Variability in -caprylate and -caproate producing microbiomes in reactors with in-line product extraction.

Medium-chain carboxylates (MCCs) are used in various industrial applications. These chemicals are typically extracted from palm oil, which is deemed not sustainable. Recent research has focused on microbial chain elongation using reactors to produce MCCs, such as -caproate (C6) and -caprylate (C8), from organic substrates such as wastes.

Exploring the Specificity of Extracellular Wastewater Peptidases to Improve the Design of Sustainable Peptide-Based Antibiotics.

New antimicrobial peptides are emerging as promising alternatives to conventional antibiotics because of their specificity for target pathogens and their potential to be rapidly hydrolyzed (, inactivated) by extracellular peptidases during biological wastewater treatment, thereby limiting the emergence and propagation of antibiotic resistance in the environment. However, little is known about the specificity of extracellular peptidases derived from wastewater microbial communities, which is a major impediment for the design of sustainable peptide-based antibiotics that can be hydrolyzed by wastewater peptidases. We used a set of natural peptides to explore the specificity of dissolved extracellular wastewater peptidases.

Singlet Oxygen Phosphorescence as a Probe for Triplet-State Dissolved Organic Matter Reactivity.

Triplet-state chromophoric dissolved organic matter (CDOM*) plays an important role in aquatic photochemistry, yet much remains unknown about the reactivity of these intermediates. To better understand the kinetic behavior and reactivity of CDOM*, we have developed an indirect observation method based on monitoring time-resolved singlet oxygen (O) phosphorescence kinetics. The underpinning principle of our approach relies on the fact that O quenches almost all triplets with near diffusion limited rate constants, resulting in the formation of O, which is kinetically linked to the precursors.

Redundancy in Anaerobic Digestion Microbiomes during Disturbances by the Antibiotic Monensin.

The antibiotic monensin is fed to dairy cows to increase milk production efficiency. A fraction of this monensin is excreted into the cow manure. Previous studies have found that cow manure containing monensin can negatively impact the performance of anaerobic digesters, especially upon first introduction.

Methane Emission in a Specific Riparian-Zone Sediment Decreased with Bioelectrochemical Manipulation and Corresponded to the Microbial Community Dynamics.

Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale.

Comparing the inhibitory thresholds of dairy manure co-digesters after prolonged acclimation periods: Part 2--correlations between microbiomes and environment.

Here, we studied the microbiome succession and time-scale variability of four mesophilic anaerobic reactors in a co-digestion study with the objective to find links between changing environmental conditions and the microbiome composition. The changing environmental conditions were ensured by gradual increases in loading rates and mixing ratios of three co-substrates with a constant manure-feeding scheme during an operating period longer than 900 days. Each co-substrate (i.

Correlation between microbial community and granule conductivity in anaerobic bioreactors for brewery wastewater treatment.

Prior investigation of an upflow anaerobic sludge blanket (UASB) reactor treating brewery wastes suggested that direct interspecies electron transfer (DIET) significantly contributed to interspecies electron transfer to methanogens. To investigate DIET in granules further, the electrical conductivity and bacterial community composition of granules in fourteen samples from four different UASB reactors treating brewery wastes were investigated. All of the UASB granules were electrically conductive whereas control granules from ANAMMOX (ANaerobic AMMonium OXidation) reactors and microbial granules from an aerobic bioreactor designed for phosphate removal were not.

Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation.

Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period.

Metabolite transfer with the fermentation product 2,3-butanediol enhances virulence by Pseudomonas aeruginosa.

The respiratory tract of cystic fibrosis (CF) patients harbor persistent microbial communities (CF airway microbiome) with Pseudomonas aeruginosa emerging as a dominant pathogen. Within a polymicrobial infection, interactions between co-habitant microbes can be important for pathogenesis, but even when considered, these interactions are not well understood. Here, we show with in vitro experiments that, compared with glucose, common fermentation products from co-habitant bacteria significantly increase virulence factor production, antimicrobial activity and biofilm formation of P.

Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut.

Gut mucosal barrier breakdown and inflammation have been associated with high levels of flagellin, the principal bacterial flagellar protein. Although several gut commensals can produce flagella, flagellin levels are low in the healthy gut, suggesting the existence of control mechanisms. We find that mice lacking the flagellin receptor Toll-like receptor 5 (TLR5) exhibit a profound loss of flagellin-specific immunoglobulins (Igs) despite higher total Ig levels in the gut.

Substrate type drives variation in reactor microbiomes of anaerobic digesters.

The goal of this study was to obtain causative information about beta-diversity (differentiation between microbiomes) by comparing sequencing information between studies rather than just knowledge about alpha-diversity (microbiome richness). Here, published sequencing data were merged representing 78 anaerobic digester samples originating from 28 different studies for an overall comparison of beta-diversity (measured using unweighted UniFrac). It was found that digester microbiomes based on bacterial sequences clustered by substrate type, independent of the study of origin, and that this clustering could be attributed to distinct bacterial lineages.

Shaping reactor microbiomes to produce the fuel precursor n-butyrate from pretreated cellulosic hydrolysates.

