ruminants. Such activity could be beneficial in preventing microbial imbalance and a reduction of rumen function efficiency in the case of nutritional transitions. Further studies with conventional animals will soon be performed in order to verify these dings.

  19. A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease.

    PubMed

    Holmans, Peter; Moskvina, Valentina; Jones, Lesley; Sharma, Manu; Vedernikov, Alexey; Buchel, Finja; Saad, Mohamad; Sadd, Mohamad; Bras, Jose M; Bettella, Francesco; Nicolaou, Nayia; Simón-Sánchez, Javier; Mittag, Florian; Gibbs, J Raphael; Schulte, Claudia; Durr, Alexandra; Guerreiro, Rita; Hernandez, Dena; Brice, Alexis; Stefánsson, Hreinn; Majamaa, Kari; Gasser, Thomas; Heutink, Peter; Wood, Nicholas W; Martinez, Maria; Singleton, Andrew B; Nalls, Michael A; Hardy, John; Morris, Huw R; Williams, Nigel M

    2013-03-01

    Parkinson's disease (PD) is the second most common neurodegenerative disease affecting 1-2% in people >60 and 3-4% in people >80. Genome-wide association (GWA) studies have now implicated significant evidence for association in at least 18 genomic regions. We have studied a large PD-meta analysis and identified a significant excess of SNPs (P < 1 × 10(-16)) that are associated with PD but fall short of the genome-wide significance threshold. This result was independent of variants at the 18 previously implicated regions and implies the presence of additional polygenic risk alleles. To understand how these loci increase risk of PD, we applied a pathway-based analysis, testing for biological functions that were significantly enriched for genes containing variants associated with PD. Analysing two independent GWA studies, we identified that both had a significant excess in the number of functional categories enriched for PD-associated genes (minimum P = 0.014 and P = 0.006, respectively). Moreover, 58 categories were significantly enriched for associated genes in both GWA studies (P < 0.001), implicating genes involved in the 'regulation of leucocyte/lymphocyte activity' and also 'cytokine-mediated signalling' as conferring an increased susceptibility to PD. These results were unaltered by the exclusion of all 178 genes that were present at the 18 genomic regions previously reported to be strongly associated with PD (including the HLA locus). Our findings, therefore, provide independent support to the strong association signal at the HLA locus and imply that the immune-related genetic susceptibility to PD is likely to be more widespread in the genome than previously appreciated.

  20. Differential responses of needle and branch order-based root decay to nitrogen addition: dominant effects of acid-unhydrolyzable residue and microbial enzymes

    NASA Astrophysics Data System (ADS)

    Kou, Liang; Chen, Weiwei; Zhang, Xinyu; Gao, Wenlong; Yang, Hao; Li, Dandan; Li, Shenggong

    2016-04-01

    Both chemical differences between foliage and different orders of fine roots and their contrasting decomposing microenvironments may affect their decomposition. However, little is known about how foliage and branch order-based root decomposition responds to increased N availability and the response mechanisms behind. The effects of different doses of N addition on the decomposition of needles and order-based roots of Pinus elliottii (slash pine) were monitored using the litterbag method for 524 days in a subtropical slash pine plantation in south China. The acid-unhydrolyzable residue (AUR) concentration and microbial extracellular enzymatic activities (EEA) in decomposing needles and roots were also determined. Our results indicate that the responses of needle and order-based root decomposition were N-dose-specific. The decomposition of both needles and lower-order roots was inhibited under the high N dose rate. The retarded decomposition of lower-order roots could be explained more by the increased binding of AUR to inorganic N ions, while the retarded decomposition of needles could be explained more by the reduced microbial EEA. Further, in contrast to lower-order roots, N addition had no effect on the decomposition of higher-order roots. We conclude that the decomposition of foliage and fine roots may fail to mirror each other at ambient conditions or in response to N deposition due to their contrasting decomposition microenvironments and tissue chemistry. Given the differential effects of N addition on order-based roots, our findings highlight the need to consider the tissue chemistry heterogeneity within branching fine root systems when predicting the responses of root decomposition to N loading.

  1. Influence of powdered activated carbon addition on water quality, sludge properties, and microbial characteristics in the biological treatment of commingled industrial wastewater.

    PubMed

    Hu, Qing-Yuan; Li, Meng; Wang, Can; Ji, Min

    2015-09-15

    A powdered activated carbon-activated sludge (PAC-AS) system, a traditional activated sludge (AS) system, and a powdered activated carbon (PAC) system were operated to examine the insights into the influence of PAC addition on biological treatment. The average COD removal efficiencies of the PAC-AS system (39%) were nearly double that of the AS system (20%). Compared with the average efficiencies of the PAC system (7%), COD removal by biodegradation in the PAC-AS system was remarkably higher than that in the AS system. The analysis of the influence of PAC on water quality and sludge properties showed that PAC facilitated the removal of hydrophobic matter and metabolic acidic products, and also enhanced the biomass accumulation, sludge settleability, and specific oxygen uptake rate inside the biological system. The microbial community structures in the PAC-AS and AS systems were monitored. The results showed that the average well color development in the PAC-AS system was higher than that in the AS system. The utilization of various substrates by microorganisms in the two systems did not differ. The dissimilarity index was far less than one; thus, showing that the microbial community structures of the two systems were the same.

  2. Influence of powdered activated carbon addition on water quality, sludge properties, and microbial characteristics in the biological treatment of commingled industrial wastewater.

    PubMed

    Hu, Qing-Yuan; Li, Meng; Wang, Can; Ji, Min

    2015-09-15

    A powdered activated carbon-activated sludge (PAC-AS) system, a traditional activated sludge (AS) system, and a powdered activated carbon (PAC) system were operated to examine the insights into the influence of PAC addition on biological treatment. The average COD removal efficiencies of the PAC-AS system (39%) were nearly double that of the AS system (20%). Compared with the average efficiencies of the PAC system (7%), COD removal by biodegradation in the PAC-AS system was remarkably higher than that in the AS system. The analysis of the influence of PAC on water quality and sludge properties showed that PAC facilitated the removal of hydrophobic matter and metabolic acidic products, and also enhanced the biomass accumulation, sludge settleability, and specific oxygen uptake rate inside the biological system. The microbial community structures in the PAC-AS and AS systems were monitored. The results showed that the average well color development in the PAC-AS system was higher than that in the AS system. The utilization of various substrates by microorganisms in the two systems did not differ. The dissimilarity index was far less than one; thus, showing that the microbial community structures of the two systems were the same. PMID:25863578

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

    PubMed

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

    2011-08-10

    The potential of the waste from beer fermentation broth (WBFB) for the production of bio-ethanol using a simultaneous saccharification and fermentation process without any extra additions of saccharification enzymes, microbial cells or carbohydrate was tested. The major microbial cells in WBFB were isolated and identified. The variations in compositions of WBFB with stock time were investigated. There was residual activity of starch hydrolyzing enzymes in WBFB. The effects of reaction modes e.g. static and shaking on bio-ethanol production were studied. After 7 days of cultivation using the supernatant of WBFB at 30 °C the ethanol concentration reached 103.8 g/L in shaking culture and 91.5 g/L in static culture. Agitation experiments conducted at a temperature-profile process in which temperature was increased from 25 to 67 °C shortened the simultaneous process time. The original WBFB was more useful than the supernatant of WBFB in getting the higher concentration of ethanol and reducing the fermentation time. From this whole study it was found that WBFB is a cheap and suitable source for bio-ethanol production. PMID:22112515

  4. Factors affecting the microbial and chemical composition of silage. III. Effect of urea additions on maize silage.

    PubMed

    Mahmoud, S A; Abd-el-Hafez, A; Zaki, M M; Saleh, E A

    1978-01-01

    The effect of urea additions on the microbiological and chemical properties of silage, produced from young maize plants (Darawa stage), was studied. Urea treatments, i.e., 0.25%, 0.50%, 0.75%, and 1.00%, stimulated higher densities of the desired microorganisms than the control, while undesired organisms showed lower counts (proteolytic and saccharolytic anaerobes). Addition of 0.25 to 0.50% or urea resulted in the production of high quality silage with pleasant small and high nutritive value, as confirmed by the various microbiological and chemical analyses conducted. Higher levels (0.75 and 1.00%) of urea decreased the quality of the product. PMID:29417

  5. Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol.

    PubMed

    Sheppard, Micah J; Kunjapur, Aditya M; Wenck, Spencer J; Prather, Kristala L J

    2014-09-24

    Increasingly complex metabolic pathways have been engineered by modifying natural pathways and establishing de novo pathways with enzymes from a variety of organisms. Here we apply retro-biosynthetic screening to a modular pathway design to identify a redox neutral, theoretically high yielding route to a branched C6 alcohol. Enzymes capable of converting natural E. coli metabolites into 4-methyl-pentanol (4MP) via coenzyme A (CoA)-dependent chemistry were taken from nine different organisms to form a ten-step de novo pathway. Selectivity for 4MP is enhanced through the use of key enzymes acting on acyl-CoA intermediates, a carboxylic acid reductase from Nocardia iowensis and an alcohol dehydrogenase from Leifsonia sp. strain S749. One implementation of the full pathway from glucose demonstrates selective carbon chain extension and acid reduction with 4MP constituting 81% (90±7 mg l(-1)) of the observed alcohol products. The highest observed 4MP titre is 192±23 mg l(-1). These results demonstrate the ability of modular pathway screening to facilitate de novo pathway engineering.

  6. Simulating the response to phosphate additions in the oligotrophic eastern Mediterranean using an idealized four-member microbial food web model

    NASA Astrophysics Data System (ADS)

    Thingstad, T.

    2005-11-01

    Elsewhere in this volume, observations of the natural microbial food web in the Cyprus Gyre, eastern Mediterranean, and its transient responses both to phosphate additions in situ and to phosphate and ammonium additions when enclosed in microcosm bottles, are reported. We here explore an idealized four-population model of the microbial part of the food web, containing features suggested in these reports to be essential for the observed responses. Such features include a steady state with P-limited growth heterotrophic bacteria and P-limited or N/P co-limited growth of phytoplankton a mechanism for luxury consumption and nutrient storage in the osmotrophs (phytoplankton and bacteria), a supply of labile organic carbon substrates in excess of bacterial carbon demand, a relatively small excess of bio-available nitrogen, and an assumption that heterotrophic bacteria are superior to phytoplankton in competing for dissolved organic nitrogen. From a P-limited steady-state dominated by heterotrophic organisms, the model responds to the in situ phosphate addition of the Lagrangian experiment with a decrease in chlorophyll, an increase in bacterial production and in bacterial biomass, and a decrease in uptake potential for phosphate. These modeled responses at the osmotroph level are qualitatively and quantitatively comparable to those observed, while detailed comparison of model and observations at the predator level appears more difficult. The model is also able to explain main traits of the dynamic patterns observed in microcosm experiments, both when different concentrations of phosphate were added to previously unperturbed water, and when water collected inside the patch of the Lagrangian experiment was enclosed and supplied with ammonia. We conclude that the idealized model contains sufficient elements to capture a useful first-order approximation to a presumably quite complex microbial food web. In this model, predator growth responds not only to food quantity, but

  7. Protein design and engineering of a de novo pathway for microbial production of 1,3-propanediol from glucose.

    PubMed

    Chen, Zhen; Geng, Feng; Zeng, An-Ping

    2015-02-01

    Protein engineering to expand the substrate spectrum of native enzymes opens new possibilities for bioproduction of valuable chemicals from non-natural pathways. No natural microorganism can directly use sugars to produce 1,3-propanediol (PDO). Here, we present a de novo route for the biosynthesis of PDO from sugar, which may overcome the mentioned limitations by expanding the homoserine synthesis pathway. The accomplishment of pathway from homoserine to PDO is achieved by protein engineering of glutamate dehydrogenase (GDH) and pyruvate decarboxylase to sequentially convert homoserine to 4-hydroxy-2-ketobutyrate and 3-hydroxypropionaldehyde. The latter is finally converted to PDO by using a native alcohol dehydrogenase. In this work, we report on experimental accomplishment of this non-natural pathway, especially by protein engineering of GDH for the key step of converting homoserine to 4-hydroxy-2-ketobutyrate. These results show the feasibility and significance of protein engineering for de novo pathway design and overproduction of desired industrial products.

  8. Responses of soil enzyme activity and microbial community compositions to nitrogen addition in bulk and microaggregate soil in the temperate steppe of Inner Mongolia

    NASA Astrophysics Data System (ADS)

    Shi, Yao; Sheng, Lianxi; Wang, Zhongqiang; Zhang, Xinyu; He, Nianpeng; Yu, Qiang

    2016-10-01

    In order to explore the responses of soil enzyme activities and microbial community compositions to long-term nitrogen (N) addition in both bulk soil and microaggregate of chestnut soil, we conducted a 7-year urea addition experiment with N treatments at 6 levels (0, 56, 112, 224, 392 and 560 kg N ha-1 yr-1) in a temperate steppe of Inner Mongolia in China. Soil properties and the activities of four enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were measured in both bulk soil and microaggregate, and phospholipid fatty acids (PLFAs) were measured in bulk soil. The results indicated that: 1) in bulk soil, N addition significantly decreased β-1,4-glucosidase (BG) and leucine aminopeptidase (LAP) activities at the treatment amounts of 224, 392 and 560 kg N ha-1 yr-1, and obviously suppressed β-1,4-N-acetylglucosaminidase (NAG) activity at the treatment amount of 560 kg N ha-1 yr-1. N addition enhanced total PLFAs (totPLFAs) and bacterial PLFAs (bacPLFAs) at the treatment amounts of 392 and 560 kg N ha-1 yr-1, respectively, but fungal PLFAs showed no response to N addition. The activities of BG, NAG and LAP were positively correlated with soil pH, but negatively correlated with the concentration of NH 4 + -N; 2) in microaggregate (53-250 μm), the activities of BG, NAG and AP showed no response to increased addition of N, but the significantly decreased LAP activity was observed at the treatment amount of 392 kg N ha-1 yr-1. These results suggested that enzyme activities were more sensitive to N addition than PLFA biomarkers in soil, and LAP activity in microaggregate may be a good indicator for evaluating N cycle response to long-term N addition.

  9. Accelerated solvent extraction of animal feedingstuffs for microbial growth inhibition screening for the presence of antimicrobial feed additives.

    PubMed

    Higgins, H C; McEvoy, J D G

    2002-09-01

    Three plate systems (combinations of indicator organism and growth medium) were evaluated for the detection of analytical standards of the banned feed additives avoparcin, bacitracin zinc, spiramycin, tylosin and virginiamycin. When authorized in the EU, the previously recommended minimum inclusion rate (MIR) for each compound was 5 mg kg(-1). One of the plate systems (Micrococcus luteus ATCC 10240, nutrient agar) detected all five additives. This plate was used in a further study that evaluated the suitability of accelerated solvent extraction (ASE) as a first step in the development of a rapid single-plate screening assay. A drug-free (negative control) feedingstuff was fortified with the compounds (0-50 mg kg(-1)), extracted by ASE and the extracts applied to the plate at each of three pH ranges - unadjusted extract (pH 5.7-5.9), pH 6.5 and 8.0. At pH 6.5, sub-MIR concentrations of virginiamycin and tylosin were detectable. Avoparcin was detectable at 6.3 mg kg(-1). The detection of zinc bacitracin was#10; pH-independent (10 mg kg(-1)). At pH 8.0, spiramycin was detectable at 5.4 mg kg(-1). Mean +/- SD analytical recoveries from fortified feedingstuffs (n = 10) ranged from 57 +/- 1.5% for avoparcin to 96 +/- 4% for virginiamycin. The five additives were also detectable following ASE extraction from a range of different feedingstuffs fortified with each of the drugs. A further 24 compounds permitted for use in animal feeds were tested. Of these, nine were detectable at their recommended MIR. It is concluded that ASE is a versatile technique suitable for the automated extraction of a range of antimicrobials from animal feedingstuffs. Employing ASE with this single-plate detection system permits the rapid antimicrobial screening of animal feedingstuffs and allows the detection of the banned additives. Whilst the method is applicable as a screening test, more specific postscreening methods would be necessary for subsequent identification (and quantification) of

  10. Microbial Disruption of Autophagy Alters Expression of the RISC Component AGO2, a Critical Regulator of the miRNA Silencing Pathway

    PubMed Central

    Sibony, Michal; Abdullah, Majd; Greenfield, Laura; Raju, Deepa; Wu, Ted; Rodrigues, David M.; Galindo-Mata, Esther; Mascarenhas, Heidi; Philpott, Dana J.; Silverberg, Mark S.

    2015-01-01

    Background: Autophagy is implicated in Crohn's disease (CD) pathogenesis. Recent evidence suggests autophagy regulates the microRNA (miRNA)-induced silencing complex (miRISC). Therefore, autophagy may play a novel role in CD by regulating expression of miRISC, thereby altering miRNA silencing. As microbes associated with CD can alter autophagy, we hypothesized that microbial disruption of autophagy affects the critical miRISC component AGO2. Methods: AGO2 expression was assessed in epithelial and immune cells, and intestinal organoids with disrupted autophagy. Microarray technology was used to determine the expression of downstream miRNAs in cells with defective autophagy. Results: Increased AGO2 was detected in autophagy-deficient ATG5−/− and ATG16−/− mouse embryonic fibroblast cells (MEFs) in comparison with wild-type MEFs. Chemical agents and VacA toxin, which disrupt autophagy, increased AGO2 expression in MEFs, epithelial cells lines, and human monocytes, respectively. Increased AGO2 was also detected in ATG7−/− intestinal organoids, in comparison with wild-type organoids. Five miRNAs were differentially expressed in autophagy-deficient MEFs. Pathway enrichment analysis of the differentially expressed miRNAs implicated signaling pathways previously associated with CD. Conclusions: Taken together, our results suggest that autophagy is involved in the regulation of the critical miRISC component AGO2 in epithelial and immune cells and primary intestinal epithelial cells. We propose a mechanism by which autophagy alters miRNA expression, which likely impacts the regulation of CD-associated pathways. Furthermore, as enteric microbial products can manipulate autophagy and AGO2, our findings suggest a novel mechanism by which enteric microbes could influence miRNA to promote disease. PMID:26332312

  11. How do Soil Microbial Enzyme Activities Respond to Changes in Temperature, Carbon, and Nutrient Additions across Gradients in Mineralogy and Nutrient Availability?

    NASA Astrophysics Data System (ADS)

    McCleery, T.; Cusack, D. F.; Reed, S.; Wieder, W. R.; Taylor, P.; Cleveland, C. C.; Chadwick, O.; Vitousek, P.

    2013-12-01

    Microbial enzyme activities are the direct agents of organic matter decomposition, and thus play a crucial role in global carbon (C) cycling. Global change factors like warming and nutrient inputs to soils have the potential to alter the activities of these enzymes, with background site conditions likely driving responses. We hypothesized that enzyme activities in sites with high background nutrient and/or carbon availability would be less sensitive to nutrient additions than nutrient-poor sites. We also hypothesized that sites poor in background nutrients and/or carbon would show greater sensitivity to changes in temperature because of a less robust microbial community. To test our hypothesis we used laboratory temperature incubations combined with long- and short-term nutrient additions to assess changes in enzyme activities for 8 common soil enzymes that acquire nitrogen (N), phosphorus (P) and C from organic matter. We collected mineral soils (0-10 cm depth) from 8 Hawaiian sites that provided maximum variation in nutrient availability and background soil C. Soils were sieved, pooled by site, and homogenized prior to a laboratory addition of a simple C (sucrose) plus N and/or P in full factorial design. The 8 soils were also incubated at 7 different temperatures from 4 - 40 degrees C. We found that temperature sensitivities varied significantly among the sites, and that the laboratory fertilizations altered enzyme activities. Across the 8 sites, laboratory sucrose+N additions nearly doubled P-acquisition enzyme activity (p < 0.05), with the strongest effect in a younger forest soil that was naturally low in N. Similarly, laboratory sucrose+N and sucrose+NP additions significantly increased N-acquiring enzyme activity (p < 0.05), with the strongest effect in a drier, nutrient poor and carbon poor soil. Carbon-acquiring enzyme activities were less responsive, but also increased significantly with additions of sucrose+N and sucrose+NP across sites, with the

  12. Microbial modeling of thermal resistance of Alicyclobacillus acidoterrestris CRA7152 spores in concentrated orange juice with nisin addition

    PubMed Central

    Peña, Wilmer Edgard Luera; de Massaguer, Pilar Rodriguez; Teixeira, Luciano Quintão

    2009-01-01

    The nisin effect on thermal death of Alicyclobacillus acidoterrestris CRA 7152 spores in concentrated orange juice (64°Brix) was studied. Concentrations of 0, 50, 75 and 100 IU of nisin/ml juice, at temperatures of 92, 95, 98 and 102°C were evaluated. The quadratic polynomial model was used to analyze the effects of the factors and their interaction. Verification of surviving spores was carried out through plating in K medium (pH 3.7). The results showed that the D values without nisin addition were 25.5, 12.9, 6.1 and 2.3 min for 92, 95, 98 and 102°C respectively. With addition of nisin into the juice there was a drop of heat resistance as the concentration was increased at a same temperature. With 30, 50, 75, 100 and 150 IU/ml at 95°C, the D values were 12.34, 11.38, 10.49, 9.49 and 9.42 min respectively, showing that a decrease in the D value up to 27% can be obtained. The second order polynomial model established with r2 = 0.995 showed that the microorganism resistance was affected by the action of temperature followed by the nisin concentration. Nisin therefore is an alternative for reducing the rigor of the A. acidoterrestris CRA 7152 thermal treatment. PMID:24031405

  13. Soil microbial biomass and community structure affected by repeated additions of sewage sludge in four Swedish long-term field experiments

    NASA Astrophysics Data System (ADS)

    Börjesson, G.; Kätterer, T.; Kirchmann, H.

    2012-04-01

    Soil organic matter is a key attribute of soil fertility. The pool of soil organic C can be increased, either by mineral fertilisers or by adding organic amendments such as sewage sludge. Sewage sludge has positive effects on agricultural soils through the supply of organic matter and essential plant nutrients, but sludge may also contain unwanted heavy metals, xenobiotic substances and pathogens. One obvious effect of long-term sewage sludge addition is a decrease in soil pH, caused by N mineralisation followed by nitrification, sulphate formation and presence of organic acids with the organic matter added. The objective of this study was to investigate the effect of sewage sludge on the microbial biomass and community structure. Materials and methods We analysed soil samples from four sites where sewage sludge has been repeatedly applied in long-term field experiments situated in different parts of Sweden; Ultuna (59°49'N, 17°39'E, started 1956), Lanna (58°21'N, 13°06'E, started 1997-98), Petersborg (55°32'N, 13°00'E, started 1981) and Igelösa (55°45'N, 13°18'E, started 1981). In these four experiments, at least one sewage sludge treatment is included in the experimental design. In the Ultuna experiment, all organic fertilisers, including sewage sludge, are applied every second year, corresponding to 4 ton C ha-1. The Lanna experiment has a similar design, with 8 ton dry matter ha-1 applied every second year. Lanna also has an additional treatment in which metal salts (Cd, Cu, Ni and Zn) are added together with sewage sludge. At Petersborg and Igelösa, two levels of sewage sludge (4 or 12 ton dry matter ha-1 every 4th year) are compared with three levels of NPK fertiliser (0 N, ½ normal N and normal N). Topsoil samples (0-20 cm depth) from the four sites were analysed for total C, total N, pH and PLFAs (phospholipid fatty acids). In addition, crop yields were recorded. Results At all four sites, sewage sludge has had a positive effect on crop yields

  14. Addition of Bacillus sp. inoculums in bedding for swine on a pilot scale: effect on microbial population and bedding temperature.

    PubMed

    Corrêa, E K; Ulguim, R R; Corrêa, L B; Castilhos, D D; Bianchi, I; Gil-Turnes, C; Lucia, T

    2012-10-01

    Thermal and microbiological characteristics of beddings for swine were compared according to their depth and of addition of inoculums. Bedding was added to boxes at 0.25 (25D) and 0.50 m (50D), with three treatments: control (no inoculums); T1, with 250 g of Bacillus cereus var. toyoii at 8.4 × 10(7) CFU; and T2, with 250 g of a pool of B. subtilis, Bacillus licheniformis and Bacillus polymyxa at 8.4 × 10(7) CFU (250 g for 25D and 500 g for 50D). Mean temperatures were 28.5 ± 3.9 at the surface and 35.2 ± 8.9 inside the beddings. The most probable number (MPN) of thermophilic bacteria was higher for T1 and T2 than for the control (P<0.05). The MPN of thermophilic bacteria and fungi was greater for D50 than for D25 (P<0.05). The use of 25D without inoculums is recommended due to the reduction of thermophilic microbiota.

  15. Brazilian propolis extract used as an additive to decrease methane emissions from the rumen microbial population in vitro.

    PubMed

    Santos, Nadine Woruby; Zeoula, Lucia Maria; Yoshimura, Emerson Henri; Machado, Erica; Macheboeuf, Didier; Cornu, Agnès

    2016-06-01

    Propolis is a product that is rich in phenolic compounds and can be utilized in animal nutrition as a dietary additive. In this study, the effects of a Brazilian green propolis extract on rumen fermentation and gas production were determined. The fate of propolis phenolic compounds in the rumen medium was also investigated. Fermentation was done in 24-h batches over three periods. Inoculates were obtained from cows fed on grassland hay and concentrate. Propolis extract in a hydroalcoholic solution was applied at increasing doses to the substrate (1 to 56 g/kg). The fermentation substrate consisted on a mixture of alfalfa hay, soybean meal, and wheat grain mixture in dry matter. After 24 h of fermentation, seven new compounds were observed in the medium in amounts that correlated to the propolis dose. The dose of propolis extract linearly decreased the pH of the medium and linearly increased propionate production, which reduced the acetate-to-propionate ratio and influenced the total production of short-chain fatty acids. Propolis also linearly reduced methane production and increased the carbon dioxide-to-methane ratio. Ammonia nitrogen levels and in vitro digestibility of organic matter were similar among the treatments. The combination of increased propionate production and decreased methane production suggests better energy utilization from the feed. PMID:27105625

  16. The Fate of Carbon Draining Permafrost Soils is Controlled by Photochemical Reactions in Addition to Microbial Degradation in Arctic Surface Waters

    NASA Astrophysics Data System (ADS)

    Kling, G. W.; Dobkowski, J.; Ward, C. P.; Crump, B. C.; Neilson, B. T.; Cory, R. M.

    2013-12-01

    Perhaps the unknown of greatest potential consequence in determining the arc of climate change in this century is the role of thawing permafrost carbon. Arctic soil temperatures are increasing and large areas of permafrost have thawed, but not all soils will thaw quietly in place. Destabilization from melting ice has caused an increase in thermokarst failures that expose buried C and release dissolved organic C (DOC) to surface waters. We found that this exposure to sunlight and surface conditions increases the reactivity of permafrost C to microbial attack by 40% compared to soil DOC held in the dark. The range of lability to microbes depends on microbial community composition and especially on prior light exposure, implying that sunlight may act as an amplification factor in converting frozen C to gases in the atmosphere. We also found that photochemical degradation accounted for the majority (up to 80%) of the degradation of DOC in the water column of lakes and streams. This was based on concurrent measurements of (1) respiration of DOM to CO2 by bacteria in the dark, (2) O2 consumed in DOM photo-oxidation, (3) CO2 produced by DOM photo-mineralization, and (4) photo-stimulated bacterial respiration. Using in-situ UV light profiles and surveys of ~70 surface waters on the North Slope of Alaska, we found that depth-integrated water column rates of photochemical DOM degradation equaled or exceeded dark bacterial respiration, by up to 7x depending on the mean depth of the water column. The total dark and light processing of DOM in these waters was estimated to be roughly 20% of the DOM exported from major rivers on the North Slope of Alaska to the Arctic Ocean. The dominant degradation pathway was the partial photo-oxidation of DOC, which was at least 2x greater than complete photo-mineralization of DOC to CO2 or than bacterial respiration to CO2. This means that the dominant fate of permafrost C released as DOC is to be partially degraded and transported through

  17. Microbial phenolic metabolites improve glucose-stimulated insulin secretion and protect pancreatic beta cells against tert-butyl hydroperoxide-induced toxicity via ERKs and PKC pathways.

    PubMed

    Fernández-Millán, Elisa; Ramos, Sonia; Alvarez, Carmen; Bravo, Laura; Goya, Luis; Martín, María Ángeles

    2014-04-01

    Oxidative stress is accepted as one of the causes of beta cell failure in type 2 diabetes. Therefore, identification of natural antioxidant agents that preserve beta cell mass and function is considered an interesting strategy to prevent or treat diabetes. Recent evidences indicated that colonic metabolites derived from flavonoids could possess beneficial effects on various tissues. The aim of this work was to establish the potential anti-diabetic properties of the microbial-derived flavonoid metabolites 3,4-dihydroxyphenylacetic acid (DHPAA), 2,3-dihydroxybenzoic acid (DHBA) and 3-hydroxyphenylpropionic acid (HPPA). To this end, we tested their ability to influence beta cell function and to protect against tert-butyl hydroperoxide-induced beta cell toxicity. DHPAA and HPPA were able to potentiate glucose-stimulated insulin secretion (GSIS) in a beta cell line INS-1E and in rat pancreatic islets. Moreover, pre-treatment of cells with both compounds protected against beta cell dysfunction and death induced by the pro-oxidant. Finally, experiments with pharmacological inhibitors indicate that these effects were mediated by the activation of protein kinase C and the extracellular regulated kinases pathways. Altogether, these findings strongly suggest that the microbial-derived flavonoid metabolites DHPAA and HPPA may have anti-diabetic potential by promoting survival and function of pancreatic beta cells. PMID:24491264

  18. Virtual Institute of Microbial Stress and Survival: Deduction of Stress Response Pathways in Metal and Radionuclide Reducing Microorganisms

    SciTech Connect

    2004-04-17

    The projects application goals are to: (1) To understand bacterial stress-response to the unique stressors in metal/radionuclide contamination sites; (2) To turn this understanding into a quantitative, data-driven model for exploring policies for natural and biostimulatory bioremediation; (3) To implement proposed policies in the field and compare results to model predictions; and (4) Close the experimental/computation cycle by using discrepancies between models and predictions to drive new measurements and construction of new models. The projects science goals are to: (1) Compare physiological and molecular response of three target microorganisms to environmental perturbation; (2) Deduce the underlying regulatory pathways that control these responses through analysis of phenotype, functional genomic, and molecular interaction data; (3) Use differences in the cellular responses among the target organisms to understand niche specific adaptations of the stress and metal reduction pathways; (4) From this analysis derive an understanding of the mechanisms of pathway evolution in the environment; and (5) Ultimately, derive dynamical models for the control of these pathways to predict how natural stimulation can optimize growth and metal reduction efficiency at field sites.

  19. Isotope Effects Associated with N2O Production By Fungal and Bacterial Nitric Oxide Reductases: Implications for Tracing Microbial Production Pathways

    NASA Astrophysics Data System (ADS)

    Ostrom, N. E.; Yang, H.; Gandhi, H.; Hegg, E. L.

    2014-12-01

    Site preference (SP), the difference in δ15N between the central (α) and outer (β) N atoms in N2O, has emerged as a conservative tracer of microbial N2O production. The key advantages of SP relative to bulk isotopes are (1) that it is independent of the isotope composition of the substrates of nitrification and denitrification and (2) has not been shown to exhibit fractionation during production. In pure microbial culture distinct SP values for N2O production from bacterial denitrification, including nitrifier-denitrification (-10 to 0 ‰), relative to hydroxylamine oxidation and fungal denitrification (33-37 ‰) provide a promising basis to resolve production pathways. In this study, we determined the δ15N, δ18O, δ15Nα, and δ15Nβ of N2O generated by purified fungal (P450nor) and bacterial nitric oxide reductases. The isotope values were used to calculate SP values, enrichment factors (e), and kinetic isotope effects (KIEs). Both O and Nα displayed normal isotope effects during enzymatic NO reduction by the P450nor with e values of -25.7‰ (KIE = 1.0264) and -12.6‰ (KIE = 1.0127), respectively. However, bulk nitrogen (average δ15N of Nα and Nβ) and Nβ exhibited inverse isotope effects with e values of 14.0‰ (KIE = 0.9862) and 36.1‰ (KIE = 0.9651), respectively. The observed inverse isotope effect in δ15Nβ is consistent with reversible binding of the first NO in the P450nor reaction mechanism. Experiments with bacterial nitric oxide reductase are ongoing, however, preliminary data indicates a inverse isotope effect in the α and β positions and a normal isotope effect in δ18O. In contrast to the constant SP observed during N2O production observed in microbial cultures, the SP measured for purified P450nor was not constant, increasing from ~15‰ to ~29‰ during the course of the reaction. Our results clearly indicate that fractionation of SP during N2O production by P450nor is not zero, and that SP values higher and lower than the

  20. Toward Additive-Free Small-Molecule Organic Solar Cells: Roles of the Donor Crystallization Pathway and Dynamics.

    PubMed

    Abdelsamie, Maged; Treat, Neil D; Zhao, Kui; McDowell, Caitlin; Burgers, Mark A; Li, Ruipeng; Smilgies, Detlef-M; Stingelin, Natalie; Bazan, Guillermo C; Amassian, Aram

    2015-12-01

    The ease with which small-molecule donors crystallize during solution processing is directly linked to the need for solvent additives. Donor molecules that get trapped in disordered (H1) or liquid crystalline (T1) mesophases require additive processing to promote crystallization, phase separation, and efficient light harvesting. A donor material (X2) that crystallizes directly from solution yields additive-free solar cells with an efficiency of 7.6%.

