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The interleukin-23 [IL-23] cytokine, derived predominantly from macrophages and dendritic cells in response to microbial stimulation, has emerged as a critical promoter of chronic intestinal inflammation. Genome-wide association studies linking variants in IL23R to disease protection, bolstered by experimental evidence from colitis models, and the successful application of therapies against the IL-12/IL-23 shared p40 subunit in the treatment of inflammatory bowel disease [IBD] all provide compelling evidence of a crucial role for IL-23 in disease pathogenesis. Moreover, targeting the p19 subunit specific for IL-23 has shown considerable promise in recent phase 2 studies in IBD. The relative importance of the diverse immunological pathways downstream of IL-23 in propagating mucosal inflammation in the gut, however, remains contentious. Here we review current understanding of IL-23 biology and explore its pleiotropic effects on T cells, and innate lymphoid, myeloid and intestinal epithelial cells in the context of the pathogenesis of IBD. We furthermore discuss these pathways in the light of recent evidence from clinical trials and indicate emerging targets amenable to therapeutic intervention and translation into clinical practice., (© The Author(s) 2022. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation.)

Still's disease, the paradigm of autoinflammation-cum-autoimmunity, predisposes for a cytokine storm with excessive T lymphocyte activation upon viral infection. Loss of function of the purine nucleoside enzyme FAMIN is the sole known cause for monogenic Still's disease. Here we discovered that a FAMIN-enabled purine metabolon in dendritic cells (DCs) restrains CD4 + and CD8 + T cell priming. DCs with absent FAMIN activity prime for enhanced antigen-specific cytotoxicity, IFNγ secretion, and T cell expansion, resulting in excessive influenza A virus-specific responses. Enhanced priming is already manifest with hypomorphic FAMIN-I254V, for which ∼6% of mankind is homozygous. FAMIN controls membrane trafficking and restrains antigen presentation in an NADH/NAD + -dependent manner by balancing flux through adenine-guanine nucleotide interconversion cycles. FAMIN additionally converts hypoxanthine into inosine, which DCs release to dampen T cell activation. Compromised FAMIN consequently enhances immunosurveillance of syngeneic tumors. FAMIN is a biochemical checkpoint that protects against excessive antiviral T cell responses, autoimmunity, and autoinflammation., Competing Interests: Declaration of interests The University of Cambridge has filed patent applications relating to this work. The authors declare no other competing financial interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Single-nucleotide variations in C13orf31 (LACC1) that encode p.C284R and p.I254V in a protein of unknown function (called 'FAMIN' here) are associated with increased risk for systemic juvenile idiopathic arthritis, leprosy and Crohn's disease. Here we set out to identify the biological mechanism affected by these coding variations. FAMIN formed a complex with fatty acid synthase (FASN) on peroxisomes and promoted flux through de novo lipogenesis to concomitantly drive high levels of fatty-acid oxidation (FAO) and glycolysis and, consequently, ATP regeneration. FAMIN-dependent FAO controlled inflammasome activation, mitochondrial and NADPH-oxidase-dependent production of reactive oxygen species (ROS), and the bactericidal activity of macrophages. As p.I254V and p.C284R resulted in diminished function and loss of function, respectively, FAMIN determined resilience to endotoxin shock. Thus, we have identified a central regulator of the metabolic function and bioenergetic state of macrophages that is under evolutionary selection and determines the risk of inflammatory and infectious disease.

Crohn's disease (CD) is associated with delayed neutrophil recruitment and bacterial clearance at sites of acute inflammation as a result of impaired secretion of proinflammatory cytokines by macrophages. To investigate the impaired cytokine secretion and confirm our previous findings, we performed transcriptomic analysis in macrophages and identified a subgroup of individuals with CD who had low expression of the autophagy receptor optineurin (OPTN). We then clarified the role of OPTN deficiency in: macrophage cytokine secretion; mouse models of bacteria-driven colitis and peritonitis; and zebrafish Salmonella infection. OPTN-deficient bone-marrow-derived macrophages (BMDMs) stimulated with heat-killed Escherichia coli secreted less proinflammatory TNFα and IL6 cytokines despite similar gene transcription, which normalised with lysosomal and autophagy inhibitors, suggesting that TNFα is mis-trafficked to lysosomes via bafilomycin-A-dependent pathways in the absence of OPTN. OPTN-deficient mice were more susceptible to Citrobacter colitis and E. coli peritonitis, and showed reduced levels of proinflammatory TNFα in serum, diminished neutrophil recruitment to sites of acute inflammation and greater mortality, compared with wild-type mice. Optn-knockdown zebrafish infected with Salmonella also had higher mortality. OPTN plays a role in acute inflammation and neutrophil recruitment, potentially via defective macrophage proinflammatory cytokine secretion, which suggests that diminished OPTN expression in humans might increase the risk of developing CD., (© 2015. Published by The Company of Biologists Ltd.)

