Microbial Recognition Via Toll-Like Receptor-Dependent and -Independent Pathways Determines the Cytokine Response of Murine Dendritic Cell Subsets to CD40 Triggering

Dendritic cells (DC) can produce Th-polarizing cytokines and direct the class of the adaptive immune response. Microbial stimuli, cytokines, chemokines, and T cell-derived signals all have been shown to trigger cytokine synthesis by DC, but it remains unclear whether these signals are functionally equivalent and whether they determine the nature of the cytokine produced or simply initiate a preprogrammed pattern of cytokine production, which may be DC subtype specific. Here, we demonstrate that microbial and T cell-derived stimuli can synergize to induce production of high levels of IL-12 p70 or IL-10 by individual murine DC subsets but that the choice of cytokine is dictated by the microbial pattern recognition receptor engaged. We show that bacterial components such as CpG-containing DNA or extracts from Mycobacterium tuberculosis predispose CD8alpha(+) and CD8alpha(-)CD4(-) DC to make IL-12 p70. In contrast, exposure of CD8alpha(+), CD4(+) and CD8alpha(-)CD4(-) DC to heat-killed yeasts leads to production of IL-10. In both cases, secretion of high levels of cytokine requires a second signal from T cells, which can be replaced by CD40 ligand. Consistent with their differential effects on cytokine production, extracts from M. tuberculosis promote IL-12 production primarily via Toll-like receptor 2 and an MyD88-dependent pathway, whereas heat-killed yeasts activate DC via a Toll-like receptor 2-, MyD88-, and Toll/IL-1R domain containing protein-independent pathway. These results show that T cell feedback amplifies innate signals for cytokine production by DC and suggest that pattern recognition rather than ontogeny determines the production of cytokines by individual DC subsets.

Hydrocarbon biodegradation and soil microbial community response to repeated oil exposure

Bioremediation strategies continue to be developed to mitigate the environmental impact of petroleum hydrocarbon contamination. This study investigated the ability of soil microbiota, adapted by prior exposure, to biodegrade petroleum. Soils from Barrow Is. (W. Australia), a class A nature reserve and home to Australia’s largest onshore oil field, were exposed to Barrow production oil (50 ml/kg soil) and incubated (25 °C) for successive phases of 61 and 100 days. Controls in which oil was not added at Phase I or II were concurrently studied and all treatments were amended with the same levels of additional nutrient and water to promote microbial activity. Prior exposure resulted in accelerated biodegradation of most, but not all, hydrocarbon constituents in the production oil. Molecular biodegradation parameters measured using gas chromatography–mass spectrometry (GC–MS) showed that several aromatic constituents were degraded more slowly with increased oil history. The unique structural response of the soil microbial community was reflected by the response of different phospholipid fatty acid (PLFA) sub-classes (e.g. branched saturated fatty acids of odd or even carbon number) measured using a ratio termed Barrow PLFA ratio (B-PLFAr). The corresponding values of a previously proposed hydrocarbon degrading alteration index showed a negative correlation with hydrocarbon exposure, highlighting the site specificity of PLFA-based ratios and microbial community dynamics. B-PLFAr values increased with each Phase I and II addition of production oil. The different hydrocarbon biodegradation rates and responses of PLFA subclasses to the Barrow production oil probably relate to the relative bioavailability of production oil hydrocarbons. These different effects suggest preferred structural and functional microbial responses to anticipated contaminants may potentially be engineered by controlled pre-exposure to the same or closely related substrates. The bioremediation of soils freshly contaminated with petroleum could benefit from the addition of exhaustively bioremediated soils rich in biota primed for the impacting hydrocarbons.