  1. Changes of Fermentation Pathways of Fecal Microbial Communities Associated with a Drug Treatment That Increases Dietary Starch in the Human Colon

    PubMed Central

    Wolin, Meyer J.; Miller, Terry L.; Yerry, Susan; Zhang, Yongchao; Bank, Shelton; Weaver, Gary A.

    1999-01-01

    Acarbose inhibits starch digestion in the human small intestine. This increases the amount of starch available for microbial fermentation to acetate, propionate, and butyrate in the colon. Relatively large amounts of butyrate are produced from starch by colonic microbes. Colonic epithelial cells use butyrate as an energy source, and butyrate causes the differentiation of colon cancer cells. In this study we investigated whether colonic fermentation pathways changed during treatment with acarbose. We examined fermentations by fecal suspensions obtained from subjects who participated in an acarbose-placebo crossover trial. After incubation with [1-13C]glucose and 12CO2 or with unlabeled glucose and 13CO2, the distribution of 13C in product C atoms was determined by nuclear magnetic resonance spectrometry and gas chromatography-mass spectrometry. Regardless of the treatment, acetate, propionate, and butyrate were produced from pyruvate formed by the Embden-Meyerhof-Parnas pathway. Considerable amounts of acetate were also formed by the reduction of CO2. Butyrate formation from glucose increased and propionate formation decreased with acarbose treatment. Concomitantly, the amounts of CO2 reduced to acetate were 30% of the total acetate in untreated subjects and 17% of the total acetate in the treated subjects. The acetate, propionate, and butyrate concentrations were 57, 20, and 23% of the total final concentrations, respectively, for the untreated subjects and 57, 13, and 30% of the total final concentrations, respectively, for the treated subjects. PMID:10388668

  2. Single and Combined Effects of Deoxynivalenol Mycotoxin and a Microbial Feed Additive on Lymphocyte DNA Damage and Oxidative Stress in Broiler Chickens

    PubMed Central

    Awad, Wageha A.; Ghareeb, Khaled; Dadak, Agnes; Hess, Michael; Böhm, Josef

    2014-01-01

    The immune and intestinal epithelial cells are particularly sensitive to the toxic effects of deoxynivalenol (DON). The aim of this experiment was to study the effects of DON and/or a microbial feed additive on the DNA damage of blood lymphocytes and on the level of thiobarbituric acid reactive substance (TBARS) as an indicator of lipid peroxidation and oxidative stress in broilers. A total of forty 1-d-old broiler chicks were randomly assigned to 1 of 4 dietary treatments (10 birds per group) for 5 wk. The dietary treatments were 1) basal diet; 2) basal diet contaminated with 10 mg DON/kg feed; 3) basal diet contaminated with 10 mg DON/kg feed and supplemented with 2.5 kg/ton of feed of Mycofix Select; 4) basal diet supplemented with Mycofix Select (2.5 kg/ton of feed). At the end of the feeding trial, blood were collected for measuring the level of lymphocyte DNA damage of blood and the TBARS level was measured in plasma, heart, kidney, duodenum and jejunum. The dietary exposure of DON caused a significant increase (P = 0.001) of DNA damage in blood lymphocytes (31.99±0.89%) as indicated in the tail of comet assay. Interestingly addition of Mycofix Select to DON contaminated diet decreased (P = 0.001) the DNA damage (19.82±1.75%) induced by DON. In order to clarify the involvement of lipid peroxidation in the DNA damage of DON, TBARS levels was measured. A significant increase (P = 0.001) in the level of TBARS (23±2 nmol/mg) was observed in the jejunal tissue suggesting that the lipid peroxidation might be involved in the DNA damage. The results indicate that DON is cytotoxic and genotoxic to the chicken intestinal and immune cells and the feed additive have potential ability to prevent DNA damage induced by DON. PMID:24498242

  3. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use.

    PubMed

    Kleiner, Manuel; Wentrup, Cecilia; Lott, Christian; Teeling, Hanno; Wetzel, Silke; Young, Jacque; Chang, Yun-Juan; Shah, Manesh; VerBerkmoes, Nathan C; Zarzycki, Jan; Fuchs, Georg; Markert, Stephanie; Hempel, Kristina; Voigt, Birgit; Becher, Dörte; Liebeke, Manuel; Lalk, Michael; Albrecht, Dirk; Hecker, Michael; Schweder, Thomas; Dubilier, Nicole

    2012-05-01

    Low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. Particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and CO(2). Remarkably little is known about the physiological strategies that enable chemosynthetic symbioses to colonize oligotrophic environments. In this study, we used metaproteomics and metabolomics to investigate the intricate network of metabolic interactions in the chemosynthetic association between Olavius algarvensis, a gutless marine worm, and its bacterial symbionts. We propose previously undescribed pathways for coping with energy and nutrient limitation, some of which may be widespread in both free-living and symbiotic bacteria. These pathways include (i) a pathway for symbiont assimilation of the host waste products acetate, propionate, succinate and malate; (ii) the potential use of carbon monoxide as an energy source, a substrate previously not known to play a role in marine invertebrate symbioses; (iii) the potential use of hydrogen as an energy source; (iv) the strong expression of high-affinity uptake transporters; and (v) as yet undescribed energy-efficient steps in CO(2) fixation and sulfate reduction. The high expression of proteins involved in pathways for energy and carbon uptake and conservation in the O. algarvensis symbiosis indicates that the oligotrophic nature of its environment exerted a strong selective pressure in shaping these associations. PMID:22517752

  4. Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use

    SciTech Connect

    Kleiner, Manuel; Wentrop, C.; Lott, C.; Teeling, Hanno; Wetzel, Silke; Young, Jacque C; Chang, Y.; Shah, Manesh B; Verberkmoes, Nathan C; Zarzycki, Jan; Fuchs, Georg; Markert, Stephanie; Hempel, Kristina

    2012-01-01

    Low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. Particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep-sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and CO2. Remarkably little is known about the physiological strategies that enable chemosynthetic symbioses to colonize oligotrophic environments. In this study, we used metaproteomics and metabolomics to investigate the intricate network of metabolic interactions in the chemosynthetic association between Olavius algarvensis, a gutless marine worm, and its bacterial symbionts. We propose novel pathways for coping with energy and nutrient limitation, some of which may be widespread in both free-living and symbiotic bacteria. These include (i) a pathway for symbiont assimilation of the host waste products acetate, propionate, succinate and malate, (ii) the potential use of carbon monoxide as an energy source, a substrate previously not known to play a role in marine invertebrate symbioses, (iii) the potential use of hydrogen as an energy source, (iv) the strong expression of high affinity uptake transporters, and (v) novel energy efficient steps in CO2 fixation and sulfate reduction. The high expression of proteins involved in pathways for energy and carbon uptake and conservation in the O. algarvensis symbiosis indicates that the oligotrophic nature of its environment exerted a strong selective pressure in shaping these associations.

  5. Microbial community and removal of nitrogen via the addition of a carrier in a pilot-scale duckweed-based wastewater treatment system.

    PubMed

    Zhao, Yonggui; Fang, Yang; Jin, Yanling; Huang, Jun; Ma, Xinrong; He, Kaize; He, Zhiming; Wang, Feng; Zhao, Hai

    2015-03-01

    Carriers were added to a pilot-scale duckweed-based (Lemna japonica 0223) wastewater treatment system to immobilize and enhance microorganisms. This system and another parallel duckweed system without carriers were operated for 1.5 years. The results indicated the addition of the carrier did not significantly affect the growth and composition of duckweed, the recovery of total nitrogen (TN), total phosphorus (TP) and CO2 or the removal of TP. However, it significantly improved the removal efficiency of TN and NH4(+)-N (by 19.97% and 15.02%, respectively). The use of 454 pyrosequencing revealed large differences of the microbial communities between the different components within a system and similarities within the same components between the two systems. The carrier biofilm had the highest bacterial diversity and relative abundance of nitrifying bacteria (3%) and denitrifying bacteria (24% of Rhodocyclaceae), which improved nitrogen removal of the system. An efficient N-removal duckweed system with enhanced microorganisms was established. PMID:25579229

  6. Microbial community and removal of nitrogen via the addition of a carrier in a pilot-scale duckweed-based wastewater treatment system.

    PubMed

    Zhao, Yonggui; Fang, Yang; Jin, Yanling; Huang, Jun; Ma, Xinrong; He, Kaize; He, Zhiming; Wang, Feng; Zhao, Hai

    2015-03-01

    Carriers were added to a pilot-scale duckweed-based (Lemna japonica 0223) wastewater treatment system to immobilize and enhance microorganisms. This system and another parallel duckweed system without carriers were operated for 1.5 years. The results indicated the addition of the carrier did not significantly affect the growth and composition of duckweed, the recovery of total nitrogen (TN), total phosphorus (TP) and CO2 or the removal of TP. However, it significantly improved the removal efficiency of TN and NH4(+)-N (by 19.97% and 15.02%, respectively). The use of 454 pyrosequencing revealed large differences of the microbial communities between the different components within a system and similarities within the same components between the two systems. The carrier biofilm had the highest bacterial diversity and relative abundance of nitrifying bacteria (3%) and denitrifying bacteria (24% of Rhodocyclaceae), which improved nitrogen removal of the system. An efficient N-removal duckweed system with enhanced microorganisms was established.

  7. Carbon dioxide addition to microbial fuel cell cathodes maintains sustainable catholyte pH and improves anolyte pH, alkalinity, and conductivity.

    PubMed

    Fornero, Jeffrey J; Rosenbaum, Miriam; Cotta, Michael A; Angenent, Largus T

    2010-04-01

    Bioelectrochemical system (BES) pH imbalances develop due to anodic proton-generating oxidation reactions and cathodic hydroxide-ion-generating reduction reactions. Until now, workers added unsustainable buffers to reduce the pH difference between the anode and cathode because the pH imbalance contributes to BES potential losses and, therefore, power losses. Here, we report that adding carbon dioxide (CO(2)) gas to the cathode, which creates a CO(2)/bicarbonate buffered catholyte system, can diminish microbial fuel cell (MFC) pH imbalances in contrast to the CO(2)/carbonate buffered catholyte system by Torres, Lee, and Rittmann [Environ. Sci. Technol. 2008, 42, 8773]. We operated an air-cathode and liquid-cathode MFC side-by-side. For the air-cathode MFC, CO(2) addition resulted in a stable catholyte film pH of 6.61 +/- 0.12 and a 152% increase in steady-state power density. By adding CO(2) to the liquid-cathode system, we sustained a steady catholyte pH (pH = 5.94 +/- 0.02) and a low pH imbalance (DeltapH = 0.65 +/- 0.18) over a 2-week period without external salt buffer addition. By migrating bicarbonate ions from the cathode to the anode (with an anion-exchange membrane), we increased the anolyte pH (DeltapH = 0.39 +/- 0.31), total alkalinity (494 +/- 6 to 582 +/- 6 as mg CaCO(3)/L), and conductivity (1.53 +/- 0.49 to 2.16 +/- 0.03 mS/cm) relative to the feed properties. We also verified with a phosphate-buffered MFC that our reaction rates were limited mainly by the reactor configuration rather than limitations due to the bicarbonate buffer.

  8. Using chemical, microbial and fluorescence techniques to understand contaminant sources and pathways to wetlands in a conservation site.

    PubMed

    Rhymes, J; Jones, L; Lapworth, D J; White, D; Fenner, N; McDonald, J E; Perkins, T L

    2015-04-01

    Nutrients and faecal contaminants can enter wetland systems in a number of ways, with both biological and potentially human-health implications. In this study we used a combination of inorganic chemistry, dissolved organic matter (DOM) fluorescence and Escherichia coli and total coliform (TC) count techniques to study the sources and multiple pathways of contamination affecting a designated sand dune site of international conservation importance, surrounded by agricultural land. Analysis of stream samples, groundwater and dune slack wetlands revealed multiple input pathways. These included riverbank seepage, runoff events and percolation of nutrients from adjacent pasture into the groundwater, as well as some on-site sources. The combined techniques showed that off-site nutrient inputs into the sand dune system were primarily from fertilisers, revealed by high nitrate concentrations, and relatively low tryptophan-like fulvic-like ratios<0.4Ramanunits (R.U.). The E. coli and TC counts recorded across the site confirm a relatively minor source of bacterial and nutrient inputs from on-site grazers. Attenuation of the nutrient concentrations in streams, in groundwater and in run-off inputs occurs within the site, restoring healthier groundwater nutrient concentrations showing that contaminant filtration by the sand dunes provides a valuable ecosystem service. However, previous studies show that this input of nutrients has a clear adverse ecological impact.

  9. Synchronized electrical stimulation of the rat medial forebrain bundle and perforant pathway generates an additive BOLD response in the nucleus accumbens and prefrontal cortex.

    PubMed

    Krautwald, Karla; Min, Hoon-Ki; Lee, Kendall H; Angenstein, Frank

    2013-08-15

    To study how a synchronized activation of two independent pathways affects the fMRI response in a common targeted brain region, blood oxygen dependent (BOLD) signals were measured during electrical stimulation of the right medial forebrain bundle (MFB), the right perforant pathway (PP) and concurrent stimulation of the two fiber systems. Repetitive electrical stimulations of the MFB triggered significant positive BOLD responses in the nucleus accumbens (NAcc), septum, anterior cingulate cortex/medial prefrontal cortex (ACC/mPFC), ventral tegmental area/substantia nigra (VTA/SN), right entorhinal cortex (EC) and colliculus superior, which, in general, declined during later stimulation trains. At the same time, negative BOLD responses were observed in the striatum. Thus, the same stimulus caused region-specific hemodynamic responses. An identical electrical stimulation of the PP generated positive BOLD responses in the right dentate gyrus/hippocampus proper/subiculum (DG/HC), the right entorhinal cortex and the left entorhinal cortex, which remained almost stable during consecutive stimulation trains. Co-stimulation of the two fiber systems resulted in an additive activation pattern, i.e., the BOLD responses were stronger during the stimulation of the two pathways than during the stimulation of only one pathway. However, during the simultaneous stimulation of the two pathways, the development of the BOLD responses to consecutive trains changed. The BOLD responses in regions that were predominantly activated by MFB stimulation (i.e., NAcc, septum and ACC/mPFC) did not decline as fast as during pure MFB stimulation, thus an additive BOLD response was only observed during later trains. In contrast, in the brain regions that were predominantly activated by PP stimulation (i.e., right EC, DG/HC), co-stimulation of the MFB only resulted in an additive effect during early trains but not later trains. Consequently, the development of the BOLD responses during consecutive

  10. The molecular basis for the post-translational addition of amino acids by L/F transferase in the N-end rule pathway.

    PubMed

    Fung, Angela Wai S; Fahlman, Richard P

    2015-01-01

    The N-end rule pathway is a conserved targeted proteolytic process observed in organisms ranging from eubacteria to mammals. The N-end rule relates the metabolic stability of a protein to its N-terminal amino acid residue. The identity of the N-terminal amino acid residue is a primary degradation signal, often referred to as an N-degron, which is recognized by the components of the N-end rule when it is a destabilizing N-terminus. N-degrons may be exposed by non-processive proteolytic cleavages or by post-translational modifications. One modification is the post-translational addition of amino acids to the N-termini of proteins, a reaction catalyzed by aminoacyl-tRNA protein transferases. The aminoacyl-tRNA protein transferase in eubacteria like Escherichia coli is L/F transferase. Recent investigations have reported unexpected observations regarding the L/F transferase catalytic mechanism and its mechanisms of substrate recognition. Additionally, recent proteome-wide identification of putative in vivo substrates facilitates hypothesis into the yet elusive biological functions of the prokaryotic N-end rule pathway. Here we summarize the recent findings on the molecular mechanisms of catalysis and substrate recognition by the E. coli L/F transferase in the prokaryotic N-end rule pathway.

  11. Investigation of the O+allyl addition/elimination reaction pathways from the OCH(2)CHCH(2) radical intermediate.

    PubMed

    Fitzpatrick, Benjamin L; Lau, Kai-Chung; Butler, Laurie J; Lee, Shih-Huang; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH(2)CHCH(2), a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH(2)CHCH(2) radicals; these undergo a facile ring opening to the OCH(2)CHCH(2) radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcalmol. To elucidate the product channels resulting from the OCH(2)CHCH(2) radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C(3)H(4)O (acrolein)+H, C(2)H(4)+HCO (formyl radical), and H(2)CO (formaldehyde)+C(2)H(3). A small signal from C(2)H(2)O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at me=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C(2)H(5)+CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to

  12. Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a mediterranean forest after a wildfire.

    PubMed

    Cobo-Díaz, José F; Fernández-González, Antonio J; Villadas, Pablo J; Robles, Ana B; Toro, Nicolás; Fernández-López, Manuel

    2015-05-01

    Wildfires are frequent in the forests of the Mediterranean Basin and have greatly influenced this ecosystem. Changes to the physical and chemical properties of the soil, due to fire and post-fire conditions, result in alterations of both the bacterial communities and the nitrogen cycle. We explored the effects of a holm oak forest wildfire on the rhizospheric bacterial communities involved in the nitrogen cycle. Metagenomic data of the genes involved in the nitrogen cycle showed that both the undisturbed and burned rhizospheres had a conservative nitrogen cycle with a larger number of sequences related to the nitrogen incorporation pathways and a lower number for nitrogen output. However, the burned rhizosphere showed a statistically significant increase in the number of sequences for nitrogen incorporation (allantoin utilization and nitrogen fixation) and a significantly lower number of sequences for denitrification and dissimilatory nitrite reductase subsystems, possibly in order to compensate for nitrogen loss from the soil after burning. The genetic potential for nitrogen incorporation into the ecosystem was assessed through the diversity of the nitrogenase reductase enzyme, which is encoded by the nifH gene. We found that nifH gene diversity and richness were lower in burned than in undisturbed rhizospheric soils. The structure of the bacterial communities involved in the nitrogen cycle showed a statistically significant increase of Actinobacteria and Firmicutes phyla after the wildfire. Both approaches showed the important role of gram-positive bacteria in the ecosystem after a wildfire.

  13. Modulation of the Arginase Pathway in the Context of Microbial Pathogenesis: A Metabolic Enzyme Moonlighting as an Immune Modulator

    PubMed Central

    Lahiri, Ayan; Chakravortty, Dipshikha

    2010-01-01

    Arginine is a crucial amino acid that serves to modulate the cellular immune response during infection. Arginine is also a common substrate for both inducible nitric oxide synthase (iNOS) and arginase. The generation of nitric oxide from arginine is responsible for efficient immune response and cytotoxicity of host cells to kill the invading pathogens. On the other hand, the conversion of arginine to ornithine and urea via the arginase pathway can support the growth of bacterial and parasitic pathogens. The competition between iNOS and arginase for arginine can thus contribute to the outcome of several parasitic and bacterial infections. There are two isoforms of vertebrate arginase, both of which catalyze the conversion of arginine to ornithine and urea, but they differ with regard to tissue distribution and subcellular localization. In the case of infection with Mycobacterium, Leishmania, Trypanosoma, Helicobacter, Schistosoma, and Salmonella spp., arginase isoforms have been shown to modulate the pathology of infection by various means. Despite the existence of a considerable body of evidence about mammalian arginine metabolism and its role in immunology, the critical choice to divert the host arginine pool by pathogenic organisms as a survival strategy is still a mystery in infection biology. PMID:20585552

  14. Novel anti-microbial peptide SR-0379 accelerates wound healing via the PI3 kinase/Akt/mTOR pathway.

    PubMed

    Tomioka, Hideki; Nakagami, Hironori; Tenma, Akiko; Saito, Yoshimi; Kaga, Toshihiro; Kanamori, Toshihide; Tamura, Nao; Tomono, Kazunori; Kaneda, Yasufumi; Morishita, Ryuichi

    2014-01-01

    We developed a novel cationic antimicrobial peptide, AG30/5C, which demonstrates angiogenic properties similar to those of LL-37 or PR39. However, improvement of its stability and cost efficacy are required for clinical application. Therefore, we examined the metabolites of AG30/5C, which provided the further optimized compound, SR-0379. SR-0379 enhanced the proliferation of human dermal fibroblast cells (NHDFs) via the PI3 kinase-Akt-mTOR pathway through integrin-mediated interactions. Furthermore SR-0379 promoted the tube formation of human umbilical vein endothelial cells (HUVECs) in co-culture with NHDFs. This compound also displays antimicrobial activities against a number of bacteria, including drug-resistant microbes and fungi. We evaluated the effect of SR-0379 in two different would-healing models in rats, the full-thickness defects under a diabetic condition and an acutely infected wound with full-thickness defects and inoculation with Staphylococcus aureus. Treatment with SR-0379 significantly accelerated wound healing when compared to fibroblast growth factor 2 (FGF2). The beneficial effects of SR-0379 on wound healing can be explained by enhanced angiogenesis, granulation tissue formation, proliferation of endothelial cells and fibroblasts and antimicrobial activity. These results indicate that SR-0379 may have the potential for drug development in wound repair, even under especially critical colonization conditions. PMID:24675668

  15. Metagenomic assessment of the potential microbial nitrogen pathways in the rhizosphere of a mediterranean forest after a wildfire.

    PubMed

    Cobo-Díaz, José F; Fernández-González, Antonio J; Villadas, Pablo J; Robles, Ana B; Toro, Nicolás; Fernández-López, Manuel

    2015-05-01

    Wildfires are frequent in the forests of the Mediterranean Basin and have greatly influenced this ecosystem. Changes to the physical and chemical properties of the soil, due to fire and post-fire conditions, result in alterations of both the bacterial communities and the nitrogen cycle. We explored the effects of a holm oak forest wildfire on the rhizospheric bacterial communities involved in the nitrogen cycle. Metagenomic data of the genes involved in the nitrogen cycle showed that both the undisturbed and burned rhizospheres had a conservative nitrogen cycle with a larger number of sequences related to the nitrogen incorporation pathways and a lower number for nitrogen output. However, the burned rhizosphere showed a statistically significant increase in the number of sequences for nitrogen incorporation (allantoin utilization and nitrogen fixation) and a significantly lower number of sequences for denitrification and dissimilatory nitrite reductase subsystems, possibly in order to compensate for nitrogen loss from the soil after burning. The genetic potential for nitrogen incorporation into the ecosystem was assessed through the diversity of the nitrogenase reductase enzyme, which is encoded by the nifH gene. We found that nifH gene diversity and richness were lower in burned than in undisturbed rhizospheric soils. The structure of the bacterial communities involved in the nitrogen cycle showed a statistically significant increase of Actinobacteria and Firmicutes phyla after the wildfire. Both approaches showed the important role of gram-positive bacteria in the ecosystem after a wildfire. PMID:25732259

  16. The Wnt and Delta-Notch signalling pathways interact to direct pair-rule gene expression via caudal during segment addition in the spider Parasteatoda tepidariorum.

    PubMed

    Schönauer, Anna; Paese, Christian L B; Hilbrant, Maarten; Leite, Daniel J; Schwager, Evelyn E; Feitosa, Natália Martins; Eibner, Cornelius; Damen, Wim G M; McGregor, Alistair P

    2016-07-01

    In short-germ arthropods, posterior segments are added sequentially from a segment addition zone (SAZ) during embryogenesis. Studies in spiders such as Parasteatoda tepidariorum have provided insights into the gene regulatory network (GRN) underlying segment addition, and revealed that Wnt8 is required for dynamic Delta (Dl) expression associated with the formation of new segments. However, it remains unclear how these pathways interact during SAZ formation and segment addition. Here, we show that Delta-Notch signalling is required for Wnt8 expression in posterior SAZ cells, but represses the expression of this Wnt gene in anterior SAZ cells. We also found that these two signalling pathways are required for the expression of the spider orthologues of even-skipped (eve) and runt-1 (run-1), at least in part via caudal (cad). Moreover, it appears that dynamic expression of eve in this spider does not require a feedback loop with run-1, as is found in the pair-rule circuit of the beetle Tribolium Taken together, our results suggest that the development of posterior segments in Parasteatoda is directed by dynamic interactions between Wnt8 and Delta-Notch signalling that are read out by cad, which is necessary but probably not sufficient to regulate the expression of eve and run-1 Our study therefore provides new insights towards better understanding the evolution and developmental regulation of segmentation in other arthropods, including insects. PMID:27287802

  17. The Wnt and Delta-Notch signalling pathways interact to direct pair-rule gene expression via caudal during segment addition in the spider Parasteatoda tepidariorum.

    PubMed

    Schönauer, Anna; Paese, Christian L B; Hilbrant, Maarten; Leite, Daniel J; Schwager, Evelyn E; Feitosa, Natália Martins; Eibner, Cornelius; Damen, Wim G M; McGregor, Alistair P

    2016-07-01

    In short-germ arthropods, posterior segments are added sequentially from a segment addition zone (SAZ) during embryogenesis. Studies in spiders such as Parasteatoda tepidariorum have provided insights into the gene regulatory network (GRN) underlying segment addition, and revealed that Wnt8 is required for dynamic Delta (Dl) expression associated with the formation of new segments. However, it remains unclear how these pathways interact during SAZ formation and segment addition. Here, we show that Delta-Notch signalling is required for Wnt8 expression in posterior SAZ cells, but represses the expression of this Wnt gene in anterior SAZ cells. We also found that these two signalling pathways are required for the expression of the spider orthologues of even-skipped (eve) and runt-1 (run-1), at least in part via caudal (cad). Moreover, it appears that dynamic expression of eve in this spider does not require a feedback loop with run-1, as is found in the pair-rule circuit of the beetle Tribolium Taken together, our results suggest that the development of posterior segments in Parasteatoda is directed by dynamic interactions between Wnt8 and Delta-Notch signalling that are read out by cad, which is necessary but probably not sufficient to regulate the expression of eve and run-1 Our study therefore provides new insights towards better understanding the evolution and developmental regulation of segmentation in other arthropods, including insects.

  18. Antifungal hydroxy fatty acids produced during sourdough fermentation: microbial and enzymatic pathways, and antifungal activity in bread.

    PubMed

    Black, Brenna A; Zannini, Emanuele; Curtis, Jonathan M; Gänzle, Michael G

    2013-03-01

    Lactobacilli convert linoleic acid to hydroxy fatty acids; however, this conversion has not been demonstrated in food fermentations and it remains unknown whether hydroxy fatty acids produced by lactobacilli have antifungal activity. This study aimed to determine whether lactobacilli convert linoleic acid to metabolites with antifungal activity and to assess whether this conversion can be employed to delay fungal growth on bread. Aqueous and organic extracts from seven strains of lactobacilli grown in modified De Man Rogosa Sharpe medium or sourdough were assayed for antifungal activity. Lactobacillus hammesii exhibited increased antifungal activity upon the addition of linoleic acid as a substrate. Bioassay-guided fractionation attributed the antifungal activity of L. hammesii to a monohydroxy C(18:1) fatty acid. Comparison of its antifungal activity to those of other hydroxy fatty acids revealed that the monohydroxy fraction from L. hammesii and coriolic (13-hydroxy-9,11-octadecadienoic) acid were the most active, with MICs of 0.1 to 0.7 g liter(-1). Ricinoleic (12-hydroxy-9-octadecenoic) acid was active at a MIC of 2.4 g liter(-1). L. hammesii accumulated the monohydroxy C(18:1) fatty acid in sourdough to a concentration of 0.73 ± 0.03 g liter(-1) (mean ± standard deviation). Generation of hydroxy fatty acids in sourdough also occurred through enzymatic oxidation of linoleic acid to coriolic acid. The use of 20% sourdough fermented with L. hammesii or the use of 0.15% coriolic acid in bread making increased the mold-free shelf life by 2 to 3 days or from 2 to more than 6 days, respectively. In conclusion, L. hammesii converts linoleic acid in sourdough and the resulting monohydroxy octadecenoic acid exerts antifungal activity in bread.

  19. Pressure-dependent competition among reaction pathways from first- and second-O2 additions in the low-temperature oxidation of tetrahydrofuran

    DOE PAGES

    Antonov, Ivan O.; Zador, Judit; Rotavera, Brandon; Papajak, Ewa; Osborn, David L.; Taatjes, Craig A.; Sheps, Leonid

    2016-07-21

    Here, we report a combined experimental and quantum chemistry study of the initial reactions in low-temperature oxidation of tetrahydrofuran (THF). Using synchrotron-based time-resolved VUV photoionization mass spectrometry, we probe numerous transient intermediates and products at P = 10–2000 Torr and T = 400–700 K. A key reaction sequence, revealed by our experiments, is the conversion of THF-yl peroxy to hydroperoxy-THF-yl radicals (QOOH), followed by a second O2 addition and subsequent decomposition to dihydrofuranyl hydroperoxide + HO2 or to γ-butyrolactone hydroperoxide + OH. The competition between these two pathways affects the degree of radical chain-branching and is likely of central importancemore » in modeling the autoignition of THF. We interpret our data with the aid of quantum chemical calculations of the THF-yl + O2 and QOOH + O2 potential energy surfaces. On the basis of our results, we propose a simplified THF oxidation mechanism below 700 K, which involves the competition among unimolecular decomposition and oxidation pathways of QOOH.« less

  20. Pressure-Dependent Competition among Reaction Pathways from First- and Second-O2 Additions in the Low-Temperature Oxidation of Tetrahydrofuran.

    PubMed

    Antonov, Ivan O; Zádor, Judit; Rotavera, Brandon; Papajak, Ewa; Osborn, David L; Taatjes, Craig A; Sheps, Leonid

    2016-08-25

    We report a combined experimental and quantum chemistry study of the initial reactions in low-temperature oxidation of tetrahydrofuran (THF). Using synchrotron-based time-resolved VUV photoionization mass spectrometry, we probe numerous transient intermediates and products at P = 10-2000 Torr and T = 400-700 K. A key reaction sequence, revealed by our experiments, is the conversion of THF-yl peroxy to hydroperoxy-THF-yl radicals (QOOH), followed by a second O2 addition and subsequent decomposition to dihydrofuranyl hydroperoxide + HO2 or to γ-butyrolactone hydroperoxide + OH. The competition between these two pathways affects the degree of radical chain-branching and is likely of central importance in modeling the autoignition of THF. We interpret our data with the aid of quantum chemical calculations of the THF-yl + O2 and QOOH + O2 potential energy surfaces. On the basis of our results, we propose a simplified THF oxidation mechanism below 700 K, which involves the competition among unimolecular decomposition and oxidation pathways of QOOH. PMID:27441526

  1. Microfluidics and microbial engineering.

    PubMed

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

    2016-02-01

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

  2. Effects of soaking with natural additives in combinations with vacuum or modified atmosphere packaging on microbial populations and shelf life of fresh truffles (Chinese Tuber indicum).

    PubMed

    Miao, Yuzhi; Chen, Cuiping; Ma, Qinqin; Wang, Yiding; Zhang, Xiaoyu; Guo, Fanglan; Li, Wei; Yong, Bin

    2014-10-01

    The objective of this study was to evaluate the relative effects and interactions of combined soaking treatment using citric acid (CTA) and apple polyphenol (APP) at mild heating temperatures for the inactivation of the external and internal microflora (mesophilic aerobic bacteria, mesophilic anaerobic bacteria, and fungi) in Chinese Tuber indicum, as well as to analyze the microbiological and sensory changes under modified atmosphere packaging (MAP)- and vacuum atmosphere packaging (VAC)-packed Chinese T. indicum stored at 4 °C for up to 55 d. Chinese T. indicum was soaked with CTA and APP alone or in combination for 10, 20, and 30 min at 35, 45, and 55 °C. A disinfection method using CTA and APP (3% CTA + 3% APP for 20 min at 45 °C) was obtained. Under this set of combination, the experimental values of microbial counts of mesophilic aerobic bacteria, mesophilic anaerobic bacteria, and fungi were 2.31 ± 0.4 log CFU/g, <1.0 log CFU/g, and <1.0 log CFU/g, respectively. Through the analysis of sensory qualities and microbial populations for MAP- or VAC-packed Chinese T. indicum, the shelf life of soaked truffles was prolonged to 45 or 40 d, respectively. The synergistic effect of CTA and APP may provide valuable insight into the reduction of microorganisms on fresh truffles.

  3. Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences

    PubMed Central

    Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu

    2013-01-01

    Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner, we present a probabilistic sampling approach to profiling functional content in a metagenomic dataset, by sampling functions of catalytically promiscuous enzymes within the context of the entire metabolic network defined by the annotated metagenome. We test our approach on metagenomic datasets from environmental and human-associated microbial communities. The results show that our approach provides a more accurate representation of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis of multiple microbial communities. In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/. PMID:23555216

  4. Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.

    PubMed

    Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu

    2013-01-01

    Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner, we present a probabilistic sampling approach to profiling functional content in a metagenomic dataset, by sampling functions of catalytically promiscuous enzymes within the context of the entire metabolic network defined by the annotated metagenome. We test our approach on metagenomic datasets from environmental and human-associated microbial communities. The results show that our approach provides a more accurate representation of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis of multiple microbial communities. In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/. PMID:23555216

  5. Reciprocal influences of microbial community and hydrogeomorphology in sandy streambeds

    NASA Astrophysics Data System (ADS)

    Mendoza-Lera, C.; Federlein, L. L.; Frossard, A.; Gessner, M. O.; Knie, M.; Mutz, M.