To maximize the production of carboxylic acids with open cultures of microbial consortia (reactor microbiomes), we performed experiments to understand which factors affect the community dynamics and performance parameters. We operated six thermophilic (55 °C) bioreactors to test how the factors: (i) biomass pretreatment; (ii) bioreactor operating conditions; and (iii) bioreactor history (after perturbations during the operating period) affected total fermentation product and n-butyrate performance parameters with corn fiber as the cellulosic biomass waste. We observed a maximum total fermentation product yield of 39%, a n-butyrate yield of 23% (both on a COD basis), a maximum total fermentation production rate of 0.

Host remodeling of the gut microbiome and metabolic changes during pregnancy.

Many of the immune and metabolic changes occurring during normal pregnancy also describe metabolic syndrome. Gut microbiota can cause symptoms of metabolic syndrome in nonpregnant hosts. Here, to explore their role in pregnancy, we characterized fecal bacteria of 91 pregnant women of varying prepregnancy BMIs and gestational diabetes status and their infants.

Relating chloroethene respiration rates in Dehalococcoides to protein and mRNA biomarkers.

Molecular biomarkers could provide critical insight into myriad in situ microbial activities. In this study we explore correlations of both mRNA and protein biomarkers with chloroethene respiration rate in Dehalococcoides. In a series of continuously fed dechlorinating mixed-culture microcosm experiments (n = 26), we varied respiratory substrates, substrate ratios and feeding rates.

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Taxonomic classification of the thousands-millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples).

Bacterial community structures are unique and resilient in full-scale bioenergy systems.

Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated the relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e.

Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration.

The quantification of trace proteins in complex environmental samples and mixed microbial communities would be a valuable monitoring tool in countless applications, including the bioremediation of groundwater contaminated with chlorinated solvents. Measuring the concentrations of specific proteins provides unique information about the activity and physiological state of organisms in a sample. We developed sensitive (< 5 fmol), selective bioindicator assays for the absolute quantification of select proteins used by Dehalococcoides spp.

Photolysis of chlortetracycline on a clay surface.

Chlortetracycline, an antibiotic commonly used as a growth promoter in livestock, enters the environment primarily through application of animal waste to open fields. The photochemical loss of chlortetracycline in sunlight-exposed soils is a potentially important process in its environmental fate, especially because it is photochemically labile and sorbs strongly to mineral surfaces. In this study, photolysis on kaolinite clay under simulated sunlight was used as a model system to elucidate the mechanistic kinetics of chlortetracycline photolysis on soil surfaces.

Meta-iodobenzylguanidine, an inhibitor of arginine-dependent mono(ADP-ribosyl)ation, prevents neointimal hyperplasia.

The association of ADP-ribosylation with cell proliferation and ischemia-reperfusion injury suggests that it may be a suitable target for therapeutic control of revascularization-induced injury. The purpose of this study was to investigate the inhibitory actions of ADP-ribosylation inhibitors on restenosis. In organ culture, the poly(ADP-ribose) polymerase (PARP) inhibitor 3,4-dihydro-5-methylisoquinolinone (PD128763) was unable to prevent neointimal hyperplasia, whereas the arginine-dependent mono(ADP-ribosyl)transferase (ART) inhibitor meta-iodobenzylguanidine (MIBG) was highly effective (EC(50) 21 microM).

Environmental photochemistry of tylosin: efficient, reversible photoisomerization to a less-active isomer, followed by photolysis.

The environmental photochemical kinetics of tylosin, a common veterinary macrolide antibiotic and growth promoter, were investigated under simulated sunlight. An efficient, reversible photoisomerization was characterized using kinetic, mass spectrometry, and proton nuclear magnetic resonance data. The photoisomerization was confirmed to occur by a rotation about the distal alkene of the ketodiene functionality.

Water hardness as a photochemical parameter: tetracycline photolysis as a function of calcium concentration, magnesium concentration, and pH.

The environmental photochemical kinetics of the antibiotic compound tetracycline were investigated. The aqueous speciation of tetracycline over a range of natural pH and water hardness values is dominated by association with Ca2+ and Mg2+ ions. The association constants necessary to calculate tetracycline aqueous speciation given knowledge of pH, [Ca2+], and [Mg2+] were measured by spectrophotometric titrations and matrix deconvolution of a series of UV-vis absorption spectra into individual component species.

Precision of Raman depolarization and optical attenuation measurements of sound tooth enamel.

The demineralization of enamel that is associated with early caries formation affects the optical properties of the enamel. Polarized Raman spectroscopy and optical coherence tomography have been used to detect these changes and potentially offer a means to detect and monitor early caries development. The total optical attenuation coefficient as measured by optical coherence tomography and the polarization anisotropy of the Raman peak arising from the symmetric nu(1) vibration of PO4(3-) at approximately 959 cm(-1) have been demonstrated as being sensitive markers of early caries.

Environmental photodegradation of mefenamic acid.

Pharmaceuticals and personal care products are an emerging class of environmental pollutants. Photolysis is expected to be a major loss process for many of these compounds in surface waters, including the common non-steroidal anti-inflammatory drug mefenamic acid. The direct photolysis solar quantum yield of mefenamic acid was observed to be 1.

Activation of MMP-2 in response to vascular injury is mediated by phosphatidylinositol 3-kinase-dependent expression of MT1-MMP.

Phosphatidylinositol 3-kinase (PI3K) is required for smooth muscle cell (SMC) proliferation. This study reports that inhibitors of PI3K also prevent SMC migration and block neointimal hyperplasia in an organ culture model of restenosis. Inhibition of neointimal formation by LY-294002 was concentration and time dependent, with 10 muM yielding the maximal effect.