Crohn's disease (CD) is a complex and highly heterogeneous chronic inflammatory disorder, primarily affecting the gastrointestinal tract. Genetic and functional studies have highlighted a key role for innate immunity in its pathogenesis. Profound systemic defects in innate immunity and acute inflammation are understood to result in markedly delayed clearance of bacteria from the tissues, leading to local chronic granulomatous inflammation and compensatory adaptive immunological changes. Macrophages, key orchestrators of acute inflammation, are likely to play an important role in the initial impaired innate immune response. Monocyte-derived macrophages from CD patients stimulated with Escherichia coli were shown to release attenuated levels of tumour necrosis factor and interferon-γ with normal secretion of interleukin-8 (IL-8), IL-10 and IL-6. In controls, the secretion of these cytokines was strongly positively correlated, which was not seen with CD macrophages. The transcriptomes of CD and control macrophages were examined in an attempt to understand the molecular basis of this defect. There were no differentially expressed genes identified between the two groups, consistent with genetic heterogeneity; however, a number of molecules were found to be under-expressed in subgroups of CD patients. The most common of these was optineurin (OPTN) which was under-expressed in approximately 10% of the CD patients. Reduced OPTN expression coincided with lower intracellular protein levels and diminished cytokine secretion after bacterial stimulation both in the patients and with small interfering RNA knockdown in THP-1 cells. Identifying and studying subgroups of patients with shared defective gene expression could aid our understanding of the mechanisms underlying highly heterogeneous diseases such as CD., (© 2014 The Authors. Immunology published by John Wiley & Sons Ltd., Immunology.)

Background: Mucosal abnormalities are potentially important in the primary pathogenesis of ulcerative colitis (UC). We investigated the mucosal transcriptomic expression profiles of biopsies from patients with UC and healthy controls, taken from macroscopically noninflamed tissue from the terminal ileum and 3 colonic locations with the objective of identifying abnormal molecules that might be involved in disease development., Methods: Whole-genome transcriptional analysis was performed on intestinal biopsies taken from 24 patients with UC, 26 healthy controls, and 14 patients with Crohn's disease. Differential gene expression analysis was performed at each tissue location separately, and results were then meta-analyzed. Significantly, differentially expressed genes were validated using quantitative polymerase chain reaction. The location of gene expression within the colon was determined using immunohistochemistry, subcellular fractionation, electron and confocal microscopy. DNA methylation was quantified by pyrosequencing., Results: Only 4 probes were abnormally expressed throughout the colon in patients with UC with Bone morphogenetic protein/Retinoic acid Inducible Neural-specific 3 (BRINP3) being the most significantly underexpressed. Attenuated expression of BRINP3 in UC was independent of current inflammation, unrelated to phenotype or treatment, and remained low at rebiopsy an average of 22 months later. BRINP3 is localized to the brush border of the colonic epithelium and expression is influenced by DNA methylation within its promoter., Conclusions: Genome-wide expression analysis of noninflamed mucosal biopsies from patients with UC identified BRINP3 as significantly underexpressed throughout the colon in a large subset of patients with UC. Low levels of this gene could predispose or contribute to the maintenance of the characteristic mucosal inflammation seen in this condition.