    2015-12-01

    Stream hydrogeomorphology is a strong determinant of streambed microbial community activity, which in turn influences stream biogeochemistry. Whether this influence is unidirectional or whether microbial communities can also modulate biogeochemical processes by affecting hydrogeomorphology is an emerging question in research on sediment-water interfaces. Using experimental flumes simulating sandy streams, we tested whether such influences can occur through altered water exchange across the sediment-water interface. Results show that microbial communities in sandy streambeds can indeed affect hydrogeomorphology by producing gas bubbles. Specifically, gas bubbles accumulating in microbial biofilms can alter the water exchange by (i) reducing sediment pore space or (ii) provoking the detachment of the microbial biofilm detachment and thus altering streambed topography. Additionally, results indicate that water exchange is the major for the structure and activity of the microbial community. Our data also indicate that the potential of microbial communities to influence water exchange can be modulated by factors such as light intensity and discharge fluctuations. These biological-physical interactions and their effects on the influence of microbial communities on hydrogeomorphology is a source of spatiotemporal variability in water exchange across the sediment-water interface. Heterogeneity in water exchange is known to increase biogeochemical pathways and, thus, ecosystem functions. These results suggest that a holistic understanding of vertical connectivity in running waters requires consideration of biological-physical interactions at the water-sediment interface.

  6. Microbially induced and microbially catalysed precipitation: two different carbonate factories

    NASA Astrophysics Data System (ADS)

    Meister, Patrick

    2016-04-01

    The landmark paper by Schlager (2003) has revealed three types of benthic carbonate production referred to as "carbonate factories", operative at different locations at different times in Earth history. The tropical or T-factory comprises the classical platforms and fringing reefs and is dominated by carbonate precipitation by autotrophic calcifying metazoans ("biotically controlled" precipitation). The cool or C-factory is also biotically controlled but via heterotrophic, calcifying metazoans in cold and deep waters at the continental margins. A further type is the mud-mound or M-factory, where carbonate precipitation is supported by microorganisms but not controlled by a specific enzymatic pathway ("biotically induced" precipitation). How exactly the microbes influence precipitation is still poorly understood. Based on recent experimental and field studies, the microbial influence on modern mud mound and microbialite growth includes two fundamentally different processes: (1) Metabolic activity of microbes may increase the saturation state with respect to a particular mineral phase, thereby indirectly driving the precipitation of the mineral phase: microbially induced precipitation. (2) In a situation, where a solution is already supersaturated but precipitation of the mineral is inhibited by a kinetic barrier, microbes may act as a catalyser, i.e. they lower the kinetic barrier: microbially catalysed precipitation. Such a catalytic effect can occur e.g. via secreted polymeric substances or specific chemical groups on the cell surface, at which the minerals nucleate or which facilitate mechanistically the bonding of new ions to the mineral surface. Based on these latest developments in microbialite formation, I propose to extend the scheme of benthic carbonate factories of Schlager et al. (2003) by introducing an additional branch distinguishing microbially induced from microbially catalysed precipitation. Although both mechanisms could be operative in a M

  7. Evaluation of microbial triglyceride oil purification requirements for the CelTherm process: an efficient biochemical pathway to renewable fuels and chemicals.

    PubMed

    Linnen, Michael; Seames, Wayne; Kubatova, Alena; Menon, Suresh; Alisala, Kashinatham; Hash, Sara

    2014-10-01

    CelTherm is a biochemical process to produce renewable fuels and chemicals from lignocellulosic biomass. The present study's objective was to determine the level of treatment/purity of the microbial triacylglyceride oil (TAG) necessary to facilitate fuel production. After a unique microbe aerobically synthesizes TAG from biomass-derived sugars, the microbes were harvested and dried then crude TAG was chemically extracted from the residual biomass. Some TAGs were further purified to hydrotreating process requirements. Both grades were then noncatalytically cracked into a petroleum-like intermediate characterized by gas chromatography. Experiments were repeated using refined soybean oil for comparison to previous studies. The products from crude microbial TAG cracking were then further refined into a jet fuel product. Fuel tests indicate that this jet fuel corresponds to specifications for JP-8 military turbine fuel. It was thus concluded that the crude microbial TAG is a suitable feedstock with no further purification required, demonstrating CelTherm's commercial potential. PMID:24781206

  8. Nitrogen Cycling Potential of a Grassland Litter Microbial Community.

    PubMed

    Nelson, Michaeline B; Berlemont, Renaud; Martiny, Adam C; Martiny, Jennifer B H

    2015-10-01

    Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems.

  9. Nitrogen Cycling Potential of a Grassland Litter Microbial Community

    PubMed Central

    Berlemont, Renaud; Martiny, Adam C.; Martiny, Jennifer B. H.

    2015-01-01

    Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems. PMID:26231641

  10. The addition of ortho-hexagon nano spinel Co3O4 to improve the performance of activated carbon air cathode microbial fuel cell.

    PubMed

    Ge, Baochao; Li, Kexun; Fu, Zhou; Pu, Liangtao; Zhang, Xi

    2015-11-01

    Commercial Co3O4 and ortho-hexagon spinel nano-Co3O4 (OHSNC) were doped in the AC at a different percentage (5%, 10% and 15%) to enhance the performance of microbial fuel cell (MFC). The maximum power density of MFC with 10% OHSNC doped cathode was 1500±14 mW m(-2), which was 97.36% and 41.24% higher than that with the bare AC air cathode and commercial Co3O4 respectively. The electrocatalytic behavior for their better performance was discussed in detail with the help of various structural and electrochemical techniques. The OHSNC was characterized via X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM). The results showed that the improved performance owed to the enhancement of both kinetics activity and the number of electron transfer in the ORR, and the internal resistance was largely reduced. Therefore, OHSNC was proved to be an excellent cathodic catalyst in AC air cathode MFC.

  11. Effect of red mud addition on tetracycline and copper resistance genes and microbial community during the full scale swine manure composting.

    PubMed

    Wang, Rui; Zhang, Junya; Sui, Qianwen; Wan, Hefeng; Tong, Juan; Chen, Meixue; Wei, Yuansong; Wei, Dongbin

    2016-09-01

    Swine manure has been considered as the reservoir of antibiotic resistance genes (ARGs). Composting is one of the most suitable technologies for treating livestock manures, and red mud was proved to have a positive effect on nitrogen conservation during composting. This study investigated the abundance of eight tetracycline and three copper resistance genes, the bacterial community during the full scale swine manure composting with or without addition of red mud. The results showed that ARGs in swine manure could be effectively removed through composting (reduced by 2.4log copies/g TS), especially during the thermophilic phase (reduced by 1.5log copies/g TS), which the main contributor might be temperature. Additionally, evolution of bacterial community could also have a great influence on ARGs. Although addition of red mud could enhance nitrogen conservation, it obviously hindered removal of ARGs (reduced by 1.7log copies/g TS) and affected shaping of bacterial community during composting.

  12. Co-digestion of manure and whey for in situ biogas upgrading by the addition of H(2): process performance and microbial insights.

    PubMed

    Luo, Gang; Angelidaki, Irini

    2013-02-01

    In situ biogas upgrading was conducted by introducing H(2) directly to the anaerobic reactor. As H(2) addition is associated with consumption of the CO(2) in the biogas reactor, pH increased to higher than 8.0 when manure alone was used as substrate. By co-digestion of manure with acidic whey, the pH in the anaerobic reactor with the addition of hydrogen could be maintained below 8.0, which did not have inhibition to the anaerobic process. The H(2) distribution systems (diffusers with different pore sizes) and liquid mixing intensities were demonstrated to affect the gas-liquid mass transfer of H(2) and the biogas composition. The best biogas composition (75:6.6:18.4) was obtained at stirring speed 150 rpm and using ceramic diffuser, while the biogas in the control reactor consisted of CH(4) and CO(2) at a ratio of 55:45. The consumed hydrogen was almost completely converted to CH(4), and there was no significant accumulation of VFA in the effluent. The study showed that addition of hydrogen had positive effect on the methanogenesis, but had no obvious effect on the acetogenesis. Both hydrogenotrophic methanogenic activity and the concentration of coenzyme F(420) involved in methanogenesis were increased. The archaeal community was also altered with the addition of hydrogen, and a Methanothermobacter thermautotrophicus related band appeared in a denaturing gradient gel electrophoresis gel from the sample of the reactor with hydrogen addition. Though the addition of hydrogen increased the dissolved hydrogen concentration, the degradation of propionate was still thermodynamically feasible at the reactor conditions.

  13. Effectiveness of Phytogenic Feed Additive as Alternative to Bacitracin Methylene Disalicylate on Hematological Parameters, Intestinal Histomorphology and Microbial Population and Production Performance of Japanese Quails.

    PubMed

    Manafi, M; Hedayati, M; Khalaji, S

    2016-09-01

    This study was conducted to evaluate the effects of phytogenic additive and antibiotic growth promoter in laying Japanese quails. One hundred and sixty five quails were divided into three groups of 5 replicates and 11 quails (8 females and 3 males) in each replicate. Treatment 1 was fed control diet, treatment 2 was fed control diet supplemented with 0.05% bacitracin methylene disalicylate as antibiotic growth promoter and treatment 3 was fed control diet supplemented with 0.1% phytogenic feed additive (PFA) for two periods of 3 weeks each from 37 to 42 weeks of age. Results showed that egg production, eggshell strength, eggshell weight, villus height and villus height to crypt depth ratio were significantly (p≤0.05) increased and feed consumption, feed conversion ratio, albumen, Haugh unit, cholesterol, low-density lipoprotein, alanine transaminase, gamma glutamyltransferase, alkaline phosphatase, high-density lipoprotein, triglyceride, number of goblet cell, crypt depth and intestinal bacterial population of Coliforms, Salmonella and E. coli were significantly (p≤0.05) decreased in PFA fed group. It is concluded that addition of PFA containing phytomolecules and organic acids as main ingredients could significantly improve the production parameters and the general health of laying quails as an alternative to antibiotic growth promoters. PMID:27189636

  14. Effectiveness of Phytogenic Feed Additive as Alternative to Bacitracin Methylene Disalicylate on Hematological Parameters, Intestinal Histomorphology and Microbial Population and Production Performance of Japanese Quails

    PubMed Central

    Manafi, M.; Hedayati, M.; Khalaji, S.

    2016-01-01

    This study was conducted to evaluate the effects of phytogenic additive and antibiotic growth promoter in laying Japanese quails. One hundred and sixty five quails were divided into three groups of 5 replicates and 11 quails (8 females and 3 males) in each replicate. Treatment 1 was fed control diet, treatment 2 was fed control diet supplemented with 0.05% bacitracin methylene disalicylate as antibiotic growth promoter and treatment 3 was fed control diet supplemented with 0.1% phytogenic feed additive (PFA) for two periods of 3 weeks each from 37 to 42 weeks of age. Results showed that egg production, eggshell strength, eggshell weight, villus height and villus height to crypt depth ratio were significantly (p≤0.05) increased and feed consumption, feed conversion ratio, albumen, Haugh unit, cholesterol, low-density lipoprotein, alanine transaminase, gamma glutamyltransferase, alkaline phosphatase, high-density lipoprotein, triglyceride, number of goblet cell, crypt depth and intestinal bacterial population of Coliforms, Salmonella and E. coli were significantly (p≤0.05) decreased in PFA fed group. It is concluded that addition of PFA containing phytomolecules and organic acids as main ingredients could significantly improve the production parameters and the general health of laying quails as an alternative to antibiotic growth promoters. PMID:27189636

  15. Microbial Transformation of 14-Anhydrodigoxigenin by Alternaria alternata.

    PubMed

    Liu, Jimei; Tang, Wanxia; Chen, Ridao; Dai, Jungui

    2015-12-01

    The microbial transformation of 14-anhydrodigoxigenin (1) by Alternaria alternata CGMCC 3.577 led to the production of seven new metabolites, 2-8. Their structures were determined by extensive spectroscopic (CD, IR, 1D- and 2D-NMR, and HR-ESI-MS) data analyses. The reactions in the bioprocess exhibited diversity, including specific oxidation, hydroxylation, reduction, epoxidation, and dehydration. In addition, a hypothetical biocatalytic pathway is proposed.

  16. Microbial ultraviolet sunscreens.

    PubMed

    Gao, Qunjie; Garcia-Pichel, Ferran

    2011-11-01

    Exposure to the shortest wavelengths in sunlight, ultraviolet light, constitutes a deleterious ecological factor for many microorganisms. The use of secondary metabolites as sunscreens has emerged as an important photoprotective mechanism in certain groups of large-celled microorganisms, such as cyanobacteria, fungi and many protists. In this Review, we describe our current understanding of microbial 'sunscreen' compounds, including scytonemin, the mycosporines and the naphthalene-based melanins. Study of these sunscreens has led to the discovery of new classes of compounds, new metabolic pathways, a deeper understanding of microbial photobiology and the potential for dermatological or biomedical applications.

  17. Addition of microbially-treated sugar beet residue and a native bacterium increases structural stability in heavy metal-contaminated Mediterranean soils.

    PubMed

    Carrasco, L; Caravaca, F; Azcón, R; Kohler, J; Roldán, A

    2009-10-15

    A mesocosm experiment was conducted to investigate the effect of the addition of Aspergillus niger-treated sugar beet waste, in the presence of rock phosphate, and inoculation with a native, metal-tolerant bacterium, Bacillus thuringiensis, on the stabilisation of soil aggregates of two mine tailings, with differing pH values, from a semiarid Mediterranean area and on the stimulation of growth of Piptatherum miliaceum. Bacterium combined with organic amendment enhanced structural stability (38% in acidic soil and 106% in neutral soil compared with their corresponding controls). Only the organic amendment increased pH, electrical conductivity, water-soluble C, water-soluble carbohydrates and plant growth, in both soils. While in neutral soil both organic amendment and bacterium increased dehydrogenase activity, only organic amendment had a significant effect in acidic soil. This study demonstrates that the use of P. miliaceum in combination with organic amendment and bacterium is a suitable tool for the stabilisation of the soil structure of degraded mine tailings, although its effectiveness is dependent on soil pH. PMID:19660785

  18. Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale.

    PubMed

    Vikram, Amit; Lipus, Daniel; Bibby, Kyle

    2016-10-01

    Controlling microbial activity is a primary concern during the management of the large volumes of wastewater (produced water) generated during high-volume hydraulic fracturing. In this study we analyzed the transcriptional activity (metatranscriptomes) of three produced water samples from the Marcellus Shale. The goal of this study was to describe active metabolic pathways of industrial concern for produced water management and reuse, and to improve understanding of produced water microbial activity. Metatranscriptome analysis revealed active biofilm formation, sulfide production, and stress management mechanisms of the produced water microbial communities. Biofilm-formation and sulfate-reduction pathways were identified in all samples. Genes related to a diverse array of stress response mechanisms were also identified with implications for biocide efficacy. Additionally, active expression of a methanogenesis pathway was identified in a sample of produced water collected prior to holding pond storage. The active microbial community identified by metatranscriptome analysis was markedly different than the community composition as identified by 16S rRNA sequencing, highlighting the value of evaluating the active microbial fraction during assessments of produced water biofouling potential and evaluation of biocide application strategies. These results indicate biofouling and corrosive microbial processes are active in produced water and should be taken into consideration while designing produced water reuse strategies. PMID:27457653

  19. Overview of differences between microbial feed additives and probiotics for food regarding regulation, growth promotion effects and health properties and consequences for extrapolation of farm animal results to humans.

    PubMed

    Bernardeau, M; Vernoux, J-P

    2013-04-01

    For many years, microbial adjuncts have been used to supplement the diets of farm animals and humans. They have evolved since the 1990s to become known as probiotics, i.e. functional food with health benefits. After the discovery of a possible link between manipulation of gut microflora in mice and obesity, a focus on the use of these beneficial microbes that act on gut microflora in animal farming was undertaken and compared with the use of probiotics for food. Beneficial microbes added to feed are classified at a regulatory level as zootechnical additives, in the category of gut flora stabilizers for healthy animals and are regulated up to strain level in Europe. Intended effects are improvement of performance characteristics, which are strain dependent and growth enhancement is not a prerequisite. In fact, increase of body weight is not commonly reported and its frequency is around 25% of the published data examined here. However, when a Body Weight Gain (BWG) was found in the literature, it was generally moderate (lower than or close to 10%) and this over a reduced period of their short industrial life. When it was higher than 10%, it could be explained as an indirect consequence of the alleviation of the weight losses linked to stressful intensive rearing conditions or health deficiency. However, regulations on feed do not consider the health effects because animals are supposed to be healthy, so there is no requirement for reporting healthy effects in the standard European dossier. The regulations governing the addition of beneficial microorganisms to food are less stringent than for feed and no dossier is required if a species has a Qualified Presumption of Safety status. The microbial strain marketed is not submitted to any regulation and its properties (including BWG) do not need to be studied. Only claims for functional or healthy properties are regulated and again growth effect is not included. However, recent studies on probiotic effects showed that BWG

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

    USGS Publications Warehouse

    Schmidt, S.K.; Cleveland, C.C.; Nemergut, D.R.; Reed, S.C.; King, A.J.; Sowell, P.

    2011-01-01

    Estimating phosphorus (P) availability is difficult—particularly in infertile soils such as those exposed after glacial recession—because standard P extraction methods may not mimic biological acquisition pathways. We developed an approach, based on microbial CO2 production kinetics and conserved carbon:phosphorus (C:P) ratios, to estimate the amount of P available for microbial growth in soils and compared this method to traditional, operationally-defined indicators of P availability. Along a primary succession gradient in the High Andes of Perú, P additions stimulated the growth-related (logistic) kinetics of glutamate mineralization in soils that had been deglaciated from 0 to 5 years suggesting that microbial growth was limited by soil P availability. We then used a logistic model to estimate the amount of C incorporated into biomass in P-limited soils, allowing us to estimate total microbial P uptake based on a conservative C:P ratio of 28:1 (mass:mass). Using this approach, we estimated that there was < 1 μg/g of microbial-available P in recently de-glaciated soils in both years of this study. These estimates fell well below estimates of available soil P obtained using traditional extraction procedures. Our results give both theoretical and practical insights into the kinetics of C and P utilization in young soils, as well as show changes in microbial P availability during early stages of soil development.

  1. Biofuel alternatives to ethanol: pumping the microbial well

    SciTech Connect

    Fortman, J. L.; Chhabra, Swapnil; Mukhopadhyay, Aindrila; Chou, Howard; Lee, Taek Soon; Steen, Eric; Keasling, Jay D.

    2009-12-02

    Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has gener-ated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel mar-ket, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we review advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.

  2. Biofuel alternatives to ethanol: pumping the microbial well

    SciTech Connect

    Fortman, J.L.; Chhabra, Swapnil; Mukhopadhyay, Aindrila; Chou, Howard; Lee, Taek Soon; Steen, Eric; Keasling, Jay D.

    2009-08-19

    Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has generated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel market, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we review advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.

  3. Microbial safety in space

    NASA Astrophysics Data System (ADS)

    Krooneman, Janneke; Harmsen, Hermie; Landini, Paolo; Zinn, Manfred; Munaut, Françoise; van der Meer, Walter; Beimfohr, Claudia; Reichert, Bas; Preuß, Andrea

    2005-10-01

    Microbial hygiene is important in our daily lives; preventing and combating microbial infections is increasingly important in society. In hospitals, strict monitoring and control is exercised for people and infrastructure alike. In modern buildings, air-conditioning system are screened for harmful bacteria such as Legionella. More recently, concerns about SARS (virus) and anthrax (bacteria) have added pressure on the scientific community to come up with adequate monitoring and control techniques to assure microbial hygiene. Additionally, the use of biotechnological recycling and cleaning processes for sustainability brings the need for reliable monitoring tools and preventive or riks-reducing strategies. In the manned space environment, similar problems need to be solved and efforts have already been made to study the behaviour of micro-organisms and microbial hygiene onboard space stations.

  4. Flat laminated microbial mat communities

    NASA Astrophysics Data System (ADS)

    Franks, Jonathan; Stolz, John F.

    2009-10-01

    Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.

  5. Global microbialization of coral reefs.

    PubMed

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

    2016-01-01

    Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC. PMID:27572833

  6. Global microbialization of coral reefs.

    PubMed

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

    2016-04-25

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

  7. Bi(OTf)3-catalyzed addition of isocyanides to 2H-chromene acetals: an efficient pathway for accessing 2-carboxamide-2H-chromenes.

    PubMed

    Lyu, Longyun; Jin, Ming Yu; He, Qijie; Xie, Han; Bian, Zhaoxiang; Wang, Jun

    2016-09-14

    Bismuth triflate (Bi(OTf)3) is identified as an efficient catalyst for the direct addition of isocyanides to 2H-chromene acetals. The large scope of isocyanides and chromene acetals makes them suitable substrates in this catalytic system. By this synthetic strategy, a polyfunctional molecular scaffold, 2-carboxamide-2H-chromenes could be prepared efficiently in one step up to 95% yield. In addition, this efficient and practical protocol proceeded smoothly in the gram scale even when the catalytic loading was reduced to 2 mol%. PMID:27503764

  8. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester—A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    PubMed Central

    Liebrich, Marietta; Kleyböcker, Anne; Kasina, Monika; Miethling-Graff, Rona; Kassahun, Andrea; Würdemann, Hilke

    2016-01-01

    The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil.

  9. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester-A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    PubMed

    Liebrich, Marietta; Kleyböcker, Anne; Kasina, Monika; Miethling-Graff, Rona; Kassahun, Andrea; Würdemann, Hilke

    2016-03-17

    The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil.

  10. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester-A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    PubMed

    Liebrich, Marietta; Kleyböcker, Anne; Kasina, Monika; Miethling-Graff, Rona; Kassahun, Andrea; Würdemann, Hilke

    2016-01-01

    The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil. PMID:27681911

  11. Process Recovery after CaO Addition Due to Granule Formation in a CSTR Co-Digester—A Tool to Influence the Composition of the Microbial Community and Stabilize the Process?

    PubMed Central

    Liebrich, Marietta; Kleyböcker, Anne; Kasina, Monika; Miethling-Graff, Rona; Kassahun, Andrea; Würdemann, Hilke

    2016-01-01

    The composition, structure and function of granules formed during process recovery with calcium oxide in a laboratory-scale fermenter fed with sewage sludge and rapeseed oil were studied. In the course of over-acidification and successful process recovery, only minor changes were observed in the bacterial community of the digestate, while granules appeared during recovery. Fluorescence microscopic analysis of the granules showed a close spatial relationship between calcium and oil and/or long chain fatty acids. This finding further substantiated the hypothesis that calcium precipitated with carbon of organic origin and reduced the negative effects of overloading with oil. Furthermore, the enrichment of phosphate minerals in the granules was shown, and molecular biological analyses detected polyphosphate-accumulating organisms as well as methanogenic archaea in the core. Organisms related to Methanoculleus receptaculi were detected in the inner zones of a granule, whereas they were present in the digestate only after process recovery. This finding indicated more favorable microhabitats inside the granules that supported process recovery. Thus, the granule formation triggered by calcium oxide addition served as a tool to influence the composition of the microbial community and to stabilize the process after overloading with oil. PMID:27681911

  12. C and Cl isotope fractionation of 1,2-dichloroethane displays unique δ¹³C/δ³⁷Cl patterns for pathway identification and reveals surprising C-Cl bond involvement in microbial oxidation.

    PubMed

    Palau, Jordi; Cretnik, Stefan; Shouakar-Stash, Orfan; Höche, Martina; Elsner, Martin; Hunkeler, Daniel

    2014-08-19

    This study investigates dual element isotope fractionation during aerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via oxidative cleavage of a C-H bond (Pseudomonas sp. strain DCA1) versus C-Cl bond cleavage by S(N)2 reaction (Xanthobacter autotrophicus GJ10 and Ancylobacter aquaticus AD20). Compound-specific chlorine isotope analysis of 1,2-DCA was performed for the first time, and isotope fractionation (ε(bulk)(Cl)) was determined by measurements of the same samples in three different laboratories using two gas chromatography-isotope ratio mass spectrometry systems and one gas chromatography-quadrupole mass spectrometry system. Strongly pathway-dependent slopes (Δδ13C/Δδ37Cl), 0.78 ± 0.03 (oxidation) and 7.7 ± 0.2 (S(N)2), delineate the potential of the dual isotope approach to identify 1,2-DCA degradation pathways in the field. In contrast to different ε(bulk)(C) values [-3.5 ± 0.1‰ (oxidation) and -31.9 ± 0.7 and -32.0 ± 0.9‰ (S(N)2)], the obtained ε(bulk)(Cl) values were surprisingly similar for the two pathways: -3.8 ± 0.2‰ (oxidation) and -4.2 ± 0.1 and -4.4 ± 0.2‰ (S(N)2). Apparent kinetic isotope effects (AKIEs) of 1.0070 ± 0.0002 (13C-AKIE, oxidation), 1.068 ± 0.001 (13C-AKIE, S(N)2), and 1.0087 ± 0.0002 (37Cl-AKIE, S(N)2) fell within expected ranges. In contrast, an unexpectedly large secondary 37Cl-AKIE of 1.0038 ± 0.0002 reveals a hitherto unrecognized involvement of C-Cl bonds in microbial C-H bond oxidation. Our two-dimensional isotope fractionation patterns allow for the first time reliable 1,2-DCA degradation pathway identification in the field, which unlocks the full potential of isotope applications for this important groundwater contaminant.

  13. The inability of phosphatidylinositol 3-kinase activation to stimulate GLUT4 translocation indicates additional signaling pathways are required for insulin-stimulated glucose uptake.

    PubMed

    Isakoff, S J; Taha, C; Rose, E; Marcusohn, J; Klip, A; Skolnik, E Y

    1995-10-24

    Recent experimental evidence has focused attention to the role of two molecules, insulin receptor substrate 1 (IRS-1) and phosphatidylinositol 3-kinase (PI3-kinase), in linking the insulin receptor to glucose uptake; IRS-1 knockout mice are insulin resistant, and pharmacological inhibitors of PI3-kinase block insulin-stimulated glucose uptake. To investigate the role of PI3-kinase and IRS-1 in insulin-stimulated glucose uptake we examined whether stimulation of insulin-sensitive cells with platelet-derived growth factor (PDGF) or with interleukin 4 (IL-4) stimulates glucose uptake; the activated PDGF receptor (PDGFR) directly binds and activates PI3-kinase, whereas the IL-4 receptor (IL-4R) activates PI3-kinase via IRS-1 or the IRS-1-related molecule 4PS. We found that stimulation of 3T3-L1 adipocytes with PDGF resulted in tyrosine phosphorylation of the PDGFR and activation of PI3-kinase in these cells. To examine whether IL-4 stimulates glucose uptake, L6 myoblasts were engineered to overexpress GLUT4 as well as both chains of the IL-4R (L6/IL-4R/GLUT4); when these L6/IL-4R/GLUT4 myoblasts were stimulated with IL-4, IRS-1 became tyrosine phosphorylated and associated with PI3-kinase. Although PDGF and IL-4 can activate PI3-kinase in the respective cell lines, they do not possess insulin's ability to stimulate glucose uptake and GLUT4 translocation to the plasma membrane. These findings indicate that activation of PI3-kinase is not sufficient to stimulate GLUT4 translocation to the plasma membrane. We postulate that activation of a second signaling pathway by insulin, distinct from PI3-kinase, is necessary for the stimulation of glucose uptake in insulin-sensitive cells.

  14. Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids

    NASA Astrophysics Data System (ADS)

    Purkamo, Lotta; Bomberg, Malin; Kietäväinen, Riikka; Salavirta, Heikki; Nyyssönen, Mari; Nuppunen-Puputti, Maija; Ahonen, Lasse; Kukkonen, Ilmo; Itävaara, Merja

    2016-05-01

    The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from groundwater of six fracture zones from 180 to 2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related operational taxonomic units (OTUs) form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteriaceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed possible "keystone" genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found in oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found in other deep Precambrian terrestrial bedrock environments.

  15. Microbial volatile emissions as insect semiochemicals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We provide a synthesis of the literature describing biochemical interactions between microorganisms and arthropods by way of microbial volatile organic compound (MVOC) production. We explored important metabolic pathways involved in MVOC production and evaluated the functionality, generality, and e...

  16. Investigation of the O+allyl addition/elimination reaction pathways from the OCH{sub 2}CHCH{sub 2} radical intermediate

    SciTech Connect

    FitzPatrick, Benjamin L.; Lau, K.-C.; Butler, Laurie J.; Lee, S.-H.; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH{sub 2}CHCH{sub 2}, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH{sub 2}CHCH{sub 2} radicals; these undergo a facile ring opening to the OCH{sub 2}CHCH{sub 2} radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH{sub 2}CHCH{sub 2} radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C{sub 3}H{sub 4}O (acrolein)+H, C{sub 2}H{sub 4}+HCO (formyl radical), and H{sub 2}CO (formaldehyde)+C{sub 2}H{sub 3}. A small signal from C{sub 2}H{sub 2}O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C{sub 2}H{sub 5}+CO, does not contribute significantly to the product branching. The higher internal energy onset of the

  17. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    PubMed Central

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  18. Multicomponent reactions of phosphines, enynedioates and benzylidene malononitriles generated highly substituted cyclopentenes through an unexpected phosphine α-addition-δ-evolvement of an anion pathway.

    PubMed

    Chuang, Shih-Ching; Sung, Shih-Ping; Deng, Jie-Cheng; Chiou, Mong-Feng; Hsu, Day-Shin

    2016-02-21

    Multicomponent reactions of phosphines, enynedioates and benzylidene malononitriles provide highly substituted syn-selective cyclopentenes appending the phosphorus ylide moiety in good yield with a diastereoselectivity of up to 100% through resonance-derived 1,5-dipolar species as the key intermediates, via the nucleophilic α(δ')-attack of phosphines toward enynedioates followed by addition to benzylidene malononitriles and 5-exo-dig cyclization. Through computational analyses, the overall reactions for the formation of syn- and anti-diastereomers are both exothermic with 65.6 and 66.3 kcal mol(-1) at the B3LYP-D3/6-31G(d) level of theory and were found to be kinetically controlled, which favours the formation of syn-diastereomers.

  19. Microbial Baeyer-Villiger oxidation of 5α-steroids using Beauveria bassiana. A stereochemical requirement for the 11α-hydroxylation and the lactonization pathway.

    PubMed

    Świzdor, Alina; Panek, Anna; Milecka-Tronina, Natalia

    2014-04-01

    Beauveria bassiana KCH 1065, as was recently demonstrated, is unusual amongst fungal biocatalysts in that it converts C19 3-oxo-4-ene and 3β-hydroxy-5-ene as well as 3β-hydroxy-5α-saturated steroids to 11α-hydroxy ring-D lactones. The Baeyer-Villiger monooxygenase (BVMO) of this strain is distinguished from other enzymes catalyzing BVO of steroidal ketones by the fact that it oxidizes solely substrates with 11α-hydroxyl group. The current study using a series of 5α-saturated steroids (androsterone, 3α-androstanediol and androstanedione) has highlighted that a small change of the steroid structure can result in significant differences of the metabolic fate. It was found that the 3α-stereochemistry of hydroxyl group restricted "normal" binding orientation of the substrate within 11α-hydroxylase and, as a result, androsterone and 3α-androstanediol were converted into a mixture of 7β-, 11α- and 7α-hydroxy derivatives. Hydroxylation of androstanedione occurred only at the 11α-position, indicating that the 3-oxo group limits the alternative binding orientation of the substrate within the hydroxylase. Only androstanedione and 3α-androstanediol were metabolized to hydroxylactones. The study uniquely demonstrated preference for oxidation of equatorial (11α-, 7β-) hydroxyketones by BVMO from B. bassiana. The time course experiments suggested that the activity of 17β-HSD is a factor determining the amount of produced ring-D lactones. The obtained 11α-hydroxylactones underwent further transformations (oxy-red reactions) at C-3. During conversion of androstanedione, a minor dehydrogenation pathway was observed with generation of 11α,17β-dihydroxy-5α-androst-1-en-3-one. The introduction of C1C2 double bond has been recorded in B. bassiana for the first time.

  20. Microbial Weathering of Olivine

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  1. Additive effect of heat on the UVB-induced tyrosinase activation and melanogenesis via ERK/p38/MITF pathway in human epidermal melanocytes.

    PubMed

    Gu, Wei-Jie; Ma, Hui-Jun; Zhao, Guang; Yuan, Xiao-Ying; Zhang, Ping; Liu, Wen; Ma, Li-Juan; Lei, Xiao-Bing

    2014-08-01

    Heat is known as an environmental factor that causes significant skin pigmentation, but its effects on melanogenesis have been poorly studied. It has been shown that mitogen-activated protein kinase (MAPK) is involved in ultraviolet B (UVB) and stress-induced melanogenesis in melanocytes. In this study, we investigated the effects of heat and UVB, on melanocyte melanogenesis, differentiation, and MAPK phosphorylation. The results showed that heat (1 h at 40 °C for 5 days) increased cell dendrites, enlarged cell bodies, and induced extracellular signal-regulated kinases (ERK)/p38/MITF activation but did not influence melanogenesis of human epidermal melanocytes from skin phototype III. UVB irradiation (20 mJ/cm(2) for 5 days) induced melanogenesis and c-jun N-terminal kinases (JNK)/p38/MITF/tyrosinase activation in melanocytes from skin phototype III. UVB combined with heat resulted in much more significant tyrosinase activation and melanogenesis as compared with UVB alone in melanocytes from skin phototype III. Furthermore, heat treatment and UVB irradiation induced JNK, ERK, and p38 activation but not melanogenic and morphological changes in melanocytes from skin phototype I. These findings suggested that heat promoted melanocyte differentiation, probably via heat-induced ERK/p38/MITF/activation. Furthermore, heat had an additive effect on the UVB-induced tyrosinase activation and melanogenesis. These results provide a new clue for dermatologists for the treatment of hypopigmented skin disease with heat combined with UVB irradiation.

