Colonization-induced host-gut microbial metabolic interaction

The gut microbiota enhances the host's metabolic capacity for processing nutrients and drugs and modulate the activities of multiple pathways in a variety of organ systems. We have probed the systemic metabolic adaptation to gut colonization for 20 days following exposure of axenic mice (n = 35) to a typical environmental microbial background using high-resolution (1)H nuclear magnetic resonance (NMR) spectroscopy to analyze urine, plasma, liver, kidney, and colon (5 time points) metabolic profiles. Acquisition of the gut microbiota was associated with rapid increase in body weight (4%) over the first 5 days of colonization with parallel changes in multiple pathways in all compartments analyzed. The colonization process stimulated glycogenesis in the liver prior to triggering increases in hepatic triglyceride synthesis. These changes were associated with modifications of hepatic Cyp8b1 expression and the subsequent alteration of bile acid metabolites, including taurocholate and tauromuricholate, which are essential regulators of lipid absorption. Expression and activity of major drug-metabolizing enzymes (Cyp3a11 and Cyp2c29) were also significantly stimulated. Remarkably, statistical modeling of the interactions between hepatic metabolic profiles and microbial composition analyzed by 16S rRNA gene pyrosequencing revealed strong associations of the Coriobacteriaceae family with both the hepatic triglyceride, glucose, and glycogen levels and the metabolism of xenobiotics. These data demonstrate the importance of microbial activity in metabolic phenotype development, indicating that microbiota manipulation is a useful tool for beneficially modulating xenobiotic metabolism and pharmacokinetics in personalized health care. IMPORTANCE: Gut bacteria have been associated with various essential biological functions in humans such as energy harvest and regulation of blood pressure. Furthermore, gut microbial colonization occurs after birth in parallel with other critical processes such as immune and cognitive development. Thus, it is essential to understand the bidirectional interaction between the host metabolism and its symbionts. Here, we describe the first evidence of an in vivo association between a family of bacteria and hepatic lipid metabolism. These results provide new insights into the fundamental mechanisms that regulate host-gut microbiota interactions and are thus of wide interest to microbiological, nutrition, metabolic, systems biology, and pharmaceutical research communities. This work will also contribute to developing novel strategies in the alteration of host-gut microbiota relationships which can in turn beneficially modulate the host metabolism.

Prebiotics modulate the effects of antibiotics on gut microbial diversity and functioning in vitro

Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs), which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation—another method used to modulate gut composition and function—could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre), inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria) or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.

Characterization of para-Nitrophenol-degrading bacterial communities in river water by using functional markers and stable isotope probing

Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [13C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations.

Tissue culture propagation alters plant-microbe interactions in tobacco rhizosphere

We have compared properties of roots from different lines (genotypes) of tobacco raised either in tissue culture or grown from seed. The different lines included unmodified plants and plants modified to express reduced activity of the enzyme cinnamoyl-CoA reductase, which has a pivotal role in lignin biosynthesis. The size and structure of the rhizosphere microbial community, characterized by adenosine triphosphate and phospholipid fatty acid analyses, were related to root chemistry (specifically the soluble carbohydrate concentration) and decomposition rate of the roots. The root material from unmodified plants decomposed faster following tissue culture compared with seed culture, and the faster decomposing material had significantly higher soluble carbohydrate concentrations. These observations are linked to the larger microbial biomass and greater diversity of the rhizosphere communities of tissue culture propagated plants.

Microbial perchlorate reduction: A precise laboratory determination of the chlorine isotope fractionation and its possible biochemical basis

Perchlorate-reducing bacteria fractionate chlorine stable isotopes giving a powerful approach to monitor the extent of microbial consumption of perchlorate in contaminated sites undergoing remediation or natural perchlorate containing sites. This study reports the full experimental data and methodology used to re-evaluate the chlorine isotope fractionation of perchlorate reduction in duplicate culture experiments of Azospira suillum strain PS at 37 degrees C (Delta Cl-37(Cr)--ClO4-) previously reported, without a supporting data set by Coleman et al. [Coleman, M.L., Ader, M., Chaudhuri, S., Coates,J.D., 2003. Microbial Isotopic Fractionation of Perchlorate Chlorine. Appl. Environ. Microbiol. 69, 4997-5000] in a reconnaissance study, with the goal of increasing the accuracy and precision of the isotopic fractionation determination. The method fully described here for the first time, allows the determination of a higher precision Delta Cl-37(Cl)--ClO4- value, either from accumulated chloride content and isotopic composition or from the residual perchlorate content and isotopic composition. The result sets agree perfectly, within error, giving average Delta Cl-37(Cl)--ClO4- = -14.94 +/- 0.15%omicron. Complementary use of chloride and perchlorate data allowed the identification and rejection of poor quality data by applying mass and isotopic balance checks. This precise Delta Cl-37(Cl)--ClO4-, value can serve as a reference point for comparison with future in situ or microcosm studies but we also note its similarity to the theoretical equilibrium isotopic fractionation between a hypothetical chlorine species of redox state +6 and perchlorate at 37 degrees C and suggest that the first electron transfer during perchlorate reduction may occur at isotopic equilibrium between art enzyme-bound chlorine and perchlorate. (C) 2008 Elsevier B.V. All rights reserved.

Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes

The aim of this study was to examine interrelationships between functional biochemical and microbial indicators of soil quality, and their suitability to differentiate areas under contrasting agricultural management regimes. The study included five 0.8 ha areas on a sandy-loam soil which had received contrasting fertility and cropping regimes over a 5 year period. These were organically managed vegetable, vegetable -cereal and arable rotations, an organically managed grass clover ley, and a conventional cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. All of the biochemical analyses, including light fraction organic matter (LFOM) C and N, labile organic N (LON), dissolved organic N and water-soluble carbohydrates showed significant differences between the areas, although the nature of the relationships between the areas varied between the different parameters, and were not related to differences in total soil organic matter content. The clearest differences were seen in LFOM C and N and LON, which were higher in the organic arable area relative to the other areas. In the case of the biological parameters, there were differences between the areas for biomass-N, ATP, chitin content, and the ratios of ATP: biomass and basal respiration: biomass. For these parameters, the precise relationships between the areas varied. However, relative to the conventionally managed area, areas under organic management generally had lower biomass-N and higher ATP contents. Arbuscular mycorrhizal fungus colonization potential was extremely low in the conventional area relative to the organic areas. Further, metabolic diversity and microbial community level physiological profiles, determined by analysis of microbial community metabolism using Biolog GN plates and the activities of eight key nutrient cycling enzymes, grouped the organic areas together, but separated them from the conventional area. We conclude that microbial parameters are more effective and consistent indicators of management induced changes to soil quality than biochemical parameters, and that a variety of biochemical and microbial analyses should be used when considering the impact of management on soil quality. (C) 2004 Elsevier Ltd. All rights reserved.

Liming upland grassland: the effects on earthworm communities and the chemical characteristics of carbon in casts

Different earthworm species have different tolerances of acid soil conditions, and the application of lime to upland grassland to improve the grazing quality may therefore alter the size and diversity of the earthworm community. Altering soil properties may also affect the chemical characteristics of organic C in earthworm casts. We surveyed the earthworm community of an upland grassland in southern Scotland at the outset of annual lime applications, and after 3 years, and used C-13 nuclear magnetic resonance (NMR) spectroscopy to assess the distribution of C between different functional groups in the organic matter. In addition, soil was incubated for 8 weeks with several earthworm species in the presence or absence of lime, and the earthworm casts were subsequently analysed by C-13 NMR spectroscopy. Liming did not significantly affect earthworm abundance or species diversity, but it did affect the chemical composition of the casts. Casts from earthworms incubated in unlimed soil had greater ratios of alkyl-C to O-alkyl-C, indicative of more decomposed, recalcitrant C, and spectra from litter-feeding species had the greatest intensities of O-alkyl-C signals. In limed soil, the largest O-alkyl-C signal intensities were not restricted to litter-feeding species, indicating an increase in the quality of organic matter ingested by geophagous species.

Determination of the impact of continuous defoliation of Lolium perenne and Trifolium repens on bacterial and fungal community structure in rhizosphere soil

To determine the effects of defoliation on microbial community structure, rhizosphere soil samples were taken pre-, and post-defoliation from the root tip and mature root regions of Trifolium repens L. and Lolium perenne L. Microbial DNA isolated from samples was used to generate polymerase chain reaction-denaturing gradient gel electrophoresis molecular profiles of bacterial and fungal communities. Bacterial plate counts were also obtained. Neither plant species nor defoliation affected the bacterial and fungal community structures in both the root tip and mature root regions, but there were significant differences in the bacterial and fungal community profiles between the two root regions for each plant. Prior to defoliation, there was no difference between plants for bacterial plate counts of soils from the root tip regions; however, counts were greater in the mature root region of L. perenne than T. repens. Bacterial plate counts for T. repens were higher in the root tip than the mature root region. After defoliation, there was no effect of plant type, position along the root or defoliation status on bacterial plate counts, although there were significant increases in bacterial plate counts with time. The results indicate that a general effect existed during maturation in the root regions of each plant, which had a greater impact on microbial community structure than either plant type or the effect of defoliation. In addition there were no generic consequences with regard to microbial populations in the rhizosphere as a response to plant defoliation.