Summary: Complex human diseases can show significant heterogeneity between patients with the same phenotypic disorder. An outlier detection strategy was developed to identify variants at the level of gene transcription that are of potential biological and phenotypic importance. Here we describe a graphical software package (z-score outlier detection (ZODET)) that enables identification and visualisation of gross abnormalities in gene expression (outliers) in individuals, using whole genome microarray data. Mean and standard deviation of expression in a healthy control cohort is used to detect both over and under-expressed probes in individual test subjects. We compared the potential of ZODET to detect outlier genes in gene expression datasets with a previously described statistical method, gene tissue index (GTI), using a simulated expression dataset and a publicly available monocyte-derived macrophage microarray dataset. Taken together, these results support ZODET as a novel approach to identify outlier genes of potential pathogenic relevance in complex human diseases. The algorithm is implemented using R packages and Java., Availability: The software is freely available from http://www.ucl.ac.uk/medicine/molecular-medicine/publications/microarray-outlier-analysis.

In this study we have developed a rapid method for the shotgun analysis of bile acids in intestinal fluid. The method is semi-quantitative, and requires little sample preparation. Bile salts might contribute to the pathogenesis of Crohn's disease. In a pilot study we demonstrate the method by analysing the bile acid content of ileal fluid from seven Crohn's disease patients and three healthy controls. The dominant bile acids observed were di and/or trihydroxycholanoates, di- and/or trihydroxycholanoylglycines, di- and/or tri-hydroxycholanoyltaurines, monosulphated dihydroxycholanoates and monosulphated dihydroxycholanoylglycine. The method can be similarly applied to samples derived from other parts of the intestine., (Copyright © 2012 Elsevier Masson SAS. All rights reserved.)

Crohn's disease is a chronic inflammatory condition largely affecting the terminal ileum and large bowel. A contributing cause is the failure of an adequate acute inflammatory response as a result of impaired secretion of pro-inflammatory cytokines by macrophages. This defective secretion arises from aberrant vesicle trafficking, misdirecting the cytokines to lysosomal degradation. Aberrant intestinal permeability is also well-established in Crohn's disease. Both the disordered vesicle trafficking and increased bowel permeability could result from abnormal lipid composition. We thus measured the sphingo- and phospholipid composition of macrophages, using mass spectrometry and stable isotope labelling approaches. Stimulation of macrophages with heat-killed Escherichia coli resulted in three main changes; a significant reduction in the amount of individual ceramide species, an altered composition of phosphatidylcholine, and an increased rate of phosphatidylcholine synthesis in macrophages. These changes were observed in macrophages from both healthy control individuals and patients with Crohn's disease. The only difference detected between control and Crohn's disease macrophages was a reduced proportion of newly-synthesised phosphatidylinositol 16:0/18:1 over a defined time period. Shotgun lipidomics analysis of macroscopically non-inflamed ileal biopsies showed a significant decrease in this same lipid species with overall preservation of sphingolipid, phospholipid and cholesterol composition., (Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.)

Background: Recent work provides evidence of a failure of acute inflammation in Crohn's disease (CD), and suggests that the primary defect operates at the level of the macrophage and cytokine release. Here we extend the characterization of the innate immune defect in CD by investigating the macrophage response to Toll-like receptor (TLR) agonists and assess potential links between genome-wide association study (GWAS) susceptibility loci, disease phenotype, and therapeutic regimens on tumor necrosis factor α (TNF) release., Methods: Peripheral blood-derived macrophages were cultured from control subjects and patients with CD, stimulated with TLR ligands, and the release of TNF measured. Genomic DNA was purified from blood and genotyped for 34 single nucleotide polymorphisms (SNPs) identified as being associated with CD by GWAS., Results: All stimuli resulted in a reduction (32%-48%) in TNF release from macrophages derived from CD patients (n = 28-101) compared to those from healthy control (HC) subjects. All phenotypes demonstrated impaired TNF release, with the greatest defect in patients with colonic disease. There was no detectable relationship between the level of TNF released and the presence of GWAS susceptibility loci in CD patients. Reduced TNF levels were not influenced by age, gender, or use of aminosalicylate (5-ASA) medication., Conclusions: This study supports the hypothesis of defective proinflammatory cytokine secretion and an innate immunodeficiency in CD. Abnormal TNF secretion is evident downstream of multiple TLRs, affects all disease phenotypes, and is unrelated to 34 polymorphisms associated with CD by GWAS., (Copyright © 2012 Crohn's & Colitis Foundation of America, Inc.)