  2. Microbial Load Monitor

    NASA Technical Reports Server (NTRS)

    Gibson, S. F.; Royer, E. R.

    1979-01-01

    The Microbial Load Monitor (MLM) is an automated and computerized system for detection and identification of microorganisms. Additionally, the system is designed to enumerate and provide antimicrobic susceptibility profiles for medically significant bacteria. The system is designed to accomplish these tasks in a time of 13 hours or less versus the traditional time of 24 hours for negatives and 72 hours or more for positives usually required for standard microbiological analysis. The MLM concept differs from other methods of microbial detection in that the system is designed to accept raw untreated clinical samples and to selectively identify each group or species that may be present in a polymicrobic sample.

  3. 40 CFR 158.2110 - Microbial pesticides data requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... of the product. (b) Additional data requirements for genetically modified microbial pesticides. Additional requirements for genetically modified microbial pesticides may include but are not limited to... patterns” under which the individual data are required, with variations including all use patterns,...

  4. 40 CFR 158.2110 - Microbial pesticides data requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... of the product. (b) Additional data requirements for genetically modified microbial pesticides. Additional requirements for genetically modified microbial pesticides may include but are not limited to... patterns” under which the individual data are required, with variations including all use patterns,...

  5. 40 CFR 158.2110 - Microbial pesticides data requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... of the product. (b) Additional data requirements for genetically modified microbial pesticides. Additional requirements for genetically modified microbial pesticides may include but are not limited to... patterns” under which the individual data are required, with variations including all use patterns,...

  6. Microbial metabolism in soil at low temperatures: Mechanisms unraveled by position-specific 13C labeling

    NASA Astrophysics Data System (ADS)

    Bore, Ezekiel

    2016-04-01

    Microbial transformation of organic substances in soil is the most important process of the C cycle. Most of the current studies base their information about transformation of organic substances on incubation studies under laboratory conditions and thus, we have a profound knowledge on SOM transformations at ambient temperatures. However, metabolic pathway activities at low temperature are not well understood, despite the fact that the processes are relevant for many soils globally and seasonally. To analyze microbial metabolism at low soil temperatures, isotopomeres of position-specifically 13C labeled glucose were incubated at three temperature; 5, -5 -20 oC. Soils were sampled after 1, 3 and 10 days and additionally after 30 days for samples at -20 °C. The 13C from individual molecule position was quantifed in respired CO2, bulk soil, extractable organic C and extractable microbial biomass by chloroform fumigation extraction (CFE) and cell membranes of microbial communities classified by 13C phospholipid fatty acid (PLFA) analysis. 13CO2 released showed a dominance of the flux from C-1 position at 5 °C. Consequently, at 5 °C, pentose phosphate pathway activity is a dominant metabolic pathway of glucose metabolization. In contrast to -5 °C and -20 oC, metabolic behaviors completely switched towards a preferential respiration of the glucose C-4 position. With decreasing temperature, microorganism strongly shifted towards metabolization of glucose via glycolysis which indicates a switch to cellular maintenance. High recoveries of 13C in extractable microbial biomass at -5 °C indicates optimal growth condition for the microorganisms. PLFA analysis showed high incorporation of 13C into Gram negative bacteria at 5 °C but decreased with temperature. Gram positive bacteria out-competed Gram negatives with decreasing temperature. This study revealed a remarkable microbial activity at temperatures below 0 °C, differing significantly from that at ambient

  7. Microbial phytase addition resulted in a greater increase in phosphorus digestibility in dry-fed compared with liquid-fed non-heat-treated wheat-barley-maize diets for pigs.

    PubMed

    Blaabjerg, K; Thomassen, A-M; Poulsen, H D

    2015-02-01

    The objective was to evaluate the effect of microbial phytase (1250 FTU/kg diet with 88% dry matter (DM)) on apparent total tract digestibility (ATTD) of phosphorus (P) in pigs fed a dry or soaked diet. Twenty-four pigs (65±3 kg) from six litters were used. Pigs were housed in metabolism crates and fed one of four diets for 12 days; 5 days for adaptation and 7 days for total, but separate collection of feces and urine. The basal diet was composed of wheat, barley, maize, soybean meal and no mineral phosphate. Dietary treatments were: basal dry-fed diet (BDD), BDD with microbial phytase (BDD+phy), BDD soaked for 24 h at 20°C before feeding (BDS) and BDS with microbial phytase (BDS+phy). Supplementation of microbial phytase increased ATTD of DM and crude protein (N×6.25) by 2 and 3 percentage units (P<0.0001; P<0.001), respectively. The ATTD of P was affected by the interaction between microbial phytase and soaking (P=0.02). This was due to a greater increase in ATTD of P by soaking of the diet containing solely plant phytase compared with the diet supplemented with microbial phytase: 35%, 65%, 44% and 68% for BDD, BDD+phy, BSD and BSD+phy, respectively. As such, supplementation of microbial phytase increased ATTD of P in the dry-fed diet, but not in the soaked diet. The higher ATTD of P for BDS compared with BDD resulted from the degradation of 54% of the phytate in BDS by wheat and barley phytases during soaking. On the other hand, soaking of BDS+phy did not increase ATTD of P significantly compared with BDD+phy despite that 76% of the phytate in BDS+phy was degraded before feeding. In conclusion, soaking of BDS containing solely plant phytase provided a great potential for increasing ATTD of P. However, this potential was not present when microbial phytase (1250 FTU/kg diet) was supplemented, most likely because soaking of BDS+phy for 24 h at 20°C did not result in a complete degradation of phytate before feeding.

  8. Decomposition of complex microbial behaviors into resource-based stress responses

    PubMed Central

    Carlson, Ross P.

    2009-01-01

    Motivation: Highly redundant metabolic networks and experimental data from cultures likely adapting simultaneously to multiple stresses can complicate the analysis of cellular behaviors. It is proposed that the explicit consideration of these factors is critical to understanding the competitive basis of microbial strategies. Results: Wide ranging, seemingly unrelated Escherichia coli physiological fluxes can be simply and accurately described as linear combinations of a few ecologically relevant stress adaptations. These strategies were identified by decomposing the central metabolism of E.coli into elementary modes (mathematically defined biochemical pathways) and assessing the resource investment cost–benefit properties for each pathway. The approach capitalizes on the inherent tradeoffs related to investing finite resources like nitrogen into different pathway enzymes when the pathways have varying metabolic efficiencies. The subset of ecologically competitive pathways represented 0.02% of the total permissible pathways. The biological relevance of the assembled strategies was tested against 10 000 randomly constructed pathway subsets. None of the randomly assembled collections were able to describe all of the considered experimental data as accurately as the cost-based subset. The results suggest these metabolic strategies are biologically significant. The current descriptions were compared with linear programming (LP)-based flux descriptions using the Euclidean distance metric. The current study's pathway subset described the experimental fluxes with better accuracy than the LP results without having to test multiple objective functions or constraints and while providing additional ecological insight into microbial behavior. The assembled pathways seem to represent a generalized set of strategies that can describe a wide range of microbial responses and hint at evolutionary processes where a handful of successful metabolic strategies are utilized

  9. Microbial production of lactic acid.

    PubMed

    Eiteman, Mark A; Ramalingam, Subramanian

    2015-05-01

    Lactic acid is an important commodity chemical having a wide range of applications. Microbial production effectively competes with chemical synthesis methods because biochemical synthesis permits the generation of either one of the two enantiomers with high optical purity at high yield and titer, a result which is particularly beneficial for the production of poly(lactic acid) polymers having specific properties. The commercial viability of microbial lactic acid production relies on utilization of inexpensive carbon substrates derived from agricultural or waste resources. Therefore, optimal lactic acid formation requires an understanding and engineering of both the competing pathways involved in carbohydrate metabolism, as well as pathways leading to potential by-products which both affect product yield. Recent research leverages those biochemical pathways, while researchers also continue to seek strains with improved tolerance and ability to perform under desirable industrial conditions, for example, of pH and temperature.

  10. Environmental Controls of Microbial Resource Partitioning in Soils

    NASA Astrophysics Data System (ADS)

    Kandeler, Ellen; Poll, Christian; Kramer, Susanne; Mueller, Karolin; Marhan, Sven

    2015-04-01

    The mineralization and flow of plant-derived carbon in soils is relevant to global carbon cycling. Current models of organismic carbon fluxes in soil assume that separate bacterial and fungal energy channels exist in soil. Recent studies disentangle the herbivore and detritivore pathways of microbial resource use, identify the key players contributing to these two different pathways, and determine to what extent microbial substrate use is affected by environmental controls. To follow the kinetics of litter and root decomposition and to quantify the contribution of key players, it is necessary to use isotopic approaches like PLFA-SIP and ergosterol-SIP. It was shown that bacteria and sugar consuming fungi initiated litter decomposition in an incubation experiment during the first two weeks, whereas higher fungi started to grow after the depletion of low molecular weight substrates. Analyses of PLFA-SIP revealed, for example, that fungi assimilated C directly from the litter, whereas bacteria took up substrates in the soil and therefore depended more on external transport processes than fungi. In addition, we will present data from a field experiment showing the incorporation of root and shoot litter C into organic and microbial C pools under field conditions over a period of two years. Similar amounts of C derived from the two resources differing in substrate quality and amount were incorporated into microbial C and ergosterol pools over time, indicating the importance of root-derived C for the soil food web. High incorporation of maize C (up to 76%) into ergosterol suggests fast and high assimilation of maize C into fungal biomass. Nevertheless, there is still a debate whether bacteria, archaea and fungi start feeding on new substrates at the same time or if their activity occurs at different successional stages. This presentation gives a summery of current knowledge on microbial resource partitioning under lab and field conditions.

  11. Microbial mercury methylation in Antarctic sea ice.

    PubMed

    Gionfriddo, Caitlin M; Tate, Michael T; Wick, Ryan R; Schultz, Mark B; Zemla, Adam; Thelen, Michael P; Schofield, Robyn; Krabbenhoft, David P; Holt, Kathryn E; Moreau, John W

    2016-01-01

    Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean. PMID:27670112

  12. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

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

  13. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

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

  14. Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

    PubMed

    Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

    2016-08-01

    Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment.

  15. Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

    PubMed

    Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

    2016-08-01

    Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. PMID:27493184

  16. Carboxylases in Natural and Synthetic Microbial Pathways▿†

    PubMed Central

    Erb, Tobias J.

    2011-01-01

    Carboxylases are among the most important enzymes in the biosphere, because they catalyze a key reaction in the global carbon cycle: the fixation of inorganic carbon (CO2). This minireview discusses the physiological roles of carboxylases in different microbial pathways that range from autotrophy, carbon assimilation, and anaplerosis to biosynthetic and redox-balancing functions. In addition, the current and possible future uses of carboxylation reactions in synthetic biology are discussed. Such uses include the possible transformation of the greenhouse gas carbon dioxide into value-added compounds and the production of novel antibiotics. PMID:22003013

  17. Microbial Signatures in Ooids from the Bahamas

    NASA Astrophysics Data System (ADS)

    Diaz, M. R.; Swart, P. K.; Devlin, Q.; Oehlert, A. M.; Saied, A.; Eberli, G. P.; Klaus, J. S.; Altabet, M.

    2013-12-01

    Microbes are abundant in sedimentary systems where their metabolic capabilities can exert a profound impact on carbonate precipitation processes by altering the alkalinity of their immediate surrounding. Using a combination of clone analysis of 16SrRNA, functional gene analysis and both inorganic and organic stable isotopic analyses, we characterized the microbial community structure of ooids and their potential functional capabilities that could lead to precipitation of carbonates. Oolitic bacterial communities were highly diverse, representing 12 different prokaryotic lineages, among which Alphaproteobacteria, Gammaproteobacteria, Actinobacteria/Bacteroidetes and Deltaproteobacteria were the most abundant. Based on functional gene analysis, a large number of genes were associated with redox dependent microbial communities with putative functional capability for mineral precipitation such as aerobic/anoxygenic photosynthesis, denitrification, ammonification, and sulfate reduction. In addition, a broad diversity of genes related to organic carbon degradation and nitrogen fixation were present, implying metabolic plasticity that enables survival under oligotrophic conditions. Carbon and nitrogen isotopic analyses, which were conducted on both bulk and intracrystalline organic matter as well as in leachate sediments, identified geochemical signatures of microbial activity. δ13C values for organic C in the bulk (-11.94 to -16.71) and intracrystalline organic matter (-12.37 to -17.66), were similar and within the range of fractionation patterns associated with cyanobacteria, algae and photosynthesizers that employ the C4 carbon fixation pathway. Nitrogen isotopic values for both bulk (δ15N: -0.314 to - 0.706) and intracrystalline organic matter (δ15N: -0.343 -1.70) also showed fractionation patterns consistent with nitrogen fixation. In addition, positive δ15N and δ18O values of the NO3- leached from the ooids provided evidence of denitrification. These findings

  18. Metabolic and practical considerations on microbial electrosynthesis.

    PubMed

    Rabaey, Korneel; Girguis, Peter; Nielsen, Lars K

    2011-06-01

    The production of biofuels and biochemicals is highly electron intensive. To divert fermentative and respiratory pathways to the product of interest, additional electrons (i.e. reducing power) are often needed. Meanwhile, the past decade has seen the breakthrough of sustainable electricity sources such as solar and wind. Microbial electrosynthesis (MES) is at the nexus of both, as it uses electrical energy as source of reducing power for microorganisms. This review addresses the key opportunities and challenges for MES. While exciting as a concept, MES needs to overcome many biological, electrochemical, logistical and economic challenges. Particularly the latter is critical, as on a 'per electron basis' MES does not yet appear to deliver a substantial benefit relative to existing approaches.

  19. Microbially-driven strategies for bioremediation of bauxite residue.

    PubMed

    Santini, Talitha C; Kerr, Janice L; Warren, Lesley A

    2015-08-15

    Globally, 3 Gt of bauxite residue is currently in storage, with an additional 120 Mt generated every year. Bauxite residue is an alkaline, saline, sodic, massive, and fine grained material with little organic carbon or plant nutrients. To date, remediation of bauxite residue has focused on the use of chemical and physical amendments to address high pH, high salinity, and poor drainage and aeration. No studies to date have evaluated the potential for microbial communities to contribute to remediation as part of a combined approach integrating chemical, physical, and biological amendments. This review considers natural alkaline, saline environments that present similar challenges for microbial survival and evaluates candidate microorganisms that are both adapted for survival in these environments and have the capacity to carry out beneficial metabolisms in bauxite residue. Fermentation, sulfur oxidation, and extracellular polymeric substance production emerge as promising pathways for bioremediation whether employed individually or in combination. A combination of bioaugmentation (addition of inocula from other alkaline, saline environments) and biostimulation (addition of nutrients to promote microbial growth and activity) of the native community in bauxite residue is recommended as the approach most likely to be successful in promoting bioremediation of bauxite residue. PMID:25867516

  20. Microbially-driven strategies for bioremediation of bauxite residue.

    PubMed

    Santini, Talitha C; Kerr, Janice L; Warren, Lesley A

    2015-08-15

    Globally, 3 Gt of bauxite residue is currently in storage, with an additional 120 Mt generated every year. Bauxite residue is an alkaline, saline, sodic, massive, and fine grained material with little organic carbon or plant nutrients. To date, remediation of bauxite residue has focused on the use of chemical and physical amendments to address high pH, high salinity, and poor drainage and aeration. No studies to date have evaluated the potential for microbial communities to contribute to remediation as part of a combined approach integrating chemical, physical, and biological amendments. This review considers natural alkaline, saline environments that present similar challenges for microbial survival and evaluates candidate microorganisms that are both adapted for survival in these environments and have the capacity to carry out beneficial metabolisms in bauxite residue. Fermentation, sulfur oxidation, and extracellular polymeric substance production emerge as promising pathways for bioremediation whether employed individually or in combination. A combination of bioaugmentation (addition of inocula from other alkaline, saline environments) and biostimulation (addition of nutrients to promote microbial growth and activity) of the native community in bauxite residue is recommended as the approach most likely to be successful in promoting bioremediation of bauxite residue.

  1. Biogeochemical Processes in Microbial Ecosystems

    NASA Technical Reports Server (NTRS)

    DesMarais, David J.

    2001-01-01

    The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

  2. Microbially driven Fenton reaction for degradation of the widespread environmental contaminant 1,4-dioxane.

    PubMed

    Sekar, Ramanan; DiChristina, Thomas J

    2014-11-01

    The carcinogenic cyclic ether compound 1,4-dioxane is employed as a stabilizer of chlorinated industrial solvents and is a widespread environmental contaminant in surface water and groundwater. In the present study, a microbially driven Fenton reaction was designed to autocatalytically generate hydroxyl (HO•) radicals that degrade 1,4-dioxane. In comparison to conventional (purely abiotic) Fenton reactions, the microbially driven Fenton reaction operated at circumneutral pH and did not the require addition of exogenous H2O2 or UV irradiation to regenerate Fe(II) as Fenton reagents. The 1,4-dioxane degradation process was driven by pure cultures of the Fe(III)-reducing facultative anaerobe Shewanella oneidensis manipulated under controlled laboratory conditions. S. oneidensis batch cultures were provided with lactate, Fe(III), and 1,4-dioxane and were exposed to alternating aerobic and anaerobic conditions. The microbially driven Fenton reaction completely degraded 1,4-dioxane (10 mM initial concentration) in 53 h with an optimal aerobic-anaerobic cycling period of 3 h. Acetate and oxalate were detected as transient intermediates during the microbially driven Fenton degradation of 1,4-dioxane, an indication that conventional and microbially driven Fenton degradation processes follow similar reaction pathways. The microbially driven Fenton reaction provides the foundation for development of alternative in situ remediation technologies to degrade environmental contaminants susceptible to attack by HO• radicals generated by the Fenton reaction.

  3. MOLECULAR MECHANISM OF MICROBIAL TECHNETIUM REDUCTION FINAL REPORT

    SciTech Connect

    DiChristina, Thomas J.

    2013-04-30

    Microbial Tc(VII) reduction is an attractive alternative strategy for bioremediation of technetium-contaminated subsurface environments. Traditional ex situ remediation processes (e.g., adsorption or ion exchange) are often limited by poor extraction efficiency, inhibition by competing ions and production of large volumes of produced waste. Microbial Tc(VII) reduction provides an attractive alternative in situ remediation strategy since the reduced end-product Tc(IV) precipitates as TcO2, a highly insoluble hydrous oxide. Despite its potential benefits, the molecular mechanism of microbial Tc(VII) reduction remains poorly understood. The main goal of the proposed DOENABIR research project is to determine the molecular mechanism of microbial Tc(VII) reduction. Random mutagenesis studies in our lab have resulted in generation of a set of six Tc(VII) reduction-deficient mutants of Shewanella oneidensis. The anaerobic respiratory deficiencies of each Tc(VII) reduction-deficient mutant was determined by anaerobic growth on various combinations of three electron donors and 14 terminal electron acceptors. Results indicated that the electron transport pathways to Tc(VII), NO3 -, Mn(III) and U(VI) share common structural or regulatory components. In addition, we have recently found that wild-type Shewanella are also able to reduce Tc(IV) as electron acceptor, producing Tc(III) as an end-product. The recent genome sequencing of a variety of technetium-reducing bacteria and the anticipated release of several additional genome sequences in the coming year, provides us with an unprecedented opportunity to determine the mechanism of microbial technetium reduction across species and genus lines.

  4. Microbial xanthophylls.

    PubMed

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

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

  5. Effects of experimental lead pollution on the microbial communities associated with Sphagnum fallax (Bryophyta).

    PubMed

    Nguyen-Viet, H; Gilbert, D; Mitchell, E A D; Badot, P-M; Bernard, N

    2007-08-01

    Ecotoxicological studies usually focus on single microbial species under controlled conditions. As a result, little is known about the responses of different microbial functional groups or individual species to stresses. In an aim to assess the response of complex microbial communities to pollution in their natural habitat, we studied the effect of a simulated lead pollution on the microbial community (bacteria, cyanobacteria, protists, fungi, and micrometazoa) living on Sphagnum fallax. Mosses were grown in the laboratory with 0 (control), 625, and 2,500 microg L(-1) of Pb(2+) diluted in a standard nutrient solution and were sampled after 0, 6, 12, and 20 weeks. The biomasses of bacteria, microalgae, testate amoebae, and ciliates were dramatically and significantly decreased in both Pb addition treatments after 6, 12, and 20 weeks in comparison with the control. The biomass of cyanobacteria declined after 6 and 12 weeks in the highest Pb treatment. The biomasses of fungi, rotifers, and nematodes decreased along the duration of the experiment but were not significantly affected by lead addition. Consequently, the total microbial biomass was lower for both Pb addition treatments after 12 and 20 weeks than in the controls. The community structure was strongly modified due to changes in the densities of testate amoebae and ciliates, whereas the relative contribution of bacteria to the microbial biomass was stable. Differences in responses among the microbial groups suggest changes in the trophic links among them. The correlation between the biomass of bacteria and that of ciliates or testate amoebae increased with increasing Pb loading. We interpret this result as an effect on the grazing pathways of these predators and by the Pb effect on other potential prey (i.e., smaller protists). The community approach used here complements classical ecotoxicological studies by providing clues to the complex effect of pollutant-affecting organisms both directly and indirectly

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

    PubMed

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

    2014-10-01

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

  7. Microbial nanowires for bioenergy applications.

    PubMed

    Malvankar, Nikhil S; Lovley, Derek R

    2014-06-01

    Microbial nanowires are electrically conductive filaments that facilitate long-range extracellular electron transfer. The model for electron transport along Shewanella oneidensis nanowires is electron hopping/tunneling between cytochromes adorning the filaments. Geobacter sulfurreducens nanowires are comprised of pili that have metal-like conductivity attributed to overlapping pi-pi orbitals of aromatic amino acids. The nanowires of Geobacter species have been implicated in direct interspecies electron transfer (DIET), which may be an important mode of syntrophy in the conversion of organic wastes to methane. Nanowire networks confer conductivity to Geobacter biofilms converting organic compounds to electricity in microbial fuel cells (MFCs) and increasing nanowire production is the only genetic manipulation shown to yield strains with improved current-producing capabilities. Introducing nanowires, or nanowire mimetics, might improve other bioenergy strategies that rely on extracellular electron exchange, such as microbial electrosynthesis. Similarities between microbial nanowires and synthetic conducting polymers suggest additional energy-related applications.

  8. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture.

    PubMed

    Wood, Stephen A; Almaraz, Maya; Bradford, Mark A; McGuire, Krista L; Naeem, Shahid; Neill, Christopher; Palm, Cheryl A; Tully, Katherine L; Zhou, Jizhong

    2015-01-01

    Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.

  9. Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture

    PubMed Central

    Wood, Stephen A.; Almaraz, Maya; Bradford, Mark A.; McGuire, Krista L.; Naeem, Shahid; Neill, Christopher; Palm, Cheryl A.; Tully, Katherine L.; Zhou, Jizhong

    2015-01-01

    Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture. PMID:25926815

  10. Use of Metabolic Inhibitors to Characterize Ecological Interactions in an Estuarine Microbial Food Web.

    PubMed

    DeLorenzo, M.E.; Lewitus, A.J.; Scott, G.I.; Ross, P.E.

    2001-10-01

    Understanding microbial food web dynamics is complicated by the multitude of competitive or interdependent trophic interactions involved in material and energy flow. Metabolic inhibitors can be used to gain information on the relative importance of trophic pathways by uncoupling selected microbial components and examining the net effect on ecosystem structure and function. A eukaryotic growth inhibitor (cycloheximide), a prokaryotic growth inhibitor (antibiotic mixture), and an inhibitor of photosynthesis (DCMU) were used to examine the trophodynamics of microbial communities from the tidal creek in North Inlet, a salt marsh estuary near Georgetown, South Carolina. Natural microbial communities were collected in the spring, summer, and fall after colonization onto polyurethane foam substrates deployed in the tidal creek. Bacterial abundance and productivity, heterotrophic ciliate and flagellate abundance, and phototrophic productivity, biomass, and biovolume were measured at five time points after inhibitor additions. The trophic responses of the estuarine microbial food web to metabolic inhibitors varied with season. In the summer, a close interdependency among phototrophs, bacteria, and protozoa was indicated, and the important influence of microzooplanktonic nutrient recycling was evident (i.e., a positive feedback loop). In the fall, phototroph and bacteria interactions were competitive rather than interdependent, and grazer nutrient regeneration did not appear to be an important regulatory factor for bacterial or phototrophic activities. The results indicate a seasonal shift in microbial food web structure and function in North Inlet, from a summer community characterized by microbial loop dynamics to a more linear trophic system in the fall. This study stresses the important role of microbial loops in driving primary and secondary production in estuaries such as North Inlet that are tidally dominated by fluctuations in nutrient supply and a summer

  11. Microbial Metabolomics

    PubMed Central

    Tang, Jane

    2011-01-01

    Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancement of technologies and post-genomic developments enable the study and analysis of metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “omics” platforms. This review focuses on metabolomics in microorganisms and utilizes selected topics to illustrate its impact on the understanding of systems microbiology. PMID:22379393

  12. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  13. Microbial metropolis.

    PubMed

    Wimpenny, Julian

    2009-01-01

    Microorganisms can form tightly knit communities such as biofilms. Many others include marine snow, anaerobic digester granules, the ginger beer plant and bacterial colonies. This chapter is devoted to a survey of the main properties of these communities, with an emphasis on biofilms. We start with attachment to surfaces and the nature of adhesion. The growing community then forms within a matrix, generally of organic macromolecules. Inevitably the environment within such a matrix is different from that outside. Organisms respond by forming crowd-detection and response units; these quorum sensing systems act as switches between planktonic life and the dramatically altered conditions found inside microbial aggregates. The community then matures and changes and may even fail and disappear. Antimicrobial resistance is discussed as an example of multicellular behavior. The multicellular lifestyle has been modeled mathematically and responded to powerful molecular biological techniques. Latterly, microbial systems have been used as models for fundamental evolutionary processes, mostly because of their high rates of reproduction and the ease of genetic manipulation. The life of most microbes is a duality between the yin of the community and the yang of planktonic existence. Sadly far less research has been devoted to adaptation to free-living forms than in the opposite direction. PMID:20943124

  14. Biological Diversity Comprising Microbial Structures of Antarctic Ice Covered Lakes

    NASA Astrophysics Data System (ADS)

    Matys, E. D.

    2015-12-01

    Analysis of microbial membrane lipids is a rapid and non-selective method for evaluating the composition of microbial communities. To fully realise the diagnostic potential of these lipids, we must first understand their structural diversity, biological sources, physiological functions, and pathways of preservation. Particular environmental conditions likely prompt the production of different membrane lipid structures. Antarctica's McMurdo Dry Valleys host numerous ice-covered lakes with sharp chemical gradients that vary in illumination, geochemical structure, and benthic mat morphologies that are structured by nutrient availability and water chemistry. The lipid contents of these benthic mats have not received extensive study nor have the communities yet been thoroughly characterized. Accordingly, a combination of lipid biomarker and nucleic acid sequence data provides the means of assessing species diversity and environmental controls on the composition and diversity of membrane lipid assemblages. We investigated the richness and diversity of benthic microbial communities and accumulated organic matter in Lake Vanda of the McMurdo Dry Valleys. We have identified diverse glycolipids, aminolipids, and phospholipids in addition to many unknown compounds that may be specific to these particular environments. Light levels fluctuate seasonally, favoring low-light-tolerant cyanobacteria and specific lipid assemblages. Adaptations to nutrient limitations are reflected in contrasting intact polar lipid assemblages. For example, under P-limiting conditions, phospholipids are subsidiary to membrane-forming lipids that do not contain P (i.e. ornithine, betaine, and sulfolipids). The bacteriohopanepolyol (BHP) composition is dominated by bacteriohopanetetrol (BHT), a ubiquitous BHP, and 2-methylhopanoids. The relative abundance of 2-methylhopanoids is unprecedented and may reflect the unusual seasonal light regime of this polar environment. By establishing correlations

  15. Combination of nifedipine and subtherapeutic dose of cyclosporin additively suppresses mononuclear cells activation of patients with rheumatoid arthritis and normal individuals via Ca2+–calcineurin–nuclear factor of activated T cells pathway

    PubMed Central

    Lai, N-S; Yu, C-L; Yin, W-Y; Yu, H-C; Huang, H-B; Tung, C-H; Lu, M-C

    2012-01-01

    Abnormal Ca2+-mediated signalling contributes to the pathogenesis of rheumatoid arthritis (RA). However, the potential implication of calcium channel blocker in RA remained unknown. We hypothesized that nifedipine, an L-type calcium channel blocker, combined with a calcineurin inhibitor, could suppress T cell activation via targeting different level of the Ca2+ signalling pathway. The percentage of activated T cells and the apoptotic rate of mononuclear cells (MNCs) was measured by flow cytometry. The MNC viability, cytokine production, cytosolic Ca2+ level and activity of the nuclear factor of activated T cells (NFAT) were measured by enzyme-linked immunosorbent assay (ELISA). The NFAT-regulated gene expression, including interleukin (IL)-2, interferon (IFN)-γ and granulocyte–macrophage colony-stimulating factor (GM-CSF), was measured by real-time polymerase chain reaction (PCR). We found that the percentage of activated T cells in anti-CD3 + anti-CD28-activated MNC was higher in RA patients. High doses of nifedipine (50 µM) increased MNCs apoptosis, inhibited T cell activation and decreased T helper type 2 (Th1) (IFN-γ)/Th2 (IL-10) cytokine production in both groups. The Ca2+ influx was lower in anti-CD3 + anti-CD28-activated MNC from RA patients than healthy volunteers and suppressed by nifedipine. When combined with a subtherapeutic dose (50 ng/ml) of cyclosporin, 1 µM nifedipine suppressed the percentage of activated T cells in both groups. Moreover, this combination suppressed more IFN-γ secretion and NFAT-regulated gene (GM-CSF and IFN-γ) expression in RA-MNCs than normal MNCs via decreasing the activity of NFATc1. In conclusion, we found that L-type Ca2+ channel blockers and subtherapeutic doses of cyclosporin act additively to suppress the Ca2+-calcineurin-NFAT signalling pathway, leading to inhibition of T cell activity. We propose that this combination may become a potential treatment of RA. PMID:22385242

  16. Microbial transformation of sesquiterpenoids.

    PubMed

    Bhatti, Haq N; Zubair, Muhammad; Rasool, Nasir; Hassan, Zahid; Ahmad, Viqar U

    2009-08-01

    Biotransformations are useful methods for producing medicinal and agricultural chemicals from both active and inactive natural products with the introduction of chemical functions into remote sites of the molecules. Research on microbial biotransformations of commonly available sesquiterpenoids into more valuable derivatives has always been of interest because of their economical potential to the perfume, food, chemical and pharmaceutical industries. Fungal transformations of sesquiterpenoids have been less frequently studied compared with many other natural products. In recent years, however, much attention has been given to the exploitation of new products with enhanced biological activity using microorganisms. This review, covering the period from 1990 to 2006, summarizes our knowledge of the biotransformations of sesquiterpenoids by various fungi. Such transformations could lead to the discovery of new reaction pathways that might be useful in the design of new value-added products.

  17. Microbial fuel cells

    SciTech Connect

    Nealson, Kenneth H; Pirbazari, Massoud; Hsu, Lewis

    2013-04-09

    A microbial fuel cell includes an anode compartment with an anode and an anode biocatalyst and a cathode compartment with a cathode and a cathode biocatalyst, with a membrane positioned between the anode compartment and the cathode compartment, and an electrical pathway between the anode and the cathode. The anode biocatalyst is capable of catalyzing oxidation of an organic substance, and the cathode biocatalyst is capable of catalyzing reduction of an inorganic substance. The reduced organic substance can form a precipitate, thereby removing the inorganic substance from solution. In some cases, the anode biocatalyst is capable of catalyzing oxidation of an inorganic substance, and the cathode biocatalyst is capable of catalyzing reduction of an organic or inorganic substance.

  18. Triclosan Alters Anti-microbial and Inflammatory Responses of Epithelial Cells

    PubMed Central

    Wallet, Mark A.; Calderon, Nadia L.; Alonso, Tess R.; Choe, Christina S.; Catalfamo, Dana L.; Lalane, Charles J.; Neiva, Kathleen G.; Panagakos, Foti; Wallet, Shannon M.