Microbial isotopic fractionation of perchlorate chlorine

Perchlorate contamination can be microbially respired to innocuous chloride and thus can be treated effectively. However, monitoring a bioremediative strategy is often difficult due to the complexities of environmental samples. Here we demonstrate that microbial respiration of perchlorate results in a significant fractionation (similar to - 15parts per thousand) of the chlorine stable isotope composition of perchlorate. This can be used to quantify the extent of biotic degradation and to separate biotic from abiotic attenuation of this contaminant.

Sustainable development, rolled-out neoliberalism and sustainable communities

Recent contributions by geographers on the relationships between states and citizens have documented the rise of rolled-out neoliberalism. Development agendas are, it is argued, increasingly dominated by the principles of market-driven reforms, social inequality, and a drive towards enhancing the economic competitiveness of the supply side of the economy. However, at the same time, a parallel set of discourses has emerged in the development literature which argues that it is principles of sustainable development that have, in practice, become dominant. The emphasis is, instead, on democratic empowerment, environmental conservation, and social justice. This paper examines the relationships between these ostensibly very different interpretations of contemporary development with an assessment of one of the Labour government's most ambitious planning agendas-the publication in February 2003 of the document Sustainable Communities: Building for the Future. The proposals are promoted as a "step change" in the planning system with a new emphasis on tackling shortages of housing in the South East and reviving the economy of the Thames Gateway area. The paper assesses the different ways in which such programmes can be interpreted and argues that contemporary development practices in countries such as Britain are constituted by a hybridity of approaches and rationalities and cannot be reduced to simple characterisations of rolled-out neoliberalism or sustainable development.

Promoting microbial immobilization of soil nitrogen during restoration of abandoned agricultural fields by organic additions

Application of organic materials to soils to enhance N immobilization into microbial biomass, thereby reducing inorganic N concentrations, was studied as a management option to accelerate the reestablishment of the native vegetation on abandoned arable fields on sandy soils the Kiskunsag National Park, Hungary. Sucrose and sawdust were used at three different topographic sites over 4 years. N availability and extractable inorganic N concentrations were significantly reduced in all sites. Soil microbial biomass C and microbial biomass N increased significantly following C additions, but the microbial C to microbial N ratio remained unaffected. It is concluded that the combined application of the rapidly utilized C source (sucrose) promoted N immobilization, whereas the addition of the slowly utilized C source (sawdust) maintained the elevated microbial biomass C and microbial biomass N in the field.

Tissue culture propagation alters plant-microbe interactions in tobacco rhizosphere

We have compared properties of roots from different lines (genotypes) of tobacco raised either in tissue culture or grown from seed. The different lines included unmodified plants and plants modified to express reduced activity of the enzyme cinnamoyl-CoA reductase, which has a pivotal role in lignin biosynthesis. The size and structure of the rhizosphere microbial community, characterized by adenosine triphosphate and phospholipid fatty acid analyses, were related to root chemistry (specifically the soluble carbohydrate concentration) and decomposition rate of the roots. The root material from unmodified plants decomposed faster following tissue culture compared with seed culture, and the faster decomposing material had significantly higher soluble carbohydrate concentrations. These observations are linked to the larger microbial biomass and greater diversity of the rhizosphere communities of tissue culture propagated plants.

Innovation dynamics and capability in open collaborative cyber communities: implications for cybersecurity

Cybersecurity is a complex challenge that has emerged alongside the evolving global socio-technical environment of social networks that feature connectivity across time and space in ways unimaginable even a decade ago. This paper reports on the preliminary findings of a NATO funded project that investigates the nature of innovation in open collaborative communities and its implications for cyber security. In this paper, the authors describe the framing of relevant issues, the articulation of the research questions, and the derivation of a conceptual framework based on open collaborative innovation that has emerged from preliminary field research in Russia and the UK.