Temperature affects microbial decomposition of cadavers (Rattus rattus) in contrasting soils

The ecology of soils associated with dead mammals (i.e. cadavers) is poorly understood. Although temperature and soil type are well known to influence the decomposition of other organic resource patches, the effect of these variables on the degradation of cadavers in soil has received little experimental investigation. To address this, cadavers of juvenile rats (Rattus rattus) were buried in one of three contrasting soils (Sodosol, Rudosol, and Vertosol) from tropical savanna ecosystems in Queensland, Australia and incubated at 29 °C, 22 °C, or 15 °C in a laboratory setting. Cadavers and soils were destructively sampled at intervals of 7 days over an incubation period of 28 days. Measurements of decomposition included cadaver mass loss, carbon dioxide–carbon (CO2–C) evolution, microbial biomass carbon (MBC), protease activity, phosphodiesterase activity, and soil pH, which were all significantly positively affected by cadaver burial. A temperature effect was observed where peaks or differences in decomposition that at occurred at higher temperature would occur at later sample periods at lower temperature. Soil type also had an important effect on some measured parameters. These findings have important implications for a largely unexplored area of soil ecology and nutrient cycling, which are significant for forensic science, cemetery planning and livestock carcass disposal.

Microbial decomposition of skeletal muscle tissue (Ovis aries) in a sandy loam soil at different temperatures

A laboratory experiment was conducted to determine the effect of temperature (2, 12, 22 °C) on the rate of aerobic decomposition of skeletal muscle tissue (Ovis aries) in a sandy loam soil incubated for a period of 42 days. Measurements of decomposition processes included skeletal muscle tissue mass loss, carbon dioxide (CO2) evolution, microbial biomass, soil pH, skeletal muscle tissue carbon (C) and nitrogen (N) content and the calculation of metabolic quotient (qCO2). Incubation temperature and skeletal muscle tissue quality had a significant effect on all of the measured process rates with 2 °C usually much lower than 12 and 22 °C. Cumulative CO2 evolution at 2, 12 and 22 °C equaled 252, 619 and 905 mg CO2, respectively. A significant correlation (P<0.001) was detected between cumulative CO2 evolution and tissue mass loss at all temperatures. Q10s for mass loss and CO2 evolution, which ranged from 1.19 to 3.95, were higher for the lower temperature range (Q10(2– 12 °C)>Q10(12–22 °C)) in the Ovis samples and lower for the low temperature range (Q10(2–12 °C)microbial catabolic requirements at lower temperature.

Valorisation of side streams from wheat milling and confectionery industries for consolidated production and extraction of microbial lipids

Crude enzymes produced via solid state fermentation (SSF) using wheat milling by-products have been employed for both fermentation media production using flour-rich waste (FRW) streams and lysis of Rhodosporidium toruloides yeast cells. Filter sterilization of crude hydrolysates was more beneficial than heat sterilization regarding yeast growth and microbial oil production. The initial carbon to free amino nitrogen ratio of crude hydrolysates was optimized (80.2 g/g) in fed-batch cultures of R. toruloides leading to a total dry weight of 61.2 g/L with microbial oil content of 61.8 % (w/w). Employing a feeding strategy where the glucose concentration was maintained in the range of 12.2 – 17.6 g/L led to the highest productivity (0.32 g/L∙h). The crude enzymes produced by SSF were utilised for yeast cell treatment leading to simultaneous release of around 80% of total lipids in the broth and production of a hydrolysate suitable as yeast extract replacement.

Acute benefits of the microbial-derived isoflavone metabolite equol on arterial stiffness in men prospectively recruited according to equol producer phenotype: a double-blind randomized controlled trial