    2012-01-01

    Periodontal diseases are a class of pathologies wherein oral microbes induce harmful immune responses in a susceptible host. Therefore, an agent which can both reduce microbial burden and lessen pathogenesis of localized inflammation would have beneficial effects in periodontal disease. 2,4,4-trichloro-2-hydroxydiphenyl-ether [triclosan] is currently used in oral care products due to broad spectrum anti-microbial and anti-inflammatory properties. Objective To determine effects of triclosan on the response of oral epithelial cells to stimulation with the inflammatory microbial product lipopolysaccharide [LPS], a ligand for toll-like receptor 4 [TLR4]. Materials/Methods Primary human oral epithelial cells were stimulated with LPS in the presence and/or absence of triclosan after which expression of pro-inflammatory cytokines, β-defensins, micro-RNAs [miRNAs] or TLR signaling pathway proteins were evaluated. Results Here we demonstrate that triclosan is a potent inhibitor of oral epithelial cell LPS-induced pro-inflammatory responses by inducing miRNA regulation of the TLR-signaling pathway. Triclosan was not a pan-suppresser of oral epithelial cell responses as β-defensin 2 [βD2] and βD3 were upregulated by triclosan following LPS-stimulation. Conclusions These data demonstrate both a novel anti-microbial mechanism by which triclosan improves plaque control and an additional anti-inflammatory property which could have beneficial effects in periodontal disease resolution. PMID:24079913

  19. In-Drift Microbial Communities

    SciTech Connect

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  20. Microbial Risk Assessment

    NASA Technical Reports Server (NTRS)

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

    2009-01-01

    Historically, microbiological spaceflight requirements have been established in a subjective manner based upon expert opinion of both environmental and clinical monitoring results and the incidence of disease. The limited amount of data, especially from long-duration missions, has created very conservative requirements based primarily on the concentration of microorganisms. Periodic reevaluations of new data from later missions have allowed some relaxation of these stringent requirements. However, the requirements remain very conservative and subjective in nature, and the risk of crew illness due to infectious microorganisms is not well defined. The use of modeling techniques for microbial risk has been applied in the food and potable water industries and has exceptional potential for spaceflight applications. From a productivity standpoint, this type of modeling can (1) decrease unnecessary costs and resource usage and (2) prevent inadequate or inappropriate data for health assessment. In addition, a quantitative model has several advantages for risk management and communication. By identifying the variable components of the model and the knowledge associated with each component, this type of modeling can: (1) Systematically identify and close knowledge gaps, (2) Systematically identify acceptable and unacceptable risks, (3) Improve communication with stakeholders as to the reasons for resource use, and (4) Facilitate external scientific approval of the NASA requirements. The modeling of microbial risk involves the evaluation of several key factors including hazard identification, crew exposure assessment, dose-response assessment, and risk characterization. Many of these factors are similar to conditions found on Earth; however, the spaceflight environment is very specialized as the inhabitants live in a small, semi-closed environment that is often dependent on regenerative life support systems. To further complicate modeling efforts, microbial dose

  1. Microbial Substrate Use at Sites of Continental Serpentinization: The Tablelands, NL, CAD and the Cedars, CA, USA

    NASA Astrophysics Data System (ADS)

    Morrill, P. L.; Rietze, A.; Kohl, L.; Miles, S.; Kavanagh, H.; Cox, A.; Brazelton, W. J.; Ishii, S.; Sherwood Lollar, B.; Schrenk, M. O.; Nealson, K. H.; Ziegler, S. E.; Ono, S.; Wang, D. T.; Lang, S. Q.; Cumming, E.

    2014-12-01

    Ultra-basic reducing springs at continental sites of serpentinization act as portals into the biogeochemistry of a subsurface ultramafic environment rich in hydrogen and methane gases. Field data and results from substrate addition microcosm experiments will be presented from two contrasting continental sites of serpentinization: the Tablelands, NL, CAN and The Cedars, CA, USA both Phanerozoic in age. These continental sites share geochemical characteristics that make these environments challenging for life, such as high pH, low Eh, scarce electron acceptors, and limited dissolved inorganic carbon for autotrophic growth. However, microbiological analyses have demonstrated that life does indeed exist in these environments. While environmental genomic studies indicated the potential metabolic capabilities of microorganisms in the sites, actual microbial metabolic activities in these environments remain unknown. To expand the understanding of biogeochemistry of the sites, we are conducting studies focusing on chemical and isotopic measurements, carbon substrate utilization, energy sources, and metabolic pathways of the microorganisms. Thus far, in situ geochemical data suggests that the methane from the Tablelands is primarily non-microbial, while the methane from The Cedars likely has some microbial contributions. To date, substrate addition microcosm experiments show no microbial production of methane from Tablelands' water and sediments. However, microbial carbon monoxide utilization has been observed in Tableland microcosms, but not in The Cedars microcosms. These results demonstrate how geochemistry and substrate addition experiments can be complementary for the determination of the processes favored at these continental sites of serpentinization.

  2. Microbial field pilot study

    SciTech Connect

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

    1992-03-01

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

  3. Microbial field pilot study

    SciTech Connect

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

    1992-03-01

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

  4. On the Functional Overlap between Complement and Anti-Microbial Peptides.

    PubMed

    Zimmer, Jana; Hobkirk, James; Mohamed, Fatima; Browning, Michael J; Stover, Cordula M

    2014-01-01

    Intriguingly, activated complement and anti-microbial peptides share certain functionalities; lytic, phagocytic, and chemo-attractant activities and each may, in addition, exert cell instructive roles. Each has been shown to have distinct LPS detoxifying activity and may play a role in the development of endotoxin tolerance. In search of the origin of complement, a functional homolog of complement C3 involved in opsonization has been identified in horseshoe crabs. Horseshoe crabs possess anti-microbial peptides able to bind to acyl chains or phosphate groups/saccharides of endotoxin, LPS. Complement activity as a whole is detectable in marine invertebrates. These are also a source of anti-microbial peptides with potential pharmaceutical applicability. Investigating the locality for the production of complement pathway proteins and their role in modulating cellular immune responses are emerging fields. The significance of local synthesis of complement components is becoming clearer from in vivo studies of parenchymatous disease involving specifically generated, complement-deficient mouse lines. Complement C3 is a central component of complement activation. Its provision by cells of the myeloid lineage varies. Their effector functions in turn are increased in the presence of anti-microbial peptides. This may point to a potentiating range of activities, which should serve the maintenance of health but may also cause disease. Because of the therapeutic implications, this review will consider closely studies dealing with complement activation and anti-microbial peptide activity in acute inflammation (e.g., dialysis-related peritonitis, appendicitis, and ischemia). PMID:25646095

  5. On the Functional Overlap between Complement and Anti-Microbial Peptides

    PubMed Central

    Zimmer, Jana; Hobkirk, James; Mohamed, Fatima; Browning, Michael J.; Stover, Cordula M.

    2015-01-01

    Intriguingly, activated complement and anti-microbial peptides share certain functionalities; lytic, phagocytic, and chemo-attractant activities and each may, in addition, exert cell instructive roles. Each has been shown to have distinct LPS detoxifying activity and may play a role in the development of endotoxin tolerance. In search of the origin of complement, a functional homolog of complement C3 involved in opsonization has been identified in horseshoe crabs. Horseshoe crabs possess anti-microbial peptides able to bind to acyl chains or phosphate groups/saccharides of endotoxin, LPS. Complement activity as a whole is detectable in marine invertebrates. These are also a source of anti-microbial peptides with potential pharmaceutical applicability. Investigating the locality for the production of complement pathway proteins and their role in modulating cellular immune responses are emerging fields. The significance of local synthesis of complement components is becoming clearer from in vivo studies of parenchymatous disease involving specifically generated, complement-deficient mouse lines. Complement C3 is a central component of complement activation. Its provision by cells of the myeloid lineage varies. Their effector functions in turn are increased in the presence of anti-microbial peptides. This may point to a potentiating range of activities, which should serve the maintenance of health but may also cause disease. Because of the therapeutic implications, this review will consider closely studies dealing with complement activation and anti-microbial peptide activity in acute inflammation (e.g., dialysis-related peritonitis, appendicitis, and ischemia). PMID:25646095

  6. Modeling Microbial Growth Dynamics, Patterns, and Coexistence on Partially Saturated Rough Surfaces

    NASA Astrophysics Data System (ADS)

    Long, T.; Or, D.

    2005-12-01

    A new modeling tool was developed to study the impact of variations in matric potential on aquatic pathways and substrate diffusion, and on microbial growth and movement on unsaturated rough surfaces. The modeling domain is composed of prescribed distributions of conical pits (sites) connected by prismatic channels (bonds) representing rough surfaces of soils or rocks. The well-defined geometry facilitates exact description of aqueous phase distribution within the roughness for a given matric potential. Microbial growth within the resulting highly variable diffusion network architectures (vary with matric potential) and interactions with nutrient diffusion patterns are simulated by coupling Reaction-Diffusion Method (RDM) and the Active Walker Method (AWM). Simulation results show direct impact of wetness conditions (matric potential values) on microbial growth rates and expansion patters for the same surface roughness. In addition to modification of mean diffusion rates for drier or wetter conditions, the network connectivity may induce significant changes in spatial patters of microbial growth. Impact of these changes on coexistence of two competing microbial species will be discussed.

  7. OptStrain: A computational framework for redesign of microbial production systems

    PubMed Central

    Pharkya, Priti; Burgard, Anthony P.; Maranas, Costas D.

    2004-01-01

    This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction of targeted compounds. These compounds may range from electrons or hydrogen in biofuel cell and environmental applications to complex drug precursor molecules. A comprehensive database of biotransformations, referred to as the Universal database (with >5700 reactions), is compiled and regularly updated by downloading and curating reactions from multiple biopathway database sources. Combinatorial optimization is then used to elucidate the set(s) of non-native functionalities, extracted from this Universal database, to add to the examined production host for enabling the desired product formation. Subsequently, competing functionalities that divert flux away from the targeted product are identified and removed to ensure higher product yields coupled with growth. This work represents an advancement over earlier efforts by establishing an integrated computational framework capable of constructing stoichiometrically balanced pathways, imposing maximum product yield requirements, pinpointing the optimal substrate(s), and evaluating different microbial hosts. The range and utility of OptStrain are demonstrated by addressing two very different product molecules. The hydrogen case study pinpoints reaction elimination strategies for improving hydrogen yields using two different substrates for three separate production hosts. In contrast, the vanillin study primarily showcases which non-native pathways need to be added into Escherichia coli. In summary, OptStrain provides a useful tool to aid microbial strain design and, more importantly, it establishes an integrated framework to accommodate future modeling developments. PMID:15520298

  8. EFFECT OF STARCH ADDITION ON THE PERFORMANCE AND SLUDGE CHARACTERIZATION OF UASB PROCESS TREATING METHANOLIC WASTEWATER

    NASA Astrophysics Data System (ADS)

    Yan, Feng; Kobayashi, Takuro; Takahashi, Shintaro; Li, Yu-You; Omura, Tatsuo

    A mesophilic(35℃) UASB reactor treating synthetic wastewater containing methanol with addition of starch was continuously operated for over 430 days by changing the organic loading rate from 2.5 to 120kg-COD/m3.d. The microbial community structure of the granules was analyzed with the molecular tools and its metabolic characteristics were evaluated using specific methanogenic activity tests. The process was successfully operated with over 98% soluble COD removal efficiency at VLR 30kg-COD/m3.d for approximately 300 days, and granulation satisfactory proceeded. The results of cloning and fluorescence in situ hybridization analysis suggest that groups related the genus Methanomethylovorans and the genus Methanosaeta were predominant in the reactor although only the genus Methanomethylovorans was predominant in the reactor treating methanolic wastewater in the previous study. Abundance of the granules over 0.5 mm in diameter in the reactor treating methanolic wastewater with addition of starch was 3 times larger than that in the reactor treating methanolic wastewater. Specific methanogenic activity tests in this study indicate that the methanol-methane pathway and the methanol-H2/CO2-methane pathway were predominant, and however, there was a certain level of activity for acetate-methane pathway unlike the reactor treating methanolic wastewater. These results suggest addition of starch might be responsible for diversifying the microbial community and encouraging the granulation.

  9. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-01-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

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

    PubMed Central

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

    2014-01-01

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

  11. Hypersaline Microbial Mat Lipid Biomarkers

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsegereda; Turk, Kendra A.; Summons, Roger E.

    2002-01-01

    Lipid biomarkers and compound specific isotopic abundances are powerful tools for studies of contemporary microbial ecosystems. Knowledge of the relationship of biomarkers to microbial physiology and community structure creates important links for understanding the nature of early organisms and paleoenvironments. Our recent work has focused on the hypersaline microbial mats in evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, sulfur oxidizing and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface. The delta C-13 of cyanobacterial biomarkers such as the monomethylalkanes and hopanoids are consistent with the delta C-13 measured for bulk mat (-10%o), while a GNS biomarker, wax esters (WXE), suggests a more depleted delta C-13 for GNS biomass (-16%o). This isotopic relationship is different than that observed in mats at Octopus Spring, Yellowstone National Park (YSNP) where GNS appear to grow photoheterotrophic ally. WXE abundance, while relatively low, is most pronounced in an anaerobic zone just below the cyanobacterial layer. The WXE isotope composition at GN suggests that these bacteria utilize photoautotrophy incorporating dissolved inorganic carbon (DIC) via the 3-hydroxypropionate pathway using H2S or H2.

  12. Microbial Protein-tyrosine Kinases*

    PubMed Central

    Chao, Joseph D.; Wong, Dennis; Av-Gay, Yossef

    2014-01-01

    Microbial ester kinases identified in the past 3 decades came as a surprise, as protein phosphorylation on Ser, Thr, and Tyr amino acids was thought to be unique to eukaryotes. Current analysis of available microbial genomes reveals that “eukaryote-like” protein kinases are prevalent in prokaryotes and can converge in the same signaling pathway with the classical microbial “two-component” systems. Most microbial tyrosine kinases lack the “eukaryotic” Hanks domain signature and are designated tyrosine kinases based upon their biochemical activity. These include the tyrosine kinases termed bacterial tyrosine kinases (BY-kinases), which are responsible for the majority of known bacterial tyrosine phosphorylation events. Although termed generally as bacterial tyrosine kinases, BY-kinases can be considered as one family belonging to the superfamily of prokaryotic protein-tyrosine kinases in bacteria. Other members of this superfamily include atypical “odd” tyrosine kinases with diverse mechanisms of protein phosphorylation and the “eukaryote-like” Hanks-type tyrosine kinases. Here, we discuss the distribution, phylogeny, and function of the various prokaryotic protein-tyrosine kinases, focusing on the recently discovered Mycobacterium tuberculosis PtkA and its relationship with other members of this diverse family of proteins. PMID:24554699

  13. Microbial field pilot study

    SciTech Connect

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

    1993-05-01

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

  14. Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages

    PubMed Central

    Shulse, Christine N.; Allen, Eric E.

    2011-01-01

    Bacterial production of long-chain omega-3 polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. The genes responsible for de novo bacterial PUFA biosynthesis, designated pfaEABCD, encode large, multi-domain protein complexes akin to type I iterative fatty acid and polyketide synthases, herein referred to as “Pfa synthases”. In addition to the archetypal Pfa synthase gene products from marine bacteria, we have identified homologous type I FAS/PKS gene clusters in diverse microbial lineages spanning 45 genera representing 10 phyla, presumed to be involved in long-chain fatty acid biosynthesis. In total, 20 distinct types of gene clusters were identified. Collectively, we propose the designation of “secondary lipids” to describe these biosynthetic pathways and products, a proposition consistent with the “secondary metabolite” vernacular. Phylogenomic analysis reveals a high degree of functional conservation within distinct biosynthetic pathways. Incongruence between secondary lipid synthase functional clades and taxonomic group membership combined with the lack of orthologous gene clusters in closely related strains suggests horizontal gene transfer has contributed to the dissemination of specialized lipid biosynthetic activities across disparate microbial lineages. PMID:21629834

  15. An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase.

    PubMed

    Yoo, Heejin; Widhalm, Joshua R; Qian, Yichun; Maeda, Hiroshi; Cooper, Bruce R; Jannasch, Amber S; Gonda, Itay; Lewinsohn, Efraim; Rhodes, David; Dudareva, Natalia

    2013-01-01

    Phenylalanine is a vital component of proteins in all living organisms, and in plants is a precursor for thousands of additional metabolites. Animals are incapable of synthesizing phenylalanine and must primarily obtain it directly or indirectly from plants. Although plants can synthesize phenylalanine in plastids through arogenate, the contribution of an alternative pathway via phenylpyruvate, as occurs in most microbes, has not been demonstrated. Here we show that plants also utilize a microbial-like phenylpyruvate pathway to produce phenylalanine, and flux through this route is increased when the entry point to the arogenate pathway is limiting. Unexpectedly, we find the plant phenylpyruvate pathway utilizes a cytosolic aminotransferase that links the coordinated catabolism of tyrosine to serve as the amino donor, thus interconnecting the extra-plastidial metabolism of these amino acids. This discovery uncovers another level of complexity in the plant aromatic amino acid regulatory network, unveiling new targets for metabolic engineering.

  16. Distribution of CO(2) fixation and acetate mineralization pathways in microorganisms from extremophilic anaerobic biotopes.

    PubMed

    Montoya, Lilia; Celis, Lourdes B; Razo-Flores, Elías; Alpuche-Solís, Angel G

    2012-11-01

    Extremophilic anaerobes are widespread in saline, acid, alkaline, and high or low temperature environments. Carbon is essential to living organisms and its fixation, degradation, or mineralization is driven by, up to now, six metabolic pathways. Organisms using these metabolisms are known as autotrophs, acetotrophs or carbon mineralizers, respectively. In anoxic and extreme environments, besides the well-studied Calvin-Benson-Bassham cycle, there are other five carbon fixation pathways responsible of autotrophy. Moreover, regarding carbon mineralization, two pathways perform this key process for carbon cycling. We might imagine that all the pathways can be found evenly distributed in microbial biotopes; however, in extreme environments, this does not occur. This manuscript reviews the most commonly reported anaerobic organisms that fix carbon and mineralize acetate in extreme anoxic habitats. Additionally, an inventory of autotrophic extremophiles by biotope is presented.

  17. Phosphazene additives

    DOEpatents

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  18. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  19. Microbial community modeling using reliability theory.

    PubMed

    Zilles, Julie L; Rodríguez, Luis F; Bartolerio, Nicholas A; Kent, Angela D

    2016-08-01

    Linking microbial community composition with the corresponding ecosystem functions remains challenging. Because microbial communities can differ in their functional responses, this knowledge gap limits ecosystem assessment, design and management. To develop models that explicitly incorporate microbial populations and guide efforts to characterize their functional differences, we propose a novel approach derived from reliability engineering. This reliability modeling approach is illustrated here using a microbial ecology dataset from denitrifying bioreactors. Reliability modeling is well-suited for analyzing the stability of complex networks composed of many microbial populations. It could also be applied to evaluate the redundancy within a particular biochemical pathway in a microbial community. Reliability modeling allows characterization of the system's resilience and identification of failure-prone functional groups or biochemical steps, which can then be targeted for monitoring or enhancement. The reliability engineering approach provides a new perspective for unraveling the interactions between microbial community diversity, functional redundancy and ecosystem services, as well as practical tools for the design and management of engineered ecosystems.

  20. Responses of Aromatic-Degrading Microbial Communities to Elevated Nitrate in Sediments.

    PubMed

    Xu, Meiying; He, Zhili; Zhang, Qin; Liu, Jin; Guo, Jun; Sun, Guoping; Zhou, Jizhong

    2015-10-20

    A high number of aromatic compounds that have been released into aquatic ecosystems have accumulated in sediment because of their low solubility and high hydrophobicity, causing significant hazards to the environment and human health. Since nitrate is an essential nitrogen component and a more thermodynamically favorable electron acceptor for anaerobic respiration, nitrate-based bioremediation has been applied to aromatic-contaminated sediments. However, few studies have focused on the response of aromatic-degrading microbial communities to nitrate addition in anaerobic sediments. Here we hypothesized that high nitrate inputs would stimulate aromatic-degrading microbial communities and their associated degrading processes, thus increasing the bioremediation efficiency in aromatic compound-contaminated sediments. We analyzed the changes of key aromatic-degrading genes in the sediment samples from a field-scale site for in situ bioremediation of an aromatic-contaminated creek in the Pearl River Delta before and after nitrate injection using a functional gene array. Our results showed that the genes involved in the degradation of several kinds of aromatic compounds were significantly enriched after nitrate injection, especially those encoding enzymes for central catabolic pathways of aromatic compound degradation, and most of the enriched genes were derived from nitrate-reducing microorganisms, possibly accelerating bioremediation of aromatic-contaminated sediments. The sediment nitrate concentration was found to be the predominant factor shaping the aromatic-degrading microbial communities. This study provides new insights into our understanding of the influences of nitrate addition on aromatic-degrading microbial communities in sediments. PMID:26390227

  1. Responses of Aromatic-Degrading Microbial Communities to Elevated Nitrate in Sediments.

    PubMed

    Xu, Meiying; He, Zhili; Zhang, Qin; Liu, Jin; Guo, Jun; Sun, Guoping; Zhou, Jizhong

    2015-10-20

    A high number of aromatic compounds that have been released into aquatic ecosystems have accumulated in sediment because of their low solubility and high hydrophobicity, causing significant hazards to the environment and human health. Since nitrate is an essential nitrogen component and a more thermodynamically favorable electron acceptor for anaerobic respiration, nitrate-based bioremediation has been applied to aromatic-contaminated sediments. However, few studies have focused on the response of aromatic-degrading microbial communities to nitrate addition in anaerobic sediments. Here we hypothesized that high nitrate inputs would stimulate aromatic-degrading microbial communities and their associated degrading processes, thus increasing the bioremediation efficiency in aromatic compound-contaminated sediments. We analyzed the changes of key aromatic-degrading genes in the sediment samples from a field-scale site for in situ bioremediation of an aromatic-contaminated creek in the Pearl River Delta before and after nitrate injection using a functional gene array. Our results showed that the genes involved in the degradation of several kinds of aromatic compounds were significantly enriched after nitrate injection, especially those encoding enzymes for central catabolic pathways of aromatic compound degradation, and most of the enriched genes were derived from nitrate-reducing microorganisms, possibly accelerating bioremediation of aromatic-contaminated sediments. The sediment nitrate concentration was found to be the predominant factor shaping the aromatic-degrading microbial communities. This study provides new insights into our understanding of the influences of nitrate addition on aromatic-degrading microbial communities in sediments.

  2. Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

    NASA Astrophysics Data System (ADS)

    Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

    2007-12-01

    The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms

  3. Microbial Synthesis of Alka(e)nes

    PubMed Central

    Wang, Weihua; Lu, Xuefeng

    2013-01-01

    Alka(e)nes are the predominant constituents of gasoline, diesel, and jet fuels. They can be produced naturally by a wide range of microorganisms. Bio-alka(e)nes can be used as drop-in biofuels. To date, five microbial pathways that convert free fatty acids or fatty acid derivatives into alka(e)nes have been identified or reconstituted. The discoveries open a door to achieve microbial production of alka(e)nes with high efficiency. The modules derived from these alka(e)ne biosynthetic pathways can be assembled as biological parts and synthetic biology strategies can be employed to optimize the metabolic pathways and improve alka(e)ne production. PMID:25023719

  4. Why should cell biologists study microbial pathogens?

    PubMed Central

    Welch, Matthew D.

    2015-01-01

    One quarter of all deaths worldwide each year result from infectious diseases caused by microbial pathogens. Pathogens infect and cause disease by producing virulence factors that target host cell molecules. Studying how virulence factors target host cells has revealed fundamental principles of cell biology. These include important advances in our understanding of the cytoskeleton, organelles and membrane-trafficking intermediates, signal transduction pathways, cell cycle regulators, the organelle/protein recycling machinery, and cell-death pathways. Such studies have also revealed cellular pathways crucial for the immune response. Discoveries from basic research on the cell biology of pathogenesis are actively being translated into the development of host-targeted therapies to treat infectious diseases. Thus there are many reasons for cell biologists to incorporate the study of microbial pathogens into their research programs. PMID:26628749

  5. Notch pathway is activated in cell culture and mouse models of mutant SOD1-related familial amyotrophic lateral sclerosis, with suppression of its activation as an additional mechanism of neuroprotection for lithium and valproate.

    PubMed

    Wang, S-Y; Ren, M; Jiang, H-Z; Wang, J; Jiang, H-Q; Yin, X; Qi, Y; Wang, X-D; Dong, G-T; Wang, T-H; Yang, Y-Q; Feng, H-L

    2015-08-20

    Amyotrophic lateral sclerosis (ALS) is an idiopathic and lethal neurodegenerative disease that currently has no effective treatment. A recent study found that the Notch signaling pathway was up-regulated in a TAR DNA-binding protein-43 (TDP-43) Drosophila model of ALS. Notch signaling acts as a master regulator in the central nervous system. However, the mechanisms by which Notch participates in the pathogenesis of ALS have not been completely elucidated. Recent studies have shown that the mood stabilizers lithium and valproic acid (VPA) are able to regulate Notch signaling. Our study sought to confirm the relationship between the Notch pathway and ALS and whether the Notch pathway contributes to the neuroprotective effects of lithium and VPA in ALS. We found that the Notch pathway was activated in in vitro and in vivo models of ALS, and suppression of Notch activation with a Notch signaling inhibitor, N-[N-(3,5-difluorophenacetyl-L-alanyl)]-S-phenylglycine t-butyl ester (DAPT) and Notch1 siRNA significantly reduced neuronal apoptotic signaling, as evidenced by the up-regulation of Bcl-2 as well as the down-regulation of Bax and cytochrome c. We also found that lithium and VPA suppressed the Notch activation associated with the superoxide dismutase-1 (SOD1) mutation, and the combination of lithium and VPA produced a more robust effect than either agent alone. Our findings indicate that the Notch pathway plays a critical role in ALS, and the neuroprotective effects of lithium and VPA against mutant SOD1-mediated neuronal damage are at least partially dependent on their suppression of Notch activation.

  6. Microbial ecology of drinking water distribution systems.

    PubMed

    Berry, David; Xi, Chuanwu; Raskin, Lutgarde

    2006-06-01

    The supply of clean drinking water is a major, and relatively recent, public health milestone. Control of microbial growth in drinking water distribution systems, often achieved through the addition of disinfectants, is essential to limiting waterborne illness, particularly in immunocompromised subpopulations. Recent inquiries into the microbial ecology of distribution systems have found that pathogen resistance to chlorination is affected by microbial community diversity and interspecies relationships. Research indicates that multispecies biofilms are generally more resistant to disinfection than single-species biofilms. Other recent findings are the increased survival of the bacterial pathogen Legionella pneumophila when present inside its protozoan host Hartmannella vermiformis and the depletion of chloramine disinfectant residuals by nitrifying bacteria, leading to increased overall microbial growth. Interactions such as these are unaccounted for in current disinfection models. An understanding of the microbial ecology of distribution systems is necessary to design innovative and effective control strategies that will ensure safe and high-quality drinking water. PMID:16701992

  7. Strategies to improve the nutritive value of rice bran in poultry diets. IV. Effects of addition of fish meal and a microbial phytase to duckling diets on bird performance and amino acid digestibility.

    PubMed

    Martin, E A; Nolan, J V; Nitsan, Z; Farrell, D J

    1998-12-01

    1. Ducklings were given diets with vegetable protein (VP) and 0 or 600 g rice bran/kg; fish meal (60 g/kg) and a phytase (+, -) were added to the diets (VP + AP). An additional 40 g soyabean meal/kg was added to the diet with rice bran (VP ++). Amino acid digestibility and mineral retention were measured in the lower ileum of ducklings killed at 23 d of age. Acid insoluble ash was used as an inert marker. Trypsin and amylase activities were also measured and weights of the pancreas and small intestine recorded at slaughter. 2. Addition of soyabean meal (VP ++) to the diet with rice bran improved growth rate and food intake compared to the diet without (VP) and gave the same food intake and growth rate as the comparable basal diet (VP) without rice bran. Fish meal improved growth rate on the diets without rice bran and improved food intake on this diet (VP + AP). Rice bran depressed growth rate and food conversion ratio (FCR); protein source affected growth rate, food intake and FCR; phytase increased food intake only. There were several interactions. 3. Determined total amino acid composition of the diets appeared to meet the essential amino acid requirements of ducklings. Rice bran depressed the ileal digestibility of virtually all amino acids and phytase had no direct effect, although there were interactions. Fish meal addition to diets with rice bran improved the apparent digestibility of several essential amino acids as well as that of dry matter and crude protein. 4. Ileal retention of some minerals and tibia ash content were reduced by rice bran. Fish meal and phytase inclusion increased P retention and ash in tibia. 5. Higher intestinal trypsin activity and increased pancreas size were seen in ducklings on diets with rice bran compared to those without. Intestinal amylase activity was reduced in ducklings given rice bran, probably because of its low starch content. 6. The stimulating effect of fish meal on duckling performance was probably caused in part by

  8. Microbial response to triepthylphosphate

    SciTech Connect

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

    1997-05-01

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

  9. Diet and Gut Microbial Function in Metabolic and Cardiovascular Disease Risk.

    PubMed

    Meyer, Katie A; Bennett, Brian J

    2016-10-01

    Over the past decade, the gut microbiome has emerged as a novel and largely unexplored source of variability for metabolic and cardiovascular disease risk, including diabetes. Animal and human studies support several possible pathways through which the gut microbiome may impact health, including the production of health-related metabolites from dietary sources. Diet is considered important to shaping the gut microbiota; in addition, gut microbiota influence the metabolism of many dietary components. In the present paper, we address the distinction between compositional and functional analysis of the gut microbiota. We focus on literature that highlights the value of moving beyond surveys of microbial composition to measuring gut microbial functioning to delineate mechanisms related to the interplay between diet and gut microbiota in cardiometabolic health. PMID:27541295

  10. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

    PubMed Central

    Whitaker, Jeanette; Ostle, Nicholas; McNamara, Niall P.; Nottingham, Andrew T.; Stott, Andrew W.; Bardgett, Richard D.; Salinas, Norma; Ccahuana, Adan J. Q.; Meir, Patrick

    2014-01-01

    Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., “positive priming effects” that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding 13C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils. PMID:25566230

  11. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru.

    PubMed

    Whitaker, Jeanette; Ostle, Nicholas; McNamara, Niall P; Nottingham, Andrew T; Stott, Andrew W; Bardgett, Richard D; Salinas, Norma; Ccahuana, Adan J Q; Meir, Patrick

    2014-01-01

    Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., "positive priming effects" that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding (13)C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils. PMID:25566230

  12. Microbial Engineering for Aldehyde Synthesis

    PubMed Central

    Kunjapur, Aditya M.

    2015-01-01

    Aldehydes are a class of chemicals with many industrial uses. Several aldehydes are responsible for flavors and fragrances present in plants, but aldehydes are not known to accumulate in most natural microorganisms. In many cases, microbial production of aldehydes presents an attractive alternative to extraction from plants or chemical synthesis. During the past 2 decades, a variety of aldehyde biosynthetic enzymes have undergone detailed characterization. Although metabolic pathways that result in alcohol synthesis via aldehyde intermediates were long known, only recent investigations in model microbes such as Escherichia coli have succeeded in minimizing the rapid endogenous conversion of aldehydes into their corresponding alcohols. Such efforts have provided a foundation for microbial aldehyde synthesis and broader utilization of aldehydes as intermediates for other synthetically challenging biochemical classes. However, aldehyde toxicity imposes a practical limit on achievable aldehyde titers and remains an issue of academic and commercial interest. In this minireview, we summarize published efforts of microbial engineering for aldehyde synthesis, with an emphasis on de novo synthesis, engineered aldehyde accumulation in E. coli, and the challenge of aldehyde toxicity. PMID:25576610

  13. Invited review: Essential oils as modifiers of rumen microbial fermentation.

    PubMed

    Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

    2007-06-01

    . Because plant extracts may act at different levels in the carbohydrate and protein degradation pathways, their careful selection and combination may provide a useful tool to manipulate rumen microbial fermentation effectively. However, additional research is required to establish the optimal dose in vivo in units of the active component, to consider the potential adaptation of microbial populations to their activities, to examine the presence of residues in the products (milk or meat), and to demonstrate improvements in animal performance.

  14. Invited review: Essential oils as modifiers of rumen microbial fermentation.

    PubMed

    Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

    2007-06-01

    . Because plant extracts may act at different levels in the carbohydrate and protein degradation pathways, their careful selection and combination may provide a useful tool to manipulate rumen microbial fermentation effectively. However, additional research is required to establish the optimal dose in vivo in units of the active component, to consider the potential adaptation of microbial populations to their activities, to examine the presence of residues in the products (milk or meat), and to demonstrate improvements in animal performance. PMID:17517698

  15. Oxidation state, bioavailability & biochemical pathway define the fate of carbon in soil

    NASA Astrophysics Data System (ADS)

    Kuzyakov, Yakov; Apostel, Carolin; Gunina, Anna; Herrmann, Anke M.; Dippold, Michaela

    2015-04-01

    Numerous experiments under laboratory and field conditions analyzed microbial utilization and mean residence time (MRT) of carbon (C) from plant and microbial residues as well as root exudates in soil. Most of these studies tested the effects of various environmental factors, such as temperature, soil moisture, texture etc. on these parameters. However, only a few studies compared the properties of the substances themselves and there is no conceptual framework based on biochemical pathways. We hypothesize that the fate of C from organic substances in soil strongly depends on the first step of their microbial utilization, specifically, on biochemical pathway and initial C oxidation state, as well as its bioavailability in soils, defined by its hydrophobicity and molecular weight. Here we introduce and evaluate a new conceptual framework based on the following parameters: 1) C oxidation state, 2) molecular weight and hydrophobicity, 3) initial biochemical pathway of a substance class in microbial cells. To assess these parameters, two databases were prepared based on the literature and own studies. The first database included only the studies with 14C or 13C position specific labeled sugars, amino acids, carboxylic acids, phenols and lipids in soil. This database allowed us to analyze microbial utilization and mineralization of organics to CO2 depending on their C oxidation state (OS) and on functional groups. Additionally, we calculated data on the bond electronegativity of all compounds investigated in these studies. The second data base included the results of 14C and 13C studies with uniformly labeled substances of various classes. This database considered the free enthalpie (Delta H) per C unit from a variety of substrates differing in their aromaticity, hydrophobicity/electronegativity and location of the substance on the van Krevelen diagram. In addition, we calculated the hydrophobicity from the electronegativity of the individual bonds and recorded their

  16. Pyrogenic organic matter can alter microbial communication

    NASA Astrophysics Data System (ADS)

    Masiello, Caroline; Gao, Xiaodong; Cheng, Hsiao-Ying; Silberg, Jonathan

    2016-04-01

    Soil microbes communicate with each other to manage a large range of processes that occur more efficiently when microbes are able to act simultaneously. This coordination occurs through the continuous production of signaling compounds that are easily diffused into and out of cells. As the number of microbes in a localized environment increases, the internal cellular concentration of these signaling compounds increases, and when a threshold concentration is reached, gene expression shifts, leading to altered (and coordinated) microbial behaviors. Many of these coordinated behaviors have biogeochemically important outcomes. For example, methanogenesis, denitrification, biofilm formation, and the development of plant-rhizobial symbioses are all regulated by a simple class of cell-cell signaling molecules known as acyl homoserine lactones (AHLs). Pyrogenic organic matter in soils can act to disrupt microbial communication through multiple pathways. In the case of AHLs, charcoal's very high surface area can sorb these signaling compounds, preventing microbes from detecting each others' presence (Masiello et al., 2014). In addition, the lactone ring in AHLs is vulnerable to pH increases accompanying PyOM inputs, with soil pH values higher than 7-8 leading to ring opening and compound destabilization. Different microbes use different classes of signaling compounds, and not all microbial signaling compounds are pH-vulnerable. This implies that PyOM-driven pH increases may trigger differential outcomes for Gram negative bacteria vs fungi, for example. A charcoal-driven reduction in microbes' ability to detect cell-cell communication compounds may lead to a shift in the ability of microbes to participate in key steps of C and N cycling. For example, an increase in an archaeon-specific AHL has been shown to lead to a cascade of metabolic processes that eventually results in the upregulation of CH4 production (Zhang et al., 2012). Alterations in similar AHL compounds leads to

  17. Microbial conversion of glycerol to 1,3-propanediol

    SciTech Connect

    Zeng, A.P.; Biebl, H.; Deckwer, W.D.

    1996-10-01

    Glycerol is a byproduct from the soap and detergent industry and possibly from future biodiesel plants. The conversion of glycerol to 1,3-propanediol (PD) is of industrial interest due to the potential use of PD for the synthesis of polyesters. We have been studying the microbial conversion of glycerol to PD with work ranging from strain isolation, medium optimization, pathway analysis, product formation kinetics and growth modeling, downstream processing and reactor scale-up (up to 2000 1). PD yields of nearly 100% of the theoretical maximum (0.72 mol/mol glycerol) and final product concentrations of about 65 g/l were achieved with both Klebsiella pneumoniae and Clostridium butyricum. In addition to summarizing our experimental results the advances of bioconversion of glycerol will be reviewed in this presentation, with emphasis on discussing further research and development needs in this area. Results of process engineering and cost analysis will also be presented.

  18. Towards a Microbial Thermoelectric Cell

    PubMed Central

    Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

    2013-01-01

    Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250–600 mV was achieved with 1.7 L baker’s yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices. PMID:23468862

  19. Towards a microbial thermoelectric cell.

    PubMed

    Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

    2013-01-01

    Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250-600 mV was achieved with 1.7 L baker's yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices.

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

    PubMed Central

    Glass, Jennifer B.; Orphan, Victoria J.

    2011-01-01

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

  1. Microbial responses to solvent and alcohol stress.

    PubMed

    Taylor, Mark; Tuffin, Marla; Burton, Stephanie; Eley, Kirstin; Cowan, Don

    2008-11-01

    Increasing fuel prices and doubts over the long-term availability of oil are currently major global concerns. Such concerns have led to national policies and objectives to develop microbially produced alcohols as fuel additives or substitutes. However, in South Africa this solution poses the further dilemma of sourcing a suitable fermentative carbohydrate that will not impact negatively on the availability of staple foods. The solution lies in the use of lignocellulosic materials, currently a waste product of the food and agriculture industries, which could be used in conjunction with a catabolically suitable production strain. In the pursuit of lignocellulosic biofuel production, conventional fermentation strains have been shown to have limited catabolic versatility. However, catabolically versatile engineered strains and novel isolates engineered with ethanologenic pathways have subsequently been shown to exhibit limitations in solvent tolerance, hindering their full potential as economically viable production strains. A considerable volume of research has been reported on the general cellular mechanisms and physiological responses to solvent shock as well as adaptive changes responsible for solvent tolerant phenotypes in mutant progeny. Here we review a number of the more common cell responses to solvents with particular focus on alcohol tolerance.

  2. Mechanisms Controlling Carbon Turnover from Diverse Microbial Groups in Temperate and Tropical Forest Soils

    NASA Astrophysics Data System (ADS)

    Throckmorton, H.; Dane, L.; Bird, J. A.; Firestone, M. K.; Horwath, W. R.

    2010-12-01

    Microorganisms represent an important intermediate along the pathway of plant litter decomposition to the formation of soil organic matter (SOM); yet little is known of the fate and stability of microbial C in soils and the importance of microbial biochemistry as a factor influencing SOM dynamics. This research investigates mechanisms controlling microbial C stabilization in a temperate forest in the Sierra Nevada of California (CA) and a tropical forest in Puerto Rico (PR). Biochemically diverse microbial groups (fungi, actinomycetes, bacteria gram (+), and bacteria gram (-)) were isolated from both sites, grown in the laboratory with C13 media, killed, and nonliving residues were added back to soils as a reciprocal transplant of microbial groups. The native microbial community in CA is dominated by fungi and in PR is dominated by bacteria, which provides an opportunity to asses the metabolic response of distinct microbial communities to the diverse microbial additions. CA and PR soils were sampled five times over a 3 and 2 year period, respectively. In CA there was no significant difference in the mean residence time (MRT) of diverse C13 microbial treatments; whereas in PR there were significant differences, whereby temperate fungi, temperate Gram (+) bacteria, and tropical actinomycetes exhibited a significantly longer MRT as compared with tropical fungi and temperate Gram (-). These results suggest that a bacterial dominated microbial community discriminates more amongst diverse substrates than a fungal-dominated community. MRT for labeled-C in CA was 5.21 ± 1.11 years, and in PR was 2.22 ± 0.45. Despite substantial differences in MRT between sites, physical fractionation of soils into light (LF), aggregated-occluded (OF), and mineral-associated (MF) fractions provided evidence that accelerated decomposition in PR (presumably due to climate) operated primarily on labeled-C unassociated with the mineral matrix (LF); labeled-C occluded within aggregates (OF) or

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

    NASA Astrophysics Data System (ADS)

    Kallenbach, Cynthia M.; Grandy, A. Stuart

    2014-05-01

    Soil microbial communities are fundamental to plant C turnover, as all C inputs eventually pass through the microbial biomass. In turn, there is increasing evidence that this biomass accumulates as a significant portion of stable soil organic matter (SOM) via physiochemical interactions with the soil matrix. However, when exploring SOM dynamics, these two processes are often regarded as discrete from one another, despite potentially important linkages between microbial C utilization and the fate of that biomass C as SOM. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil C inputs that influence microbial biomass production and microbial C allocation. Microbial physiology, such as microbial growth efficiency (MGE), growth rate and turnover have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM accumulation may not necessarily be a function of resistance to decay but the degree to which it optimizes microbial biomass production. To examine the relationship between microbial C utilization and microbial contributions to SOM, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine 1) if, in absence of plant-derived C, chemically complex SOM similar to natural soils can accumulate through the production of microbial residues and 2) how differences in C utilization of simple substrates, varying in energy yields, influence the quantity and chemistry of newly formed SOM. Over the course of the incubation, MGE

  4. Microbial Field Pilot Study

    SciTech Connect

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

    1990-11-01

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

  5. Research advances on microbial genetics in China in 2015.

    PubMed

    Jianping, Xie; Yubo, Han; Gang, Liu; Linquan, Bai

    2016-09-01

    In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled. We also illustrated the biosynthetic pathways and regulators of multiple microbial compounds, novel enzyme reactions, and new mechanisms regulating microbial gene expression. And new findings were obtained in the microbial development, evolution and population genetics. For the industrial microbiology, more understanding on the molecular basis of the microbial factory has been gained. For the pathogenic microbiology, the genetic circuits of several pathogens were depicted, and significant progresses were achieved for understanding the pathogen-host interaction and revealing the genetic mechanisms underlying antimicrobial resistance, emerging pathogens and environmental microorganisms at the genomic level. In future, the genetic diversity of microbes can be used to obtain specific products, while gut microbiome is gathering momentum. PMID:27644739

  6. Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment

    PubMed Central

    Graves, Christopher J.; Makrides, Elizabeth J.; Schmidt, Victor T.; Giblin, Anne E.; Cardon, Zoe G.

    2016-01-01

    -genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance. PMID:26944843

  7. Microbial Properties Database Editor Tutorial

    EPA Science Inventory

    A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbial-relevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pat...

  8. Updating the Wnt pathways

    PubMed Central

    Yu, Jia; Virshup, David M.

    2014-01-01

    In the three decades since the discovery of the Wnt1 proto-oncogene in virus-induced mouse mammary tumours, our understanding of the signalling pathways that are regulated by the Wnt proteins has progressively expanded. Wnts are involved in an complex signalling network that governs multiple biological processes and cross-talk with multiple additional signalling cascades, including the Notch, FGF (fibroblast growth factor), SHH (Sonic hedgehog), EGF (epidermal growth factor) and Hippo pathways. The Wnt signalling pathway also illustrates the link between abnormal regulation of the developmental processes and disease manifestation. Here we provide an overview of Wnt-regulated signalling cascades and highlight recent advances. We focus on new findings regarding the dedicated Wnt production and secretion pathway with potential therapeutic targets that might be beneficial for patients with Wnt-related diseases. PMID:25208913

  9. Global biogeography of microbial nitrogen-cycling traits in soil

    PubMed Central

    Nelson, Michaeline B.; Martiny, Jennifer B. H.

    2016-01-01

    Microorganisms drive much of the Earth’s nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils. PMID:27432978

  10. Global biogeography of microbial nitrogen-cycling traits in soil.

    PubMed

    Nelson, Michaeline B; Martiny, Adam C; Martiny, Jennifer B H

    2016-07-19

    Microorganisms drive much of the Earth's nitrogen (N) cycle, but we still lack a global overview of the abundance and composition of the microorganisms carrying out soil N processes. To address this gap, we characterized the biogeography of microbial N traits, defined as eight N-cycling pathways, using publically available soil metagenomes. The relative frequency of N pathways varied consistently across soils, such that the frequencies of the individual N pathways were positively correlated across the soil samples. Habitat type, soil carbon, and soil N largely explained the total N pathway frequency in a sample. In contrast, we could not identify major drivers of the taxonomic composition of the N functional groups. Further, the dominant genera encoding a pathway were generally similar among habitat types. The soil samples also revealed an unexpectedly high frequency of bacteria carrying the pathways required for dissimilatory nitrate reduction to ammonium, a little-studied N process in soil. Finally, phylogenetic analysis showed that some microbial groups seem to be N-cycling specialists or generalists. For instance, taxa within the Deltaproteobacteria encoded all eight N pathways, whereas those within the Cyanobacteria primarily encoded three pathways. Overall, this trait-based approach provides a baseline for investigating the relationship between microbial diversity and N cycling across global soils. PMID:27432978

  11. Physiology, biochemistry and possible applications of microbial caffeine degradation.

    PubMed

    Gummadi, Sathyanarayana N; Bhavya, B; Ashok, Nandhini

    2012-01-01

    Caffeine, a purine alkaloid is a constituent of widely consumed beverages. The scientific evidence which has proved the harm of this alkaloid has paved the way for innumerable research in the area of caffeine degradation. In addition to this, the fact that the by-products of the coffee and tea industry pollute the environment has called for the need of decaffeinating coffee and tea industry's by-products. Though physical and chemical methods for decaffeination are available, the lack of specificity for removal of caffeine in these techniques and their non-eco-friendly nature has opened the area of microbial and enzymatic degradation of caffeine. Another important application of microbial caffeine degradation apart from its advantages like specificity, eco-friendliness and cost-effectiveness is the fact that this process will enable the production of industrially and medically useful components of the caffeine degradation pathway like theobromine and theophylline. This is a comprehensive review which mainly focuses on caffeine degradation, large-scale degradation of the same and its applications in the industrial world.

  12. Physiology, biochemistry and possible applications of microbial caffeine degradation.

    PubMed

    Gummadi, Sathyanarayana N; Bhavya, B; Ashok, Nandhini

    2012-01-01

    Caffeine, a purine alkaloid is a constituent of widely consumed beverages. The scientific evidence which has proved the harm of this alkaloid has paved the way for innumerable research in the area of caffeine degradation. In addition to this, the fact that the by-products of the coffee and tea industry pollute the environment has called for the need of decaffeinating coffee and tea industry's by-products. Though physical and chemical methods for decaffeination are available, the lack of specificity for removal of caffeine in these techniques and their non-eco-friendly nature has opened the area of microbial and enzymatic degradation of caffeine. Another important application of microbial caffeine degradation apart from its advantages like specificity, eco-friendliness and cost-effectiveness is the fact that this process will enable the production of industrially and medically useful components of the caffeine degradation pathway like theobromine and theophylline. This is a comprehensive review which mainly focuses on caffeine degradation, large-scale degradation of the same and its applications in the industrial world. PMID:22139018

  13. Why Microbial Communities?

    ScienceCinema

    Fredrickson, Jim (PNNL)

    2016-07-12

    The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities. Dr. Fredrickson introduces the symposium by defining microbial communities and describing their scientific relevance as they relate to solving problems in energy, climate, and sustainability.

  14. The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information.

    PubMed

    Hayman, G Thomas; Jayaraman, Pushkala; Petri, Victoria; Tutaj, Marek; Liu, Weisong; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

    2013-01-01

    The RGD Pathway Portal provides pathway annotations for rat, human and mouse genes and pathway diagrams and suites, all interconnected via the pathway ontology. Diagram pages present the diagram and description, with diagram objects linked to additional resources. A newly-developed dual-functionality web application composes the diagram page. Curators input the description, diagram, references and additional pathway objects. The application combines these with tables of rat, human and mouse pathway genes, including genetic information, analysis tool and reference links, and disease, phenotype and other pathway annotations to pathway genes. The application increases the information content of diagram pages while expediting publication.

  15. Engineering of methionine chain elongation part of glucoraphanin pathway in E. coli.

    PubMed

    Mirza, Nadia; Crocoll, Christoph; Erik Olsen, Carl; Ann Halkier, Barbara

    2016-05-01

    The methionine-derived glucosinolate glucoraphanin is associated with the health-promoting properties of broccoli. This has developed a strong interest in producing this compound in high amounts from a microbial source. Glucoraphanin synthesis starts with a five-gene chain elongation pathway that converts methionine to dihomo-methionine, which is subsequently converted to glucoraphanin by the seven-gene glucosinolate core structure pathway. As dihomo-methionine is the precursor amino acid for glucoraphanin production, a first challenge is to establish an expression system for production of dihomo-methionine. In planta, the methionine chain elongation enzymes are physically separated within the cell with the first enzyme in the cytosol while the rest are located in the chloroplast. A de-compartmentalization approach was applied to produce dihomo-methionine by expression of the respective plant genes in Escherichia coli cytosol. Introduction of two plasmids encoding the methionine chain elongation pathway into E. coli resulted in production of 25mgL(-1) of dihomo-methionine. In addition to chain-elongated methionine products, side-products from chain elongation of leucine were produced. Methionine supplementation enhanced dihomo-methionine production to 57mgL(-1), while keeping a steady level of the chain-elongated leucine products. Engineering of the de-compartmentalized pathway of dihomo-methionine in E. coli cytosol provides an important first step for microbial production of the health-promoting glucoraphanin.

  16. Pyrosequencing for microbial identification and characterization.

    PubMed

    Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

    2013-08-22

    Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

  17. Our unique microbial identity.

    PubMed

    Gilbert, Jack A

    2015-05-14

    A recent article examines the extent of individual variation in microbial identities and how this might determine disease susceptibility, therapeutic responses and recovery from clinical interventions.

  18. Surface reflectance degradation by microbial communities

    SciTech Connect

    Cheng, Meng -Dawn; Allman, Steve L.; Graham, David E.; Cheng, Karen R.; Pfiffner, Susan Marie; Vishnivetskaya, Tatiana A.; Desjarlais, Andre Omer

    2015-11-05

    Building envelope, such as a roof, is the interface between a building structure and the environment. Understanding of the physics of microbial interactions with the building envelope is limited. In addition to the natural weathering, microorganisms and airborne particulate matter that attach to a cool roof tend to reduce the roof reflectance over time, compromising the energy efficiency advantages of the reflective coating designs. We applied microbial ecology analysis to identify the natural communities present on the exposed coatings and investigated the reduction kinetics of the surface reflectance upon the introduction of a defined mixture of both photoautotrophic and heterotrophic microorganisms representing the natural communities. The result are (1) reflectance degradation by microbial communities follows a first-order kinetic relationship and (2) more than 50% of degradation from the initial reflectance value can be caused by microbial species alone in much less time than 3 years required by the current standard ENERGY STAR® test methods.

  19. Surface reflectance degradation by microbial communities

    DOE PAGES

    Cheng, Meng -Dawn; Allman, Steve L.; Graham, David E.; Cheng, Karen R.; Pfiffner, Susan Marie; Vishnivetskaya, Tatiana A.; Desjarlais, Andre Omer

    2015-11-05

    Building envelope, such as a roof, is the interface between a building structure and the environment. Understanding of the physics of microbial interactions with the building envelope is limited. In addition to the natural weathering, microorganisms and airborne particulate matter that attach to a cool roof tend to reduce the roof reflectance over time, compromising the energy efficiency advantages of the reflective coating designs. We applied microbial ecology analysis to identify the natural communities present on the exposed coatings and investigated the reduction kinetics of the surface reflectance upon the introduction of a defined mixture of both photoautotrophic and heterotrophicmore » microorganisms representing the natural communities. The result are (1) reflectance degradation by microbial communities follows a first-order kinetic relationship and (2) more than 50% of degradation from the initial reflectance value can be caused by microbial species alone in much less time than 3 years required by the current standard ENERGY STAR® test methods.« less

  20. Ins and Outs of Microbial Adhesion

    NASA Astrophysics Data System (ADS)

    Virji, Mumtaz

    Microbial adhesion is generally a complex process, involving multiple adhesins on a single microbe and their respective target receptors on host cells. In some situations, various adhesins of a microbe may co-operate in an apparently hierarchical and sequential manner whereby the first adhesive event triggers the target cell to express receptors for additional microbial adhesins. In other instances, adhesins may act in concert leading to high avidity interactions, often a prelude to cellular invasion and tissue penetration. Mechanisms used to target the host include both lectin-like interactions and protein-protein interactions; the latter are often highly specific for the host or a tissue within the host. This reflective chapter aims to offer a point of view on microbial adhesion by presenting some experiences and thoughts especially related to respiratory pathogens and explore if there can be any future hope of controlling bacterial infections via preventing adhesion or invasion stages of microbial pathogenesis.

  1. Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes generated furans appending reactive phosphorus ylides through cumulated trienoates as key intermediates: a phosphine α-addition-δ-evolvement of an anion pathway.

    PubMed

    Deng, Jie-Cheng; Chuang, Shih-Ching

    2014-11-01

    Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes have been demonstrated, providing trisubstituted furans appending reactive phosphorus ylides, through cumulated trienoates as key intermediates. The proposed trienoate intermediates, 1,5-dipolar species formed via nucleophilic α-attack of phosphines toward diynedioates (α-addition-δ-evolvement of an anion, abbreviated αAδE), undergo addition to aryl aldehydes followed by 5-endo-dig cyclization, proton transfer, and resonance to give trisubstituted furans. Furthermore, the phosphorus ylides are oxidized to α-keto ester furans and utilized as Wittig reagents.

  2. Subsurface microbial habitats on Mars

    NASA Technical Reports Server (NTRS)

    Boston, P. J.; Mckay, C. P.

    1991-01-01

    We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

  3. Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

    NASA Astrophysics Data System (ADS)

    Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

    2014-06-01

    Microbial degradation of chitin in soil substantially contributes to carbon cycling in terrestrial ecosystems. Chitin is globally the second most abundant biopolymer after cellulose and can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities is unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, and carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation, along with ammonification, were likely responsible for anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of less than 50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions on community level.

  4. Microbial responses to chitin and chitosan in oxic and anoxic agricultural soil slurries

    NASA Astrophysics Data System (ADS)

    Wieczorek, A. S.; Hetz, S. A.; Kolb, S.

    2014-02-01

    Chitin is the second most abundant biopolymer in terrestrial ecosystems and is subject to microbial degradation. Chitin can be deacetylated to chitosan or can be hydrolyzed to N,N'-diacetylchitobiose and oligomers of N-acetylglucosamine by aerobic and anaerobic microorganisms. Which pathway of chitin hydrolysis is preferred by soil microbial communities has previously been unknown. Supplementation of chitin stimulated microbial activity under oxic and anoxic conditions in agricultural soil slurries, whereas chitosan had no effect. Thus, the soil microbial community likely was more adapted to chitin as a substrate. In addition, this finding suggested that direct hydrolysis of chitin was preferred to the pathway that starts with deacetylation. Chitin was apparently degraded by aerobic respiration, ammonification, and nitrification to carbon dioxide and nitrate under oxic conditions. When oxygen was absent, fermentation products (acetate, butyrate, propionate, hydrogen, carbon dioxide) and ammonia were detected, suggesting that butyric and propionic acid fermentation were along with ammonification likely responsible for apparent anaerobic chitin degradation. In total, 42 different chiA genotypes were detected of which twenty were novel at an amino acid sequence dissimilarity of >50%. Various chiA genotypes responded to chitin supplementation and affiliated with a novel deep-branching bacterial chiA genotype (anoxic conditions), genotypes of Beta- and Gammaproteobacteria (oxic and anoxic conditions), and Planctomycetes (oxic conditions). Thus, this study provides evidence that detected chitinolytic bacteria were catabolically diverse and occupied different ecological niches with regard to oxygen availability enabling chitin degradation under various redox conditions at the level of the community.

  5. Heterologous expression of mitochondria-targeted microbial nitrilase enzymes increases cyanide tolerance in Arabidopsis.

    PubMed

    Molojwane, E; Adams, N; Sweetlove, L J; Ingle, R A

    2015-07-01

    Anthropogenic activities have resulted in cyanide (CN) contamination of both soil and water in many areas of the globe. While plants possess a detoxification pathway that serves to degrade endogenously generated CN, this system is readily overwhelmed, limiting the use of plants in bioremediation. Genetic engineering of additional CN degradation pathways in plants is one potential strategy to increase their tolerance to CN. Here we show that heterologous expression of microbial nitrilase enzymes targeted to the mitochondria increases CN tolerance in Arabidopsis. Root length in seedlings expressing either a CN dihydratase from Bacillus pumilis or a CN hydratase from Neurospora crassa was increased by 45% relative in wild-type plants in the presence of 50 μm KCN. We also demonstrate that in contrast to its strong inhibitory effects on seedling establishment, seed germination of the Col-0 ecotype of Arabidopsis is unaffected by CN.

  6. Microbial limitation in a changing world: A stoichiometric approach for predicting microbial resource limitation and fluxes

    NASA Astrophysics Data System (ADS)

    Midgley, M.; Phillips, R.

    2014-12-01

    Microbes mediate fluxes of carbon (C), nitrogen (N), and phosphorus (P) in soils depending on ratios of available C, N, and P relative to microbial demand. Hence, characterizing microbial C and nutrient limitation in soils is critical for predicting how ecosystems will respond to human alterations of climate and nutrient availability. Here, we take a stoichiometric approach to assessing microbial C, N, and P limitation by using threshold element ratios (TERs). TERs enable shifting resource limitation to be assessed by matching C, N and P ratios from microbial biomass, extracellular enzyme activities, and soil nutrient concentrations. We assessed microbial nutrient limitation in temperate forests dominated by trees that associate with one of two mycorrhizal symbionts: arbsucular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. We found that both ECM and AM microbial communities were co-limited by C and N, supporting conventional wisdom that microbes are C-limited and temperate forests are N-limited. However, AM microbial communities were relatively more C-limited than ECM communities (P=0.001). In response to chronic field N fertilization, both AM and ECM communities became relatively more P-limited (P=0.011), but they remained N- and C-limited overall. Thus, realistic levels of N deposition may not dampen microbial N limitation. Reflecting differences in relative limitation, N mineralization rates were higher in AM soils than in ECM soils (P=0.004) while C mineralization rates were higher in ECM soils than in AM soils (P=0.023). There were no significant differences in P flux between AM and ECM soils or detectable mineralization responses to N addition, indicating that mineralization rates are closely tied to C and nutrient limitation. Overall, we found that 1) microbial resource limitation can be detected without resource addition; and 2) TERs and ratios of labile resources are viable tools for predicting mineralization responses to resource additions.

  7. WikiPathways: capturing the full diversity of pathway knowledge

    PubMed Central

    Kutmon, Martina; Riutta, Anders; Nunes, Nuno; Hanspers, Kristina; Willighagen, Egon L.; Bohler, Anwesha; Mélius, Jonathan; Waagmeester, Andra; Sinha, Sravanthi R.; Miller, Ryan; Coort, Susan L.; Cirillo, Elisa; Smeets, Bart; Evelo, Chris T.; Pico, Alexander R.

    2016-01-01

    WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access. PMID:26481357

  8. Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics.

    PubMed

    Warden, John G; Casaburi, Giorgio; Omelon, Christopher R; Bennett, Philip C; Breecker, Daniel O; Foster, Jamie S

    2016-01-01

    Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ(13)C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite

  9. Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics

    PubMed Central

    Warden, John G.; Casaburi, Giorgio; Omelon, Christopher R.; Bennett, Philip C.; Breecker, Daniel O.; Foster, Jamie S.

    2016-01-01

    Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ13C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite

  10. Microbial community response to seawater amendment in low-salinity tidal sediments.

    PubMed

    Edmonds, Jennifer W; Weston, Nathaniel B; Joye, Samantha B; Mou, Xiaozhen; Moran, Mary Ann

    2009-10-01

    Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical changes as porewater salinity was increased from 0 to 10 over 35 days. As reported in Weston et al. (Biogeochemistry, 77:375-408, 62), porewater chemistry was monitored, and cores were sacrificed at 0, 9, 15, and 35 days, at which time we completed terminal restriction fragment length polymorphism and 16S rRNA clone library analyses of sediment microbial communities. The biogeochemical study documented changes in mineralization pathways in response to artificial seawater additions, with a decline in methanogenesis, a transient increase in iron reduction, and finally a dominance of sulfate reduction. Here, we report that, despite these dramatic and significant changes in microbial activity at the biogeochemical level, no significant differences were found between microbial community composition of control vs. seawater-amended treatments for either Bacterial or Archaeal members. Further, taxa in the seawater-amended treatment community did not become more "marine-like" through time. Our experiment suggests that, as seawater intrudes into freshwater sediments, observed changes in metabolic activity and carbon mineralization on the time scale of weeks are driven more by shifts in gene expression and regulation than by changes in the composition of

  11. Inflight microbial analysis technology

    NASA Technical Reports Server (NTRS)

    Pierson, Duane L.; Brown, Harlan D.

    1987-01-01

    This paper provides an assessment of functional characteristics needed in the microbial water analysis system being developed for Space Station. Available technology is reviewed with respect to performing microbial monitoring, isolation, or identification functions. An integrated system composed of three different technologies is presented.

  12. Diel Metagenomics and Metatranscriptomics of Elkhorn Slough Hypersaline Microbial Mat

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    To understand the variation in gene expression associated with the daytime oxygenic phototrophic and nighttime fermentation regimes seen in hypersaline microbial mats, a contiguous mat piece was subjected to sampling at regular intervals over a 24-hour diel period. Additionally, to understand the impact of sulfate reduction on biohydrogen consumption, molybdate was added to a parallel experiment in the same run. 4 metagenome and 12 metatranscriptome Illumina HiSeq lanes were completed over day / night, and control / molybdate experiments. Preliminary comparative examination of noon and midnight metatranscriptomic samples mapped using bowtie2 to reference genomes has revealed several notable results about the dominant mat-building cyanobacterium Microcoleus chthonoplastes PCC 7420. Dominant cyanobacterium M. chthonoplastes PCC 7420 shows expression in several pathways for nitrogen scavenging, including nitrogen fixation. Reads mapped to M. chthonoplastes PCC 7420 shows expression of two starch storage and utilization pathways, one as a starch-trehalose-maltose-glucose pathway, another through UDP-glucose-cellulose-β-1,4 glucan-glucose pathway. The overall trend of gene expression was primarily light driven up-regulation followed by down-regulation in dark, while much of the remaining expression profile appears to be constitutive. Co-assembly of quality-controlled reads from 4 metagenomes was performed using Ray Meta with progressively smaller K-mer sizes, with bins identified and filtered using principal component analysis of coverages from all libraries and a %GC filter, followed by reassembly of the remaining co-assembly reads and binned reads. Despite having relatively similar abundance profiles in each metagenome, this binning approach was able to distinctly resolve bins from dominant taxa, but also sulfate reducing bacteria that are desired for understanding molybdate inhibition. Bins generated from this iterative assembly process will be used for downstream

  13. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics

    PubMed Central

    Burow, Luke C; Woebken, Dagmar; Marshall, Ian PG; Lindquist, Erika A; Bebout, Brad M; Prufert-Bebout, Leslie; Hoehler, Tori M; Tringe, Susannah G; Pett-Ridge, Jennifer; Weber, Peter K; Spormann, Alfred M; Singer, Steven W

    2013-01-01

    Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO2 and H2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS. PMID:23190731

  14. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics.

    PubMed

    Burow, Luke C; Woebken, Dagmar; Marshall, Ian P G; Lindquist, Erika A; Bebout, Brad M; Prufert-Bebout, Leslie; Hoehler, Tori M; Tringe, Susannah G; Pett-Ridge, Jennifer; Weber, Peter K; Spormann, Alfred M; Singer, Steven W

    2013-04-01

    Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO2 and H2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS. PMID:23190731

  15. Methanogenic pathways of coal-bed gas in the Powder River Basin, United States: The geologic factor

    USGS Publications Warehouse

    Flores, R.M.; Rice, C.A.; Stricker, G.D.; Warden, A.; Ellis, M.S.

    2008-01-01

    Coal-bed gas of the Tertiary Fort Union and Wasatch Formations in the Powder River Basin in Wyoming and Montana, U.S. was interpreted as microbial in origin by previous studies based on limited data on the gas and water composition and isotopes associated with the coal beds. To fully evaluate the microbial origin of the gas and mechanisms of methane generation, additional data for 165 gas and water samples from 7 different coal-bed methane-bearing coal-bed reservoirs were collected basinwide and correlated to the coal geology and stratigraphy. The C1/(C2 + C3) ratio and vitrinite reflectance of coal and organic shale permitted differentiation between microbial gas and transitional thermogenic gas in the central part of the basin. Analyses of methane ??13C and ??D, carbon dioxide ??13C, and water ??D values indicate gas was generated primarily from microbial CO2 reduction, but with significant gas generated by microbial methyl-type fermentation (aceticlastic) in some areas of the basin. Microbial CO2 reduction occurs basinwide, but is generally dominant in Paleocene Fort Union Formation coals in the central part of the basin, whereas microbial methyl-type fermentation is common along the northwest and east margins. Isotopically light methane ??13C is distributed along the basin margins where ??D is also depleted, indicating that both CO2-reduction and methyl-type fermentation pathways played major roles in gas generation, but gas from the latter pathway overprinted gas from the former pathway. More specifically, along the northwest basin margin gas generation by methyl-type fermentation may have been stimulated by late-stage infiltration of groundwater recharge from clinker areas, which flowed through highly fractured and faulted coal aquifers. Also, groundwater recharge controlled a change in gas composition in the shallow Eocene Wasatch Formation with the increase of nitrogen and decrease of methane composition of the coal-bed gas. Other geologic factors, such as

  16. Microbial astronauts: assembling microbial communities for advanced life support systems

    NASA Technical Reports Server (NTRS)

    Roberts, M. S.; Garland, J. L.; Mills, A. L.

    2004-01-01

    Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

  17. Microbial astronauts: assembling microbial communities for advanced life support systems.

    PubMed

    Roberts, M S; Garland, J L; Mills, A L

    2004-02-01

    Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

  18. [Microbial denitrogenation of fuel oil].