There is much speculation with regard to the potential cardioprotective benefits of equol, a microbial-derived metabolite of the isoflavone daidzein, which is produced in the large intestine after soy intake in 30% of Western populations. Although cross-sectional and retrospective data support favorable associations between the equol producer (EP) phenotype and cardiometabolic health, few studies have prospectively recruited EPs to confirm this association. The aim was to determine whether the acute vascular benefits of isoflavones differ according to EP phenotype and subsequently investigate the effect of providing commercially produced S-(–)equol to non-EPs. We prospectively recruited male EPs and non-EPs (n = 14/ group) at moderate cardiovascular risk into a double-blind, placebocontrolled crossover study to examine the acute effects of soy isoflavones (80-mg aglycone equivalents) on arterial stiffness [carotid-femoral pulse-wave velocity (cfPWV)], blood pressure, endothelial function (measured by using the EndoPAT 2000; Itamar Medical), and nitric oxide at baseline (0 h) and 6 and 24 h after intake. In a separate assessment, non-EPs consumed 40 mg S-(–)equol with identical vascular measurements performed 2 h after intake. After soy intake, cfPWV significantly improved in EPs at 24 h (cfPWV change from 0 h: isoflavone, 20.2 6 0.2 m/s; placebo, 0.6 6 0.2 m/s; P , 0.01), which was significantly associated with plasma equol concentrations (R = 20.36, P = 0.01). No vascular effects were observed in EPs at 6 h or in non-EPs at any time point. Similarly, no benefit of commercially produced S-(–)equol was observed in non-EPs despite mean plasma equol concentrations reaching 3.2 mmol/L. Acute soy intake improved cfPWV in EPs, equating to an 11–12% reduced risk of cardiovascular disease if sustained. However, a single dose of commercially produced equol had no cardiovascular benefits in non-EPs. These data suggest that the EP phenotype is critical in unlocking the vascular benefits of equol in men, and long-term trials should focus on confirming the implications of EP phenotype on cardiovascular health. This trial was registered at clinicaltrials.gov as NCT01530893. Am J Clin Nutr doi: 10.3945/ajcn.115.125690.

Formulation of fermentation media from flour-rich waste streams for microbial lipid production by Lipomyces starkeyi

Flour-rich waste (FRW) and by-product streams generated by bakery, confectionery and wheat milling plants could be employed as the sole raw materials for generic fermentation media production, suitable for microbial oil synthesis. Wheat milling by-products were used in solid state fermentations (SSF) of Aspergillus awamori for the production of crude enzymes, mainly glucoamylase and protease. Enzyme-rich SSF solids were subsequently employed for hydrolysis of FRW streams into nutrient-rich fermentation media. Batch hydrolytic experiments using FRW concentrations up to 205 g/L resulted in higher than 90%(w/w) starch to glucose conversion yields and 40% (w/w) total Kjeldahl nitrogen to free amino nitro-gen conversion yields. Starch to glucose conversion yields of 98.2, 86.1 and 73.4% (w/w) were achieved when initial FRW concentrations of 235, 300 and 350 g/L were employed in fed-batch hydrolytic experiments, respectively. Crude hydrolysates were used as fermentation media in shake flask cultures with the oleaginous yeast Lipomyces starkeyi DSM 70296 reaching a total dry weight of 30.5 g/L with a microbial oil content of 40.4% (w/w), higher than that achieved in synthetic media. Fed-batch bioreactor cultures led to a total dry weight of 109.8 g/L with a microbial oil content of 57.8% (w/w) and productivity of 0.4 g/L/h.

Design and techno-economic evaluation of microbial oil production as a renewable resource for biodiesel and oleochemical production

Experimental results from the open literature have been employed for the design and techno-economic evaluation of four process flowsheets for the production of microbial oil or biodiesel. The fermentation of glucose-based media using the yeast strain Rhodosporidium toruloides has been considered. Biodiesel production was based on the exploitation of either direct transesterification (without extraction of lipids from microbial biomass) or indirect transesterifaction of extracted microbial oil. When glucose-based renewable resources are used as carbon source for an annual production capacity of 10,000 t microbial oil and zero cost of glucose (assuming development of integrated biorefineries in existing industries utilising waste or by-product streams) the estimated unitary cost of purified microbial oil is $3.4/kg. Biodiesel production via indirect transesterification of extracted microbial oil proved more cost-competitive process compared to the direct conversion of dried yeast cells. For a price of glucose of $400/t oil production cost and biodiesel production cost are estimated to be $5.5/kg oil and $5.9/kg biodiesel, correspondingly. Industrial implementation of microbial oil production from oleaginous yeast is strongly dependent on the feedstock used and on the fermentation stage where significantly higher productivities and final microbial oil concentrations should be achieved.

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

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