    PubMed

    Li, Shan-shan; Ma, Ting; Li, Guo-qiang; Liang, Feng-lai; Liu, Ru-lin

    2006-12-01

    The amount of organic nitrides contained in fuel oil is smaller than the one of organic sulfur compounds, but the existence of them is enough to affect the invariability of oil product greatly , and has a big effect on the color of oil. They also contribute to catalyst poisoning during the refining of crude oil, thus reducing the catalyzing rate of the catalyst and increasing process costs. Further more, some nitrogen organic compounds possess mutagenic and toxic activities. The combustion of these contaminants form nitrogen oxides (NOx), releasing of which to the air will cause the formation of acid rain and hence to air pollution. The classical hydroprocessing methods of nitrogen removal are costly and complicated, so the scientists are more and more interested in microbial denitrogenation. The aspects as follows are introduced, including the aromatic nitrogen compounds of fuel oil, the varieties of denitrogenation techincs, the classes of microbial denitrogenation and its biochemical pathways, molecular genetics developments of carbazole-degradative genes, and our opinion of the research direction in the future.

  19. Microbial Changes during Pregnancy, Birth, and Infancy

    PubMed Central

    Nuriel-Ohayon, Meital; Neuman, Hadar; Koren, Omry

    2016-01-01

    Several healthy developmental processes such as pregnancy, fetal development, and infant development include a multitude of physiological changes: weight gain, hormonal, and metabolic changes, as well as immune changes. In this review, we present an additional important factor which both influences and is affected by these physiological processes—the microbiome. We summarize the known changes in microbiota composition at a variety of body sites including gut, vagina, oral cavity, and placenta, throughout pregnancy, fetal development, and early childhood. There is still a lot to be discovered; yet several pieces of research point to the healthy desired microbial changes. Future research is likely to unravel precise roles and mechanisms of the microbiota in gestation; perhaps linking the metabolic, hormonal, and immune changes together. Although some research has started to link microbial dysbiosis and specific microbial populations with unhealthy pregnancy complications, it is important to first understand the context of the natural healthy microbial changes occurring. Until recently the placenta and developing fetus were considered to be germ free, containing no apparent microbiome. We present multiple study results showing distinct microbiota compositions in the placenta and meconium, alluding to early microbial colonization. These results may change dogmas and our overall understanding of the importance and roles of microbiota from the beginning of life. We further review the main factors shaping the infant microbiome—modes of delivery, feeding, weaning, and exposure to antibiotics. Taken together, we are starting to build a broader understanding of healthy vs. abnormal microbial alterations throughout major developmental time-points. PMID:27471494

  20. Microbial Changes during Pregnancy, Birth, and Infancy.

    PubMed

    Nuriel-Ohayon, Meital; Neuman, Hadar; Koren, Omry

    2016-01-01

    Several healthy developmental processes such as pregnancy, fetal development, and infant development include a multitude of physiological changes: weight gain, hormonal, and metabolic changes, as well as immune changes. In this review, we present an additional important factor which both influences and is affected by these physiological processes-the microbiome. We summarize the known changes in microbiota composition at a variety of body sites including gut, vagina, oral cavity, and placenta, throughout pregnancy, fetal development, and early childhood. There is still a lot to be discovered; yet several pieces of research point to the healthy desired microbial changes. Future research is likely to unravel precise roles and mechanisms of the microbiota in gestation; perhaps linking the metabolic, hormonal, and immune changes together. Although some research has started to link microbial dysbiosis and specific microbial populations with unhealthy pregnancy complications, it is important to first understand the context of the natural healthy microbial changes occurring. Until recently the placenta and developing fetus were considered to be germ free, containing no apparent microbiome. We present multiple study results showing distinct microbiota compositions in the placenta and meconium, alluding to early microbial colonization. These results may change dogmas and our overall understanding of the importance and roles of microbiota from the beginning of life. We further review the main factors shaping the infant microbiome-modes of delivery, feeding, weaning, and exposure to antibiotics. Taken together, we are starting to build a broader understanding of healthy vs. abnormal microbial alterations throughout major developmental time-points. PMID:27471494

  1. Sulfide-Driven Microbial Electrosynthesis

    SciTech Connect

    Gong, YM; Ebrahim, A; Feist, AM; Embree, M; Zhang, T; Lovley, D; Zengler, K

    2013-01-01

    Microbial electrosynthesis, the conversion of carbon dioxide to organic molecules using electricity, has recently been demonstrated for acetogenic microorganisms, such as Sporomusa ovata. The energy for reduction of carbon dioxide originates from the hydrolysis of water on the anode, requiring a sufficiently low potential. Here we evaluate the use of sulfide as an electron source for microbial electrosynthesis. Abiotically oxidation of sulfide on the anode yields two electrons. The oxidation product, elemental sulfur, can be further oxidized to sulfate by Desulfobulbus propionicus, generating six additional electrons in the process. The eight electrons generated from the combined abiotic and biotic steps were used to reduce carbon dioxide to acetate on a graphite cathode by Sporomusa ovata at a rate of 24.8 mmol/day.m(2). Using a strain of Desulfuromonas as biocatalyst on the anode resulted in an acetate production rate of 49.9 mmol/day.m(2), with a Coulombic efficiency of over 90%. These results demonstrate that sulfide can serve effectively as an alternative electron donor for microbial electrosynthesis.

  2. Anode Biofilms of Geoalkalibacter ferrihydriticus Exhibit Electrochemical Signatures of Multiple Electron Transport Pathways.

    PubMed

    Yoho, Rachel A; Popat, Sudeep C; Rago, Laura; Guisasola, Albert; Torres, César I

    2015-11-17

    Thriving under alkaliphilic conditions, Geoalkalibacter ferrihydriticus (Glk. ferrihydriticus) provides new applications in treating alkaline waste streams as well as a possible new model organism for microbial electrochemistry. We investigated the electrochemical response of biofilms of the alkaliphilic anode-respiring bacterium (ARB) Glk. ferrihydriticus voltammetry (CV), electrochemical impedance spectroscopy (EIS), and chronoamperometry. We observed there to be at least four dominant electron transfer pathways, with their contribution to the overall current produced dependent on the set anode potential. These pathways appear to be manifested at midpoint potentials of approximately -0.14 V, -0.2 V, -0.24 V, and -0.27 V vs standard hydrogen electrode. The individual contributions of the pathways change upon equilibration from a set anode potential to another anode potential. Additionally, the contribution of each pathway to the overall current produced is reversible when the anode potential is changed back to the original set potential. The pathways involved in anode respiration in Glk. ferrihydriticus biofilms follow a similar, but more complicated, pattern as compared to those in the model ARB, Geobacter sulfurreducens. This greater diversity of electron transport pathways in Glk. ferrihydriticus could be related to its wider metabolic capability (e.g., higher pH and larger set of possible substrates, among others). PMID:26488071

  3. Anode Biofilms of Geoalkalibacter ferrihydriticus Exhibit Electrochemical Signatures of Multiple Electron Transport Pathways.

    PubMed

    Yoho, Rachel A; Popat, Sudeep C; Rago, Laura; Guisasola, Albert; Torres, César I

    2015-11-17

    Thriving under alkaliphilic conditions, Geoalkalibacter ferrihydriticus (Glk. ferrihydriticus) provides new applications in treating alkaline waste streams as well as a possible new model organism for microbial electrochemistry. We investigated the electrochemical response of biofilms of the alkaliphilic anode-respiring bacterium (ARB) Glk. ferrihydriticus voltammetry (CV), electrochemical impedance spectroscopy (EIS), and chronoamperometry. We observed there to be at least four dominant electron transfer pathways, with their contribution to the overall current produced dependent on the set anode potential. These pathways appear to be manifested at midpoint potentials of approximately -0.14 V, -0.2 V, -0.24 V, and -0.27 V vs standard hydrogen electrode. The individual contributions of the pathways change upon equilibration from a set anode potential to another anode potential. Additionally, the contribution of each pathway to the overall current produced is reversible when the anode potential is changed back to the original set potential. The pathways involved in anode respiration in Glk. ferrihydriticus biofilms follow a similar, but more complicated, pattern as compared to those in the model ARB, Geobacter sulfurreducens. This greater diversity of electron transport pathways in Glk. ferrihydriticus could be related to its wider metabolic capability (e.g., higher pH and larger set of possible substrates, among others).

  4. Quantifying microbial activity in deep subsurface sediments using a tritium based hydrognease enzyme assay

    NASA Astrophysics Data System (ADS)

    Adhikari, R.; Nickel, J.; Kallmeyer, J.

    2012-12-01

    Microbial life is widespread in Earth's subsurface and estimated to represent a significant fraction of Earth's total living biomass. However, very little is known about subsurface microbial activity and its fundamental role in biogeochemical cycles of carbon and other biologically important elements. Hydrogen is one of the most important elements in subsurface anaerobic microbial metabolism. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways. They either consume or produce protons for ATP synthesis. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy generating metabolic processes to electron acceptors such as CO2 or sulfate. H2ase enzyme targets a key metabolic compound in cellular metabolism therefore the assay can be used as a measure for total microbial activity without the need to identify any specific metabolic process. Using the highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey, in marine sediments of the Barents Sea and in deep subseafloor sediments from the Nankai Trough. H2ase activity could be quantified at all depths of all sites but the activity distribution varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3d-1 down to a depth of 1.60 m. At all sites the sulfate reduction rate profile followed the upper part of the H2ase activity profile until sulfate reduction reached the minimum detection limit (ca. 10 pmol cm-3d-1). H2ase activity could still be quantified after the decline of sulfate reduction, indicating that

  5. Relating nanomaterial properties and microbial toxicity

    SciTech Connect

    Suresh, Anil K; Pelletier, Dale A; Doktycz, Mitchel John

    2013-01-01

    Nanomaterials are meeting diverse needs in consumer and industrial products. Metal and metal oxide nanoparticles are among the most commonly used materials and their potential for adversely affecting environmental systems raises concern. Complex microbial consortia underlie environmental processes, and the potential toxicity of nanoparticles to microbial systems, and the consequent impacts on trophic balances, is particularly worrisome. The diverse array of metal and metal oxides, the different sizes and shapes that can be prepared and the variety of possible surface coatings complicate toxicity assessments. Further complicating toxicity interpretations are the diversity of microbial systems and their metabolic capabilities. Here, we review various studies focused on nanoparticle-microbial interactions in an effort to correlate the physical-chemical properties of engineered metal and metal oxide nanoparticles to their biological response. Gaining a predictive understanding of nanoparticle toxicity, based on the physical-chemical properties of the material, will be key to the design and responsible use of nanotechnologies. General conclusions regarding the parent material of the nanoparticle and nanoparticle s size and shape on potential toxicity can be made. However, the surface coating of the material, which can be altered significantly by environmental conditions, can ameliorate or promote microbial toxicity. Understanding nanoparticle transformations and how the nanoparticle surface can be designed to control toxicity represents a key area for further study. Additionally, the vast array of microbial species and their intrinsic metabolic capabilities complicates extrapolations of nanoparticle toxicity. A molecular-based understanding of the various microbial responses to nanoparticle-induced stress is needed. Ultimately, to interpret the effect and eventual fate of engineered materials in the environment, an understanding of the relationship between nanoparticle

  6. Exploring the response of West Siberian wetland methane emissions to potential future changes in climate, vegetation, and soil microbial metabolism

    NASA Astrophysics Data System (ADS)

    Bohn, Theodore; Kaplan, Jed; Lettenmaier, Dennis

    2015-04-01

    Methane emissions from northern peatlands depend strongly on environmental conditions, wetland plant species assemblages (via root zone oxidation and plant-aided transport), and soil microbial behavior (via metabolic pathways). While the responses of wetland methane emissions to potential future climate change have been extensively explored, the effects of future changes in plant species and soil microbial metabolism are not as well studied. We ran the Variable Infiltration Capacity (VIC) land surface model over the West Siberian Lowland (WSL), with methane emissions parameters that vary spatially with dominant plant species, and forced with outputs from 32 CMIP5 models for the RCP4.5 scenario. We compared the effects of changes in climate and vegetation (in terms of both leaf area index and species abundances) on predicted wetland CH4 emissions for the period 2071-2100, relative to the period 1981-2010. We also explored possible acclimatization of soil microbial communities to these changes. We evaluated the effects of climate change, potential northward migration of plant species, and potential microbial acclimatization on end-of-century methane emissions over the WSL, in terms of both total annual emissions and the spatial distribution of emissions. Our results suggest that, while microbial acclimatization mitigates the effects of warmer temperatures, the northward migration of plant species enhances the response to warming (due to plant-aided transport), and additionally shifts the location of maximal emissions northward, where the possible release of ancient carbon with permafrost thaw is a concern. Our work indicates the importance of better constraining the responses of wetland plants and soil microbial communities to changes in climate as they are critical determinants of the region's future methane emissions.

  7. Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation in microbial fuel cells.

    PubMed

    Zhang, Baogang; Tian, Caixing; Liu, Ying; Hao, Liting; Liu, Ye; Feng, Chuanping; Liu, Yuqian; Wang, Zhongli

    2015-03-01

    Simultaneous microbial and electrochemical reductions of vanadium (V) with bioelectricity generation were realized in microbial fuel cells (MFCs). With initial V(V) concentrations of 75 mg/l and 150 mg/l in anolyte and catholyte, respectively, stable power output of 419±11 mW/m(2) was achieved. After 12h operation, V(V) concentration in the catholyte decreased to the value similar to that of the initial one in the anolyte, meanwhile it was nearly reduced completely in the anolyte. V(IV) was the main reduction product, which subsequently precipitated, acquiring total vanadium removal efficiencies of 76.8±2.9%. Microbial community analysis revealed the emergence of the new species of Deltaproteobacteria and Bacteroidetes as well as the enhanced Spirochaetes mainly functioned in the anode. This study opens new pathways to successful remediation of vanadium contamination.

  8. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

    SciTech Connect

    Ruvindy, Rendy; White, Richard A.; Neilan, Brett A.; Burns, Brendan P.

    2015-05-29

    Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

  9. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics.

    PubMed

    Ruvindy, Rendy; White, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

    2016-01-01

    Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats. PMID:26023869

  10. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics.

    PubMed

    Ruvindy, Rendy; White, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

    2016-01-01

    Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

  11. Mineralization and Detoxification of the Carcinogenic Azo Dye Congo Red and Real Textile Effluent by a Polyurethane Foam Immobilized Microbial Consortium in an Upflow Column Bioreactor.

    PubMed

    Lade, Harshad; Govindwar, Sanjay; Paul, Diby

    2015-06-01

    A microbial consortium that is able to grow in wheat bran (WB) medium and decolorize the carcinogenic azo dye Congo red (CR) was developed. The microbial consortium was immobilized on polyurethane foam (PUF). Batch studies with the PUF-immobilized microbial consortium showed complete removal of CR dye (100 mg·L-1) within 12 h at pH 7.5 and temperature 30 ± 0.2 °C under microaerophilic conditions. Additionally, 92% American Dye Manufactureing Institute (ADMI) removal for real textile effluent (RTE, 50%) was also observed within 20 h under the same conditions. An upflow column reactor containing PUF-immobilized microbial consortium achieved 99% CR dye (100 mg·L-1) and 92% ADMI removal of RTE (50%) at 35 and 20 mL·h-l flow rates, respectively. Consequent reduction in TOC (83 and 79%), COD (85 and 83%) and BOD (79 and 78%) of CR dye and RTE were also observed, which suggested mineralization. The decolorization process was traced to be enzymatic as treated samples showed significant induction of oxidoreductive enzymes. The proposed biodegradation pathway of the dye revealed the formation of lower molecular weight compounds. Toxicity studies with a plant bioassay and acute tests indicated that the PUF-immobilized microbial consortium favors detoxification of the dye and textile effluents. PMID:26086710

  12. Mineralization and Detoxification of the Carcinogenic Azo Dye Congo Red and Real Textile Effluent by a Polyurethane Foam Immobilized Microbial Consortium in an Upflow Column Bioreactor

    PubMed Central

    Lade, Harshad; Govindwar, Sanjay; Paul, Diby

    2015-01-01

    A microbial consortium that is able to grow in wheat bran (WB) medium and decolorize the carcinogenic azo dye Congo red (CR) was developed. The microbial consortium was immobilized on polyurethane foam (PUF). Batch studies with the PUF-immobilized microbial consortium showed complete removal of CR dye (100 mg·L−1) within 12 h at pH 7.5 and temperature 30 ± 0.2 °C under microaerophilic conditions. Additionally, 92% American Dye Manufactureing Institute (ADMI) removal for real textile effluent (RTE, 50%) was also observed within 20 h under the same conditions. An upflow column reactor containing PUF-immobilized microbial consortium achieved 99% CR dye (100 mg·L−1) and 92% ADMI removal of RTE (50%) at 35 and 20 mL·h−l flow rates, respectively. Consequent reduction in TOC (83 and 79%), COD (85 and 83%) and BOD (79 and 78%) of CR dye and RTE were also observed, which suggested mineralization. The decolorization process was traced to be enzymatic as treated samples showed significant induction of oxidoreductive enzymes. The proposed biodegradation pathway of the dye revealed the formation of lower molecular weight compounds. Toxicity studies with a plant bioassay and acute tests indicated that the PUF-immobilized microbial consortium favors detoxification of the dye and textile effluents. PMID:26086710

  13. Mineralization and Detoxification of the Carcinogenic Azo Dye Congo Red and Real Textile Effluent by a Polyurethane Foam Immobilized Microbial Consortium in an Upflow Column Bioreactor.

    PubMed

    Lade, Harshad; Govindwar, Sanjay; Paul, Diby

    2015-06-16

    A microbial consortium that is able to grow in wheat bran (WB) medium and decolorize the carcinogenic azo dye Congo red (CR) was developed. The microbial consortium was immobilized on polyurethane foam (PUF). Batch studies with the PUF-immobilized microbial consortium showed complete removal of CR dye (100 mg·L-1) within 12 h at pH 7.5 and temperature 30 ± 0.2 °C under microaerophilic conditions. Additionally, 92% American Dye Manufactureing Institute (ADMI) removal for real textile effluent (RTE, 50%) was also observed within 20 h under the same conditions. An upflow column reactor containing PUF-immobilized microbial consortium achieved 99% CR dye (100 mg·L-1) and 92% ADMI removal of RTE (50%) at 35 and 20 mL·h-l flow rates, respectively. Consequent reduction in TOC (83 and 79%), COD (85 and 83%) and BOD (79 and 78%) of CR dye and RTE were also observed, which suggested mineralization. The decolorization process was traced to be enzymatic as treated samples showed significant induction of oxidoreductive enzymes. The proposed biodegradation pathway of the dye revealed the formation of lower molecular weight compounds. Toxicity studies with a plant bioassay and acute tests indicated that the PUF-immobilized microbial consortium favors detoxification of the dye and textile effluents.

  14. Systems Biology of Microbial Exopolysaccharides Production

    PubMed Central

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran. PMID:26734603

  15. Environments that Induce Synthetic Microbial Ecosystems

    PubMed Central

    Klitgord, Niels; Segrè, Daniel

    2010-01-01

    Interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. Both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. Understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. In parallel to natural communities, it is possible to explore interactions in artificial microbial ecosystems, e.g. pairs of genetically engineered mutualistic strains. Here we computationally generate artificial microbial ecosystems without re-engineering the microbes themselves, but rather by predicting their growth on appropriately designed media. We use genome-scale stoichiometric models of metabolism to identify media that can sustain growth for a pair of species, but fail to do so for one or both individual species, thereby inducing putative symbiotic interactions. We first tested our approach on two previously studied mutualistic pairs, and on a pair of highly curated model organisms, showing that our algorithms successfully recapitulate known interactions, robustly predict new ones, and provide novel insight on exchanged molecules. We then applied our method to all possible pairs of seven microbial species, and found that it is always possible to identify putative media that induce commensalism or mutualism. Our analysis also suggests that symbiotic interactions may arise more readily through environmental fluctuations than genetic modifications. We envision that our approach will help generate microbe-microbe interaction maps useful for understanding microbial consortia dynamics and evolution, and for exploring the full potential of natural metabolic pathways for metabolic engineering applications. PMID:21124952

  16. Systems Biology of Microbial Exopolysaccharides Production.

    PubMed

    Ates, Ozlem

    2015-01-01

    Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran. PMID:26734603

  17. Expansion of Microbial Forensics.

    PubMed

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

    2016-08-01

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

  18. Microbial Cell Imaging

    SciTech Connect

    Doktycz, Mitchel John; Sullivan, Claretta; Mortensen, Ninell P; Allison, David P

    2011-01-01

    Atomic force microscopy (AFM) is finding increasing application in a variety of fields including microbiology. Until the emergence of AFM, techniques for ivnestigating processes in single microbes were limited. From a biologist's perspective, the fact that AFM can be used to generate high-resolution images in buffers or media is its most appealing feature as live-cell imaging can be pursued. Imaging living cells by AFM allows dynamic biological events to be studied, at the nanoscale, in real time. Few areas of biological research have as much to gain as microbiology from the application of AFM. Whereas the scale of microbes places them near the limit of resolution for light microscopy. AFM is well suited for the study of structures on the order of a micron or less. Although electron microscopy techniques have been the standard for high-resolution imaging of microbes, AFM is quickly gaining favor for several reasons. First, fixatives that impair biological activity are not required. Second, AFM is capable of detecting forces in the pN range, and precise control of the force applied to the cantilever can be maintained. This combination facilitates the evaluation of physical characteristics of microbes. Third, rather than yielding the composite, statistical average of cell populations, as is the case with many biochemical assays, the behavior of single cells can be monitored. Despite the potential of AFM in microbiology, there are several limitations that must be considered. For example, the time required to record an image allows for the study of gross events such as cell division or membrane degradation from an antibiotic but precludes the evaluation of biological reactions and events that happen in just fractions of a second. Additionally, the AFM is a topographical tool and is restricted to imaging surfaces. Therefore, it cannot be used to look inside cells as with opticla and transmission electron microscopes. other practical considerations are the limitation on

  19. Fracture Sealing with Microbially-Induced Calcium Carbonate Precipitation: A Field Study.

    PubMed

    Phillips, Adrienne J; Cunningham, Alfred B; Gerlach, Robin; Hiebert, Randy; Hwang, Chiachi; Lomans, Bartholomeus P; Westrich, Joseph; Mantilla, Cesar; Kirksey, Jim; Esposito, Richard; Spangler, Lee

    2016-04-01

    A primary environmental risk from unconventional oil and gas development or carbon sequestration is subsurface fluid leakage in the near wellbore environment. A potential solution to remediate leakage pathways is to promote microbially induced calcium carbonate precipitation (MICP) to plug fractures and reduce permeability in porous materials. The advantage of microbially induced calcium carbonate precipitation (MICP) over cement-based sealants is that the solutions used to promote MICP are aqueous. MICP solutions have low viscosities compared to cement, facilitating fluid transport into the formation. In this study, MICP was promoted in a fractured sandstone layer within the Fayette Sandstone Formation 340.8 m below ground surface using conventional oil field subsurface fluid delivery technologies (packer and bailer). After 24 urea/calcium solution and 6 microbial (Sporosarcina pasteurii) suspension injections, the injectivity was decreased (flow rate decreased from 1.9 to 0.47 L/min) and a reduction in the in-well pressure falloff (>30% before and 7% after treatment) was observed. In addition, during refracturing an increase in the fracture extension pressure was measured as compared to before MICP treatment. This study suggests MICP is a promising tool for sealing subsurface fractures in the near wellbore environment. PMID:26911511

  20. Fracture Sealing with Microbially-Induced Calcium Carbonate Precipitation: A Field Study.

    PubMed

    Phillips, Adrienne J; Cunningham, Alfred B; Gerlach, Robin; Hiebert, Randy; Hwang, Chiachi; Lomans, Bartholomeus P; Westrich, Joseph; Mantilla, Cesar; Kirksey, Jim; Esposito, Richard; Spangler, Lee

    2016-04-01

    A primary environmental risk from unconventional oil and gas development or carbon sequestration is subsurface fluid leakage in the near wellbore environment. A potential solution to remediate leakage pathways is to promote microbially induced calcium carbonate precipitation (MICP) to plug fractures and reduce permeability in porous materials. The advantage of microbially induced calcium carbonate precipitation (MICP) over cement-based sealants is that the solutions used to promote MICP are aqueous. MICP solutions have low viscosities compared to cement, facilitating fluid transport into the formation. In this study, MICP was promoted in a fractured sandstone layer within the Fayette Sandstone Formation 340.8 m below ground surface using conventional oil field subsurface fluid delivery technologies (packer and bailer). After 24 urea/calcium solution and 6 microbial (Sporosarcina pasteurii) suspension injections, the injectivity was decreased (flow rate decreased from 1.9 to 0.47 L/min) and a reduction in the in-well pressure falloff (>30% before and 7% after treatment) was observed. In addition, during refracturing an increase in the fracture extension pressure was measured as compared to before MICP treatment. This study suggests MICP is a promising tool for sealing subsurface fractures in the near wellbore environment.

  1. T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut.

    PubMed

    Brugman, Sylvia; Schneeberger, Kerstin; Witte, Merlijn; Klein, Mark R; van den Bogert, Bartholomeus; Boekhorst, Jos; Timmerman, Harro M; Boes, Marianne L; Kleerebezem, Michiel; Nieuwenhuis, Edward E S

    2014-01-01

    Dysbiosis of the intestinal microbial community is considered a risk factor for development of chronic intestinal inflammation as well as other diseases such as diabetes, obesity and even cancer. Study of the innate and adaptive immune pathways controlling bacterial colonization has however proven difficult in rodents, considering the extensive cross-talk between bacteria and innate and adaptive immunity. Here, we used the zebrafish to study innate and adaptive immune processes controlling the microbial community. Zebrafish lack a functional adaptive immune system in the first weeks of life, enabling study of the innate immune system in the absence of adaptive immunity. We show that in wild type zebrafish, the initial lack of adaptive immunity associates with overgrowth of Vibrio species (a group encompassing fish and human pathogens), which is overcome upon adaptive immune development. In Rag1-deficient zebrafish (lacking adaptive immunity) Vibrio abundance remains high, suggesting that adaptive immune processes indeed control Vibrio species. Using cell transfer experiments, we confirm that adoptive transfer of T lymphocytes, but not B lymphocytes into Rag1-deficient recipients suppresses outgrowth of Vibrio. In addition, ex vivo exposure of intestinal T lymphocytes to Rag1-deficient microbiota results in increased interferon-gamma expression by these T lymphocytes, compared to exposure to wild type microbiota. In conclusion, we show that T lymphocytes control microbial composition by effectively suppressing the outgrowth of Vibrio species in the zebrafish intestine. PMID:25536157

  2. Biostimulation of Iron Reduction and Uranium Immobilization: Microbial and Mineralogical Controls

    SciTech Connect

    Joel E. Kostka; Lainie Petrie; Nadia North; David L. Balkwill; Joseph W. Stucki; Lee Kerkhof

    2004-03-17

    The overall objective of our project is to understand the microbial and geochemical mechanisms controlling the reduction and immobilization of U(VI) during biostimulation in subsurface sediments of the Field Research Center (FRC) which are cocontaminated with uranium and nitrate. The focus will be on activity of microbial populations (metal- and nitrate-reducing bacteria) and iron minerals which are likely to make strong contributions to the fate of uranium during in situ bioremediation. The project will: (1) quantify the relationships between active members of the microbial communities, iron mineralogy, and nitrogen transformations in the field and in laboratory incubations under a variety of biostimulation conditions, (2) purify and physiologically characterize new model metal-reducing bacteria isolated from moderately acidophilic FRC subsurface sediments, and (3) elucidate the biotic and abiotic mechanisms by which FRC aluminosilicate clay minerals are reduced and dissolved under environmental conditions resembling those during biostimulation. Active microbial communities will be assessed using quantitative molecular techniques along with geochemical measurements to determine the different terminal-electron-accepting pathways. Iron minerals will be characterized using a suite of physical, spectroscopic, and wet chemical methods. Monitoring the activity and composition of the denitrifier community in parallel with denitrification intermediates during nitrate removal will provide a better understanding of the indirect effects of nitrate reduction on uranium speciation. Through quantification of the activity of specific microbial populations and an in-depth characterization of Fe minerals likely to catalyze U sorption/precipitation, we will provide important inputs for reaction-based biogeochemical models which will provide the basis for development of in situ U bioremediation strategies. In collaboration with Jack Istok and Lee Krumholz, we have begun to study the

  3. Methylerythritol Phosphate Pathway of Isoprenoid Biosynthesis

    PubMed Central

    Zhao, Lishan; Chang, Wei-chen; Xiao, Youli; Liu, Hung-wen; Liu, Pinghua

    2016-01-01

    Isoprenoids are a class of natural products with more than 50,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway (the methylerythritol phosphate (MEP) pathway) and a modified mevalonate (MVA) pathway. In this review, mechanistic insights on the MEP pathway enzymes are summarized. Since many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both the MVA and MEP pathway-based synthetic biology efforts are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations. PMID:23746261

  4. Mass dependent stable isotope fractionation of mercury during mer mediated microbial degradation of monomethylmercury

    NASA Astrophysics Data System (ADS)

    Kritee, K.; Barkay, Tamar; Blum, Joel D.

    2009-03-01

    Controlling bioaccumulation of toxic monomethylmercury (MMHg) in aquatic food chains requires differentiation between biotic and abiotic pathways that lead to its production and degradation. Recent mercury (Hg) stable isotope measurements of natural samples suggest that Hg isotope ratios can be a powerful proxy for tracing dominant Hg transforming pathways in aquatic ecosystems. Specifically, it has been shown that photo-degradation of MMHg causes both mass dependent (MDF) and mass independent fractionation (MIF) of Hg isotopes. Because the extent of MDF and MIF observed in natural samples (e.g., fish, soil and sediments) can potentially be used to determine the relative importance of pathways leading to MMHg accumulation, it is important to determine the potential role of microbial pathways in contributing to the fractionation, especially MIF, observed in these samples. This study reports the extent of fractionation of Hg stable isotopes during degradation of MMHg to volatile elemental Hg and methane via the microbial Hg resistance ( mer) pathway in Escherichia coli carrying a mercury resistance ( mer) genetic system on a multi-copy plasmid. During experimental microbial degradation of MMHg, MMHg remaining in reactors became progressively heavier (increasing δ202Hg) with time and underwent mass dependent Rayleigh fractionation with a fractionation factor α202/198 = 1.0004 ± 0.0002 (2SD). However, MIF was not observed in any of the microbial MMHg degradation experiments indicating that the isotopic signature left by mer mediated MMHg degradation is significantly different from fractionation observed during DOC mediated photo-degradation of MMHg. Additionally, a clear suppression of Hg isotope fractionation, both during reduction of Hg(II) and degradation of MMHg, was observed when the cell densities increased, possibly due to a reduction in substrate bioavailability. We propose a multi-step framework for understanding the extent of fractionation seen in our MMHg

  5. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  6. Modular construction of a functional artificial epothilone polyketide pathway.

    PubMed

    Osswald, Corina; Zipf, Gregor; Schmidt, Gisela; Maier, Josef; Bernauer, Hubert S; Müller, Rolf; Wenzel, Silke C

    2014-10-17

    Natural products of microbial origin continue to be an important source of pharmaceuticals and agrochemicals exhibiting potent activities and often novel modes of action. Due to their inherent structural complexity chemical synthesis is often hardly possible, leaving fermentation as the only viable production route. In addition, the pharmaceutical properties of natural products often need to be optimized for application by sophisticated medicinal chemistry and/or biosynthetic engineering. The latter requires a detailed understanding of the biosynthetic process and genetic tools to modify the producing organism that are often unavailable. Consequently, heterologous expression of complex natural product pathways has been in the focus of development over recent years. However, piecing together existing DNA cloned from natural sources and achieving efficient expression in heterologous circuits represent several limitations that can be addressed by synthetic biology. In this work we have redesigned and reassembled the 56 kb epothilone biosynthetic gene cluster from Sorangium cellulosum for expression in the high GC host Myxococcus xanthus. The codon composition was adapted to a modified codon table for M. xanthus, and unique restriction sites were simultaneously introduced and others eliminated from the sequence in order to permit pathway assembly and future interchangeability of modular building blocks from the epothilone megasynthetase. The functionality of the artificial pathway was demonstrated by successful heterologous epothilone production in M. xanthus at significant yields that have to be improved in upcoming work. Our study sets the stage for future engineering of epothilone biosynthesis and production optimization using a highly flexible assembly strategy. PMID:23654254

  7. Microbial Source Tracking

    EPA Science Inventory

    Bacterial indicators of fecal contamination provide the basis for assessing the microbial quality of environmental waters. While the indicator concept has overall helped reduce waterborne outbreaks in recreational waters, the public health value of currently used indicator bacter...

  8. Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data.

    PubMed

    Vital, Marius; Howe, Adina Chuang; Tiedje, James M

    2014-04-22

    Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial Genome database. Genomes of 225 bacteria with a potential to produce butyrate were identified, including many previously unknown candidates. The majority of candidates belong to distinct families within the Firmicutes, but members of nine other phyla, especially from Actinobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, and Thermotogae, were also identified as potential butyrate producers. The established gene catalogue (3,055 entries) was used to screen for butyrate synthesis pathways in 15 metagenomes derived from stool samples of healthy individuals provided by the HMP (Human Microbiome Project) consortium. A high percentage of total genomes exhibited a butyrate-producing pathway (mean, 19.1%; range, 3.2% to 39.4%), where the acetyl-coenzyme A (CoA) pathway was the most prevalent (mean, 79.7% of all pathways), followed by the lysine pathway (mean, 11.2%). Diversity analysis for the acetyl-CoA pathway showed that the same few firmicute groups associated with several Lachnospiraceae and Ruminococcaceae were dominating in most individuals, whereas the other pathways were associated primarily with Bacteroidetes. IMPORTANCE Microbiome research has revealed new, important roles of our gut microbiota for

  9. Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment.

    PubMed

    Valentín-Vargas, Alexis; Root, Robert A; Neilson, Julia W; Chorover, Jon; Maier, Raina M

    2014-12-01

    Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost

  10. Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

    PubMed Central

    Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

    2014-01-01

    Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost

  11. Dialogue between E. coli free radical pathways and the mitochondria of C. elegans

    PubMed Central

    Govindan, J. Amaranath; Jayamani, Elamparithi; Zhang, Xinrui; Mylonakis, Eleftherios; Ruvkun, Gary

    2015-01-01

    The microbial world presents a complex palette of opportunities and dangers to animals, which have developed surveillance and response strategies to hints of microbial intent. We show here that the mitochondrial homeostatic response pathway of the nematode Caenorhabditis elegans responds to Escherichia coli mutations that activate free radical detoxification pathways. Activation of C. elegans mitochondrial responses could be suppressed by additional mutations in E. coli, suggesting that C. elegans responds to products of E. coli to anticipate challenges to its mitochondrion. Out of 50 C. elegans gene inactivations known to mediate mitochondrial defense, we found that 7 genes were required for C. elegans response to a free radical producing E. coli mutant, including the bZip transcription factor atfs-1 (activating transcription factor associated with stress). An atfs-1 loss-of-function mutant was partially resistant to the effects of free radical-producing E. coli mutant, but a constitutively active atfs-1 mutant growing on wild-type E. coli inappropriately activated the pattern of mitochondrial responses normally induced by an E. coli free radical pathway mutant. Carbonylated proteins from free radical-producing E. coli mutant may directly activate the ATFS-1/bZIP transcription factor to induce mitochondrial stress response: feeding C. elegans with H2O2-treated E. coli induces the mitochondrial unfolded protein response, and inhibition of a gut peptide transporter partially suppressed C. elegans response to free radical damaged E. coli. PMID:26392561

  12. Dialogue between E. coli free radical pathways and the mitochondria of C. elegans.

    PubMed

    Govindan, J Amaranath; Jayamani, Elamparithi; Zhang, Xinrui; Mylonakis, Eleftherios; Ruvkun, Gary

    2015-10-01

    The microbial world presents a complex palette of opportunities and dangers to animals, which have developed surveillance and response strategies to hints of microbial intent. We show here that the mitochondrial homeostatic response pathway of the nematode Caenorhabditis elegans responds to Escherichia coli mutations that activate free radical detoxification pathways. Activation of C. elegans mitochondrial responses could be suppressed by additional mutations in E. coli, suggesting that C. elegans responds to products of E. coli to anticipate challenges to its mitochondrion. Out of 50 C. elegans gene inactivations known to mediate mitochondrial defense, we found that 7 genes were required for C. elegans response to a free radical producing E. coli mutant, including the bZip transcription factor atfs-1 (activating transcription factor associated with stress). An atfs-1 loss-of-function mutant was partially resistant to the effects of free radical-producing E. coli mutant, but a constitutively active atfs-1 mutant growing on wild-type E. coli inappropriately activated the pattern of mitochondrial responses normally induced by an E. coli free radical pathway mutant. Carbonylated proteins from free radical-producing E. coli mutant may directly activate the ATFS-1/bZIP transcription factor to induce mitochondrial stress response: feeding C. elegans with H2O2-treated E. coli induces the mitochondrial unfolded protein response, and inhibition of a gut peptide transporter partially suppressed C. elegans response to free radical damaged E. coli.

  13. Ocean microbial metagenomics

    NASA Astrophysics Data System (ADS)

    Kerkhof, Lee J.; Goodman, Robert M.

    2009-09-01

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

  14. The Lectin Pathway of Complement and Rheumatic Heart Disease

    PubMed Central

    Beltrame, Marcia Holsbach; Catarino, Sandra Jeremias; Goeldner, Isabela; Boldt, Angelica Beate Winter; de Messias-Reason, Iara José

    2014-01-01

    The innate immune system is the first line of host defense against infection and is comprised of humoral and cellular mechanisms that recognize potential pathogens within minutes or hours of entry. The effector components of innate immunity include epithelial barriers, phagocytes, and natural killer cells, as well as cytokines and the complement system. Complement plays an important role in the immediate response against microorganisms, including Streptococcus sp. The lectin pathway is one of three pathways by which the complement system can be activated. This pathway is initiated by the binding of mannose-binding lectin (MBL), collectin 11 (CL-K1), and ficolins (Ficolin-1, Ficolin-2, and Ficolin-3) to microbial surface oligosaccharides and acetylated residues, respectively. Upon binding to target molecules, MBL, CL-K1, and ficolins form complexes with MBL-associated serine proteases 1 and 2 (MASP-1 and MASP-2), which cleave C4 and C2 forming the C3 convertase (C4b2a). Subsequent activation of complement cascade leads to opsonization, phagocytosis, and lysis of target microorganisms through the formation of the membrane-attack complex. In addition, activation of complement may induce several inflammatory effects, such as expression of adhesion molecules, chemotaxis and activation of leukocytes, release of reactive oxygen species, and secretion of cytokines and chemokines. In this chapter, we review the general aspects of the structure, function, and genetic polymorphism of lectin-pathway components and discuss most recent understanding on the role of the lectin pathway in the predisposition and clinical progression of Rheumatic Fever. PMID:25654073

  15. Microbial Fuel Cells and Microbial Electrolyzers

    SciTech Connect

    Borole, Abhijeet P

    2015-01-01

    Microbial Fuel Cells and microbial electrolyzers represent an upcoming technology for production of electricity and hydrogen using a hybrid electrocatalytic-biocatalytic approach. The combined catalytic efficiency of these processes has potential to make this technology highly efficient among the various renewable energy production alternatives. This field has attracted electrochemists, biologists and many other disciplines due to its potential to contribute to the energy, water and environment sectors. A brief introduction to the technology is provided followed by current research needs from a bioelectrochemical perspective. Insights into the operation and limitations of these systems achieved via cyclic voltammetry and impedance spectroscopy are discussed along with the power management needs to develop the application aspects. Besides energy production, other potential applications in bioenergy, bioelectronics, chemical production and remediation are also highlighted.

  16. Microbial Production of Isoprenoids Enabled by Synthetic Biology

    PubMed Central

    Immethun, Cheryl M.; Hoynes-O’Connor, Allison G.; Balassy, Andrea; Moon, Tae Seok

    2013-01-01

    Microorganisms transform inexpensive carbon sources into highly functionalized compounds without toxic by-product generation or significant energy consumption. By redesigning the natural biosynthetic pathways in an industrially suited host, microbial cell factories can produce complex compounds for a variety of industries. Isoprenoids include many medically important compounds such as antioxidants and anticancer and antimalarial drugs, all of which have been produced microbially. While a biosynthetic pathway could be simply transferred to the production host, the titers would become economically feasible when it is rationally designed, built, and optimized through synthetic biology tools. These tools have been implemented by a number of research groups, with new tools pledging further improvements in yields and expansion to new medically relevant compounds. This review focuses on the microbial production of isoprenoids for the health industry and the advancements though synthetic biology. PMID:23577007

  17. Introducing a new bioengineered bug: Methylobacterium extorquens tuned as a microbial bioplastic factory.

    PubMed

    Höfer, Philipp; Vermette, Patrick; Groleau, Denis

    2011-01-01

    Discussion on and use of methanol as chemical feedstock and as alternative fuel has gained momentum during the past years. Consequently, microorganism and product design based on ''methylotrophism'' is in vogue as reflected by increasing research and development activities in methanol-related areas. A recent example of microorganism and product development is the use of recombinant Methylobacterium extorquens ATCC 55366 strains in the production of second generation biopolyesters. Feeding n-alkenoic acids in addition to methanol yielded functionalized polyhydroxyalkanoates (PHAs) and uncovered how M. extorquens copes with fatty acids. While some parts of the degradation pathway remain unclear, possible metabolic routes are suggested that may explain the significant loss of double bonds prior to polymerization of PHA precursors and occurrence of odd-numbered monomers derived from even-numbered n-alkenoic acids. In addition, microbial discoloration upon fatty acid feeding is discussed and future directions for further genetic modification of M. extorquens are provided. 

  18. Biodesulfurization: a model system for microbial physiology research.

    PubMed

    Kilbane, John J; Stark, Benjamin

    2016-08-01

    Biological desulfurization (biodesulfurization) of dibenzothiophene (DBT) by the 4S pathway is a model system for an enviromentally benign way to lower the sulfur content of petroleum. Despite a large amount of effort the efficiency of the 4S pathway is still too low for a commercial oil biodesulfurization process, but the 4S pathway could potentially be used now for commercial processes to produce surfactants, antibiotics, polythioesters and other chemicals and for the detoxification of some chemical warfare agents. Proteins containing disulfide bonds are resistant to temperature, pH, and solvents, but the production of disulfide-rich proteins in microbial hosts is challenging. The study of the 4S pathway can provide insights as to how to maximize the production of disulfide-rich proteins. Engineering of the operon encoding the 4S pathway to contain a greater content of methionine and cysteine may be able to link use of DBT as a sole sulfur source to increasing 4S pathway activity by increasing the nutritional demand for sulfur. This strategy could result in the development of biocatalysts suitable for use in an oil biodesulfurization process, but the study of the 4S pathway can also lead to a better understanding of microbial physiology to optimize activity of a mult-step co-factor-requiring pathway, as well as the production of highly stable industrially relevant enzymes for numerous applications. PMID:27357405

  19. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

    PubMed

    Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B; Bayer, Christoph; Thorseth, Ingunn H; Schleper, Christa; Steen, Ida H; Ovreas, Lise

    2014-09-01

    Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments.

  20. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

    PubMed

    Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B; Bayer, Christoph; Thorseth, Ingunn H; Schleper, Christa; Steen, Ida H; Ovreas, Lise

    2014-09-01

    Deep-sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high-temperature venting systems have been studied extensively, the microbiotas associated with low-temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian-Greenland Sea, applying an integrated 'omics' approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction-independent three-domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico-chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments. PMID:24112684

  1. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    PubMed

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  2. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    PubMed

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems. PMID:26509157

  3. Microbial community transitions across the deep sediment-basement interface

    NASA Astrophysics Data System (ADS)

    Labonté, J.; Lever, M. A.; Orcutt, B.

    2015-12-01

    Previous studies of microbial abundance and geochemistry in deep marine sediments indicate a stimulation of microbial activity near the sediment-basement interface; yet, the extent to which microbial communities in bottom sediments and underlying crustal habitats interact is unclear. We conducted tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement samples to try to identify patterns in microbial community shifts across sediment-basement interfaces, focusing on samples from the subsurface of the Juan de Fuca Ridge flank (IODP Expedition 327). Our results demonstrate that sediment and the basaltic crust harbor microbial communities that are phylogenetically connected, but the eveness is characteristic of the environment. We will discuss the microbial community transitions that occur horizontally along fluid flow pathways and vertically across the sediment basement interface, as well as the possible implications regarding the controls of microbial community composition along deep sediment-basement interfaces in hydrothermal systems. We will also highlight efforts to overcome sample contamination in crustal subsurface samples.

  4. Pathways of tau fibrillization.

    PubMed

    Kuret, Jeff; Chirita, Carmen N; Congdon, Erin E; Kannanayakal, Theresa; Li, Guibin; Necula, Mihaela; Yin, Haishan; Zhong, Qi

    2005-01-01

    New methods for analyzing tau fibrillization have yielded insights into the biochemical transitions involved in the process. Here we review the parallels between the sequential progression of tau fibrillization observed macroscopically in Alzheimer's disease (AD) lesions and the pathway of tau aggregation observed in vitro with purified tau preparations. In addition, pharmacological agents for further dissection of fibrillization mechanism and lesion formation are discussed. PMID:15615636

  5. Microbial field pilot study

    SciTech Connect

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

    1991-01-01

    The objective of this project is to perform a microbially enhanced oil recovery field pilot test in the Southeast Vassar Vertz Sand Unit (SEVVSU) in Payne County, Oklahoma. Indigenous, anaerobic, nitrate-reducing bacteria will be stimulated to selectively plug flow paths which have been preferentially swept by a prior waterflood. This will force future flood water to invade bypassed regions or the reservoir and increase sweep efficiency. Injection of nutrient stimulates the growth and metabolism of reservoir bacteria, which produces beneficial products to enhance oil recovery. Sometimes, chemical treatments are used to clean or condition injection water. Such a chemical treatment has been initiated by Sullivan and Company at the Southeast Vassar Vertz Sand Unit. The unit injection water was treated with a mixture of water, methanol, isopropyl alcohol, and three proprietary chemicals. To determine if the chemicals would have an impact on the pilot, it was important to determine the effects of the chemical additives on the growth and metabolism of the bacteria from wells in this field. Two types of media were used: a mineral salts medium with molasses and nitrate, and this medium with 25 ppm of the treatment chemicals added. Samples were collected anaerobically from each of two wells, 1A-9 and 7-2. A sample from each well was inoculated and cultured in the broth tubes of molasses-nitrate medium with and without the chemicals. Culturing temperature was 35{degrees}C. Absorbance, pressure and cell number were checked to determine if the chemicals affected the growth and metabolism of bacteria in the brine samples. 12 figs.

  6. Deep subsurface microbial processes

    USGS Publications Warehouse

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

    1995-01-01

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

  7. Humans differ in their personal microbial cloud.

    PubMed

    Meadow, James F; Altrichter, Adam E; Bateman, Ashley C; Stenson, Jason; Brown, G Z; Green, Jessica L; Bohannan, Brendan J M

    2015-01-01

    Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 10(6) biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5-4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

  8. Humans differ in their personal microbial cloud

    PubMed Central

    Altrichter, Adam E.; Bateman, Ashley C.; Stenson, Jason; Brown, GZ; Green, Jessica L.; Bohannan, Brendan J.M.

    2015-01-01

    Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud. PMID:26417541

  9. Metabolic interactions and dynamics in microbial communities

    NASA Astrophysics Data System (ADS)

    Segre', Daniel

    Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

  10. Relating nanomaterial properties and microbial toxicity

    NASA Astrophysics Data System (ADS)

    Suresh, Anil K.; Pelletier, Dale A.; Doktycz, Mitchel J.

    2012-12-01

    Metal and metal oxide nanoparticles are among the most commonly used nanomaterials and their potential for adversely affecting environmental systems raises concern. Complex microbial consortia underlie environmental processes, and the potential toxicity of nanoparticles to microbial systems, and the consequent impacts on trophic balances, is particularly worrisome. The diverse array of metal and metal oxides, the different sizes and shapes that can be prepared and the variety of possible surface coatings complicate assessments of toxicity. Further muddling biocidal interpretations are the diversity of microbes and their intrinsic tolerances to stresses. Here, we review a range of studies focused on nanoparticle-microbial interactions in an effort to correlate the physical-chemical properties of engineered metal and metal oxide nanoparticles to their biological response. General conclusions regarding the parent material of the nanoparticle and the nanoparticle's size and shape on potential toxicity can be made. However, the surface coating of the material, which can be altered significantly by environmental conditions, can ameliorate or promote microbial toxicity. Understanding nanoparticle transformations and how the nanoparticle surface can be designed to control toxicity represents a key area for further study. Additionally, the vast array of microbial species and the structuring of these species within communities complicate extrapolations of nanoparticle toxicity in real world settings. Ultimately, to interpret the effect and eventual fate of engineered materials in the environment, an understanding of the relationship between nanoparticle properties and responses at the molecular, cellular and community levels will be essential.

  11. Humans differ in their personal microbial cloud.

    PubMed

    Meadow, James F; Altrichter, Adam E; Bateman, Ashley C; Stenson, Jason; Brown, G Z; Green, Jessica L; Bohannan, Brendan J M

    2015-01-01

    Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 10(6) biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5-4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud. PMID:26417541

  12. Microbial Life in a Liquid Asphalt Desert

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

    Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 107 cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

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

    PubMed

    Chen, Jian; Xie, Huijun; Zhuang, Xuliangli; Zhuang, Guoqiang; Bai, Zhihui; Zhang, Hongxun

    2008-01-01

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

  14. Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

    PubMed Central

    Xie, Wei; Wang, Fengping; Guo, Lei; Chen, Zeling; Sievert, Stefan M; Meng, Jun; Huang, Guangrui; Li, Yuxin; Yan, Qingyu; Wu, Shan; Wang, Xin; Chen, Shangwu; He, Guangyuan; Xiao, Xiang; Xu, Anlong

    2011-01-01

    Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin–Benson–Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative

  15. Linking Microbial Activity with Arsenic Fate during Cow Dung Disposal of Arsenic-Bearing Wastes

    NASA Astrophysics Data System (ADS)

    Clancy, T. M.; Reddy, R.; Tan, J.; Hayes, K. F.; Raskin, L.

    2014-12-01

    To address widespread arsenic contamination of drinking water sources numerous technologies have been developed to remove arsenic. All technologies result in the production of an arsenic-bearing waste that must be evaluated and disposed in a manner to limit the potential for environmental release and human exposure. One disposal option that is commonly recommended for areas without access to landfills is the mixing of arsenic-bearing wastes with cow dung. These recommendations are made based on the ability of microorganisms to create volatile arsenic species (including mono-, di-, and tri-methylarsine gases) to be diluted in the atmosphere. However, most studies of environmental microbial communities have found only a small fraction (<0.1 %) of the total arsenic present in soils or rice paddies is released via volatilization. Additionally, past studies often have not monitored arsenic release in the aqueous phase. Two main pathways for microbial arsenic volatilization are known and include methylation of arsenic during methanogenesis and methylation by arsenite S-adenosylmethionine methyltransferase. In this study, we compare the roles of these two pathways in arsenic volatilization and aqueous mobilization through mesocosm experiments with cow dung and arsenic-bearing wastes produced during drinking water treatment in West Bengal, India. Arsenic in gaseous, aqueous, and solid phases was measured. Consistent with previous reports, less than 0.02% of the total arsenic present was volatilized. A much higher amount (~5%) of the total arsenic was mobilized into the liquid phase. Through the application of molecular tools, including 16S rRNA sequencing and quantification of gene transcripts involved in methanogenesis, this study links microbial community activity with arsenic fate in potential disposal environments. These results illustrate that disposal of arsenic-bearing wastes by mixing with cow dung does not achieve its end goal of promoting arsenic volatilization

  16. Microbial toxicity and characterization of DNAN (bio)transformation product mixtures.

    PubMed

    Olivares, Christopher I; Sierra-Alvarez, Reyes; Alvarez-Nieto, Cristina; Abrell, Leif; Chorover, Jon; Field, Jim A

    2016-07-01

    2,4-Dinitroanisole (DNAN) is an emerging insensitive munitions compound. It undergoes rapid (bio)transformation in soils and anaerobic sludge. The primary transformation pathway catalyzed by a combination of biotic and abiotic factors is nitrogroup reduction followed by coupling of reactive intermediates to form azo-dimers. Additional pathways include N-acetylation and O-demethoxylation. Toxicity due to (bio)transformation products of DNAN has received little attention. In this study, the toxicity of DNAN (bio)transformation monomer products and azo-dimer and trimer surrogates to acetoclastic methanogens and the marine bioluminescent bacterium, Allivibrio fischeri, were evaluated. Methanogens were severely inhibited by 3-nitro-4-methoxyaniline (MENA), with a 50%-inhibiting concentration (IC50) of 25 μM, which is more toxic than DNAN with the same assay, but posed a lower toxicity to Allivibrio fischeri (IC50 = 219 μM). On the other hand, N-(5-amino-2-methoxyphenyl) acetamide (Ac-DAAN) was the least inhibitory test-compound for both microbial targets. Azo-dimer and trimer surrogates were very highly toxic to both microbial systems, with a toxicity similar or stronger than that of DNAN. A semi-quantitative LC-QTOF-MS method was employed to determine product mixture profiles at different stages of biotransformation, and compared with the microbial toxicity of the product-mixtures formed. Methanogenic toxicity increased due to putative reactive nitroso-intermediates as DNAN was reduced. However, the inhibition later attenuated as dimers became the predominant products in the mixtures. In contrast, A. fischeri tolerated the initial biotransformation products but were highly inhibited by the predominant azo-dimer products formed at longer incubation times, suggesting these ultimate products are more toxic than DNAN.

  17. Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

    PubMed Central

    Nagpal, Sunil; Haque, Mohammed Monzoorul; Mande, Sharmila S.

    2016-01-01

    Background The overall metabolic/functional potential of any given environmental niche is a function of the sum total of genes/proteins/enzymes that are encoded and expressed by various interacting microbes residing in that niche. Consequently, prior (collated) information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectly (re)constructing/ inferring the metabolic/ functional potential of a given microbial community (given its taxonomic abundance profile). In this study, we present Vikodak—a multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one or more environmental sample datasets. With the underlying assumptions of co-metabolism and independent contributions of different microbes in a community, a concerted effort has been made to accommodate microbial co-existence patterns in various modules incorporated in Vikodak. Results Validation experiments on over 1400 metagenomic samples have confirmed the utility of Vikodak in (a) deciphering enzyme abundance profiles of any KEGG metabolic pathway, (b) functional resolution of distinct metagenomic environments, (c) inferring patterns of functional interaction between resident microbes, and (d) automating statistical comparison of functional features of studied microbiomes. Novel features incorporated in Vikodak also facilitate automatic removal of false positives and spurious functional predictions. Conclusions With novel provisions for comprehensive functional analysis, inclusion of microbial co-existence pattern based algorithms, automated inter-environment comparisons; in-depth analysis of individual metabolic pathways and greater flexibilities at the user end, Vikodak is expected to be an important value addition to the family of existing tools for 16S based function prediction. Availability and Implementation A web implementation of Vikodak

  18. [Effects of nitrogen addition on red soil microbes in the Cinnamomum camphora plantation].

    PubMed

    Yu, Pei-Yi; Zhu, Fan; Su, Shao-Feng; Wang, Zhi-Yong; Yan, Wen-De

    2013-08-01

    In order to investigate the effects of nitrogen addition on the red soil microbial communities in Cinnamomum camphora plantation, three treatments of nitrogen addition were designated as control (N0: 0 g x m(-2)), low nitrogen (N1: 5 g x m(-2)) and high nitrogen (N2 :15 g x m(-2)). Soil microbial numbers, microbial biomass carbon (C), biomass N and microbial community functional diversity were analyzed using the methods of plate counting, chloroform fumigation and BIOLOG system, respectively. The results showed that the numbers of bacteria in N1 and N2 were significantly higher than the control 1 month after nitrogen addition, but significantly lower than the control 13 months after nitrogen addition, and the number of fungi and actinomycetes were not significantly changed after nitrogen addition. The soil microbial biomass C, N increased with the increase of nitrogen at 1 month, but the soil microbial biomass C increased significantly 13 months after nitrogen addition when compared with 1 month after nitrogen addition. The soil microbial biomass N was lower 13 months after nitrogen addition when compared with 1 month after nitrogen addition, but the difference was not significant (P > 0.05). The variation of the carbon utilization efficiency of soil microbial communities was resulted from the nitrogen addition. The indices of Shannon index, Simpson index and McIntosh index were calculated to show the differences in nitrogen treatments and in times, which turned out to be insignificant.

  19. Microbial bioinformatics 2020.

    PubMed

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! PMID:27471065

  20. Microbial reduction of uranium

    USGS Publications Warehouse

    Lovley, D.R.; Phillips, E.J.P.; Gorby, Y.A.; Landa, E.R.

    1991-01-01

    REDUCTION of the soluble, oxidized form of uranium, U(VI), to insoluble U(IV) is an important mechanism for the immobilization of uranium in aquatic sediments and for the formation of some uranium ores1-10. U(VI) reduction has generally been regarded as an abiological reaction in which sulphide, molecular hydrogen or organic compounds function as the reductant1,2,5,11. Microbial involvement in U(VI) reduction has been considered to be limited to indirect effects, such as microbial metabolism providing the reduced compounds for abiological U(VI) reduction and microbial cell walls providing a surface to stimulate abiological U(VI) reduction1,12,13. We report here, however, that dissimilatory Fe(III)-reducing microorganisms can obtain energy for growth by electron transport to U(VI). This novel form of microbial metabolism can be much faster than commonly cited abiological mechanisms for U(VI) reduction. Not only do these findings expand the known potential terminal electron acceptors for microbial energy transduction, they offer a likely explanation for the deposition of uranium in aquatic sediments and aquifers, and suggest a method for biological remediation of environments contaminated with uranium.

  1. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    PubMed Central

    2013-01-01

    The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research. PMID:23957006

  2. qPCR analysis of carbon, nitrogen, and arsenic cycling in Zetaproteobacteria-dominated microbial mats

    NASA Astrophysics Data System (ADS)

    Jesser, K. J.; Fullerton, H.; Hilton, T. S.; Kimber, J.; Hager, K.; Moyer, C. L.

    2013-12-01

    The recently discovered Zetaproteobacteria represent a novel class of Proteobacteria which oxidize Fe(II) to Fe(III) to fix CO2 at hydrothermal vents. Zetaproteobacteria were first discovered at Lo'ihi Seamount, located 35 km southeast of the big island of Hawai'i and characterized by low-temperature diffuse hydrothermal vents. The hydrothermal vents at Lo'ihi are surrounded by luxuriant iron-rich microbial mats dominated by Zetaproteobacteria. We aim to use real-time quantitative PCR (qPCR) to quantify functional genes associated with the microbial carbon, nitrogen, and arsenic cycles in complex Zetaproteobacteria- dominated iron mat communities. Unique qPCR primer sets have been developed based on Illumina next-generation sequence data from an iron mat collected in 2009 at Lo'ihi. These primers target the sequences for arsenate reductase and nitrite reductase, genes associated with arsenic detoxification and denitrification, respectively. Additionally, we are utilizing published primer sets to quantify genes associated with autotrophic carbon and nitrogen fixation pathways. Genomic DNA was isolated from microbial mats at multiple vent sites with varying temperatures and fluid flow during our 2013 expedition to Lo'ihi. The qPCR data for these samples can be used to draw correlations among fine scale mat structures and nutrient cycling processes across diverse mat morphologies, as previous research has identified unique microbial communities and metabolic strategies associated with distinct mat morphologies. This work will enable us to better identify samples for further molecular analysis, and may provide insights into the evolutionary history and metabolic functionality of various mat morphotypes. We hypothesize that Zetaproteobacteria act as ecosystem engineers, driving the structure and function of iron mat ecosystems.

  3. Monitoring and Modeling Microbial Sulfate Reduction and Inhibition in a Mesoscale Tank Experiment

    NASA Astrophysics Data System (ADS)

    Hubbard, C. G.; Wu, Y.; Li, L.; Piceno, Y. M.; Cheng, Y.; Bill, M.; Coates, J. D.; Andersen, G. L.; Conrad, M. E.; Ajo Franklin, J. B.

    2014-12-01

    Subsurface biogeochemical cycling at the field-scale is controlled by a complex interplay between hydrological, geochemical and biological parameters. Mesoscale tank experiments can help to bridge the gap in complexity and understanding between well constrained batch and column experiments, and the interpretation of field data. In this contribution we present the results of a tank experiment investigating microbial sulfate reduction and inhibition in a porous media (20-30 mesh Ottawa sand). Microbial sulfate reduction is a process of wide biogeochemical significance, including in the context of oil reservoirs where the generation of sulfide can result in corrosion of steel infrastructure and additional downstream processing. Inhibition of sulfate reduction is therefore a high priority for this industry. Tracer experiments were conducted at the start and end of the experiment to constrain flow pathways and heterogeneities. The tank was inoculated with a San Francisco Bay mud/water enrichment utilizing acetate as the electron donor and continuous flow was initiated using bay-water with 10 mM acetate. Samples were taken from an array of 12 steel boreholes and showed spatiotemporal heterogeneities in the development of sulfidogenesis, reaching a peak of ~5 mM dissolved sulfide 71 days after inoculation. 10 mM perchlorate was then added to the influent to inhibit sulfidogenesis and dissolved sulfide decreased to ~0.03 mM by day 95. Stable isotope analysis of dissolved sulfate showed an increase in δ34S by ~10‰ compared with influent values but δ34S did not return to influent values by day 95, which may be indicative of the mixing between new and residual sulfate in the tank. Ongoing microbial community analyses are being used to help constrain microbial metabolisms. Finally, all the data is being integrated into a reactive transport model to better constrain the observed interplay between hydrology, geochemistry and biology.

  4. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  5. The Microbial Olympics.

    PubMed

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

    2012-08-01

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

  6. Clerkship pathway

    PubMed Central

    MacLellan, Anne-Marie; Brailovsky, Carlos; Miller, François; Leboeuf, Sylvie

    2012-01-01

    Abstract Objective To identify factors that help predict success for international medical graduates (IMGs) who train in Canadian residency programs and pass the Canadian certification examinations. Design A retrospective analysis of 58 variables in the files of IMGs who applied to the Collège des médecins du Québec between 2000 and 2008. Setting Quebec. Participants Eight hundred ten IMGs who applied to the Collège des médecins du Québec through either the “equivalency pathway” (ie, starting training at a residency level) or the “clerkship pathway” (ie, relearning at the level of a medical student in the last 2 years of the MD diploma). Main outcome measures Success factors in achieving certification. Data were analyzed using descriptive statistics and ANOVA (analysis of variance). Results International medical graduates who chose the “clerkship pathway” had greater success on certification examinations than those who started at the residency level did. Conclusion There are several factors that influence IMGs’ success on certification examinations, including integration issues, the acquisition of clinical decision-making skills, and the varied educational backgrounds. These factors perhaps can be better addressed by a regular clerkship pathway, in which IMGs benefit from learner-centred teaching and have more time for reflection on and understanding of the North American approach to medical education. The clerkship pathway is a useful strategy for assuring the integration of IMGs in the North American health care system. A 2-year relearning period in medical school at a clinical clerkship level deserves careful consideration. PMID:22859630

  7. Microbial hotspots and hot moments in soil

    NASA Astrophysics Data System (ADS)

    Kuzyakov, Yakov; Blagodatskaya, Evgenia

    2015-04-01

    increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. Finally, we estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil.

  8. Reactome from a WikiPathways Perspective.

    PubMed

    Bohler, Anwesha; Wu, Guanming; Kutmon, Martina; Pradhana, Leontius Adhika; Coort, Susan L; Hanspers, Kristina; Haw, Robin; Pico, Alexander R; Evelo, Chris T

    2016-05-01

    Reactome and WikiPathways are two of the most popular freely available databases for biological pathways. Reactome pathways are centrally curated with periodic input from selected domain experts. WikiPathways is a community-based platform where pathways are created and continually curated by any interested party. The nascent collaboration between WikiPathways and Reactome illustrates the mutual benefits of combining these two approaches. We created a format converter that converts Reactome pathways to the GPML format used in WikiPathways. In addition, we developed the ComplexViz plugin for PathVisio which simplifies looking up complex components. The plugin can also score the complexes on a pathway based on a user defined criterion. This score can then be visualized on the complex nodes using the visualization options provided by the plugin. Using the merged collection of curated and converted Reactome pathways, we demonstrate improved pathway coverage of relevant biological processes for the analysis of a previously described polycystic ovary syndrome gene expression dataset. Additionally, this conversion allows researchers to visualize their data on Reactome pathways using PathVisio's advanced data visualization functionalities. WikiPathways benefits from the dedicated focus and attention provided to the content converted from Reactome and the wealth of semantic information about interactions. Reactome in turn benefits from the continuous community curation available on WikiPathways. The research community at large benefits from the availability of a larger set of pathways for analysis in PathVisio and Cytoscape. The pathway statistics results obtained from PathVisio are significantly better when using a larger set of candidate pathways for analysis. The conversion serves as a general model for integration of multiple pathway resources developed using different approaches. PMID:27203685

  9. Reactome from a WikiPathways Perspective

    PubMed Central

    Bohler, Anwesha; Wu, Guanming; Pradhana, Leontius Adhika; Hanspers, Kristina; Haw, Robin; Pico, Alexander R.

    2016-01-01

    Reactome and WikiPathways are two of the most popular freely available databases for biological pathways. Reactome pathways are centrally curated with periodic input from selected domain experts. WikiPathways is a community-based platform where pathways are created and continually curated by any interested party. The nascent collaboration between WikiPathways and Reactome illustrates the mutual benefits of combining these two approaches. We created a format converter that converts Reactome pathways to the GPML format used in WikiPathways. In addition, we developed the ComplexViz plugin for PathVisio which simplifies looking up complex components. The plugin can also score the complexes on a pathway based on a user defined criterion. This score can then be visualized on the complex nodes using the visualization options provided by the plugin. Using the merged collection of curated and converted Reactome pathways, we demonstrate improved