We describe a case of a 56 year old man with no previous medical history who presented with sudden onset dyspnoea, expressive dysphasia, and right arm sensory loss and paresis. A diagnosis of bilateral pulmonary embolism and transient cerebral ischaemic attack was confirmed by CT pulmonary angiogram and MRI. Paradoxical embolism through an occult patent foramen ovale (PFO) was subsequently proven by contrast echocardiography. This case highlights a number of short and long-term management conundrums, that to date are incompletely addressed by clinical trials. These include timing of anticoagulation in patients with both venous thromboembolism and cerebral infarction, and the risk:benefit ratio of surgical closure of patent foramen ovale.

Crohn's disease and ulcerative colitis are idiopathic chronic inflammatory diseases that primarily affect the gastrointestinal tract. The underlying causes remain poorly understood, but there is a growing body of evidence advocating a likely primary pathogenic role for immunodeficiency in the development of Crohn's lesions. Concordantly, a number of congenital immunodeficiencies disrupting the cellular innate immune system strongly predispose to noninfectious, Crohn's-like inflammatory bowel disease. There are case reports and series suggesting that the same may be true for some of the congenital adaptive and complement immunodeficiencies. This review considers and critiques these potential associations.

Crohn's disease is a chronic inflammatory disorder primarily affecting the gastrointestinal tract. Its clinical manifestations arise from a substantial infiltration of the intestinal mucosa by activated leukocytes and the downstream consequences of chronic inflammation. The underlying cause driving this immunological reaction remains poorly understood. A number of hypotheses have been proposed, most of which postulate a primary over-activation of the immune response, based on the pathological appearances of active Crohn's lesions. Interestingly, none of these theories have been mechanistically proven. It is possible that the immunological events responsible for disease initiation are quite different from those contributing to its persistence and propagation. A substantial body of data has emerged in recent years to suggest that the primary defect in Crohn's disease is actually one of relative immunodeficiency. This review considers the evidence for such a phenomenon in contrast to alternative prevailing hypotheses and attempts to address some of the potential paradoxes that it generates.

Background: Crohn's Disease (CD) is a chronic relapsing disorder characterized by granulomatous inflammation of the gastrointestinal tract. Although its pathogenesis is complex, we have recently shown that CD patients have a systemic defect in macrophage function, which results in the defective clearance of bacteria from inflammatory sites., Methodology/principal Findings: Here we have identified a number of additional macrophage defects in CD following diacylglycerol (DAG) homolog phorbol-12-myristate-13-acetate (PMA) activation. We provide evidence for decreased DNA fragmentation, reduced mitochondrial membrane depolarization, impaired reactive oxygen species production, diminished cytochrome c release and increased IL-6 production compared to healthy subjects after PMA exposure. The observed macrophage defects in CD were stimulus-specific, as normal responses were observed following p53 activation and endoplasmic reticulum stress., Conclusion: These findings add to a growing body of evidence highlighting disordered macrophage function in CD and, given their pivotal role in orchestrating inflammatory responses, defective apoptosis could potentially contribute to the pathogenesis of CD.

The pathogenesis of Crohn's disease (CD) has remained an enigma for at least a century. There was considerable optimism that genetic linkage and genome-wide association (GWA) studies had identified genes causally responsible. However, the realisation that these genes make a relatively minor contribution to the development of CD has led to the acceptance of a 'missing heritability'. In contrast to the weak genetic effects, patients with CD almost without exception exhibit a gross phenotype, namely a profound systemic failure of the acute inflammatory response. This results in markedly delayed clearance of bacteria from the tissues, leading to local chronic granulomatous inflammation and compensatory adaptive immunological changes, as well as constitutional symptoms.

The cause of Crohn's disease (CD) remains poorly understood. Counterintuitively, these patients possess an impaired acute inflammatory response, which could result in delayed clearance of bacteria penetrating the lining of the bowel and predispose to granuloma formation and chronicity. We tested this hypothesis in human subjects by monitoring responses to killed Escherichia coli injected subcutaneously into the forearm. Accumulation of (111)In-labeled neutrophils at these sites and clearance of (32)P-labeled bacteria from them were markedly impaired in CD. Locally increased blood flow and bacterial clearance were dependent on the numbers of bacteria injected. Secretion of proinflammatory cytokines by CD macrophages was grossly impaired in response to E. coli or specific Toll-like receptor agonists. Despite normal levels and stability of cytokine messenger RNA, intracellular levels of tumor necrosis factor (TNF) were abnormally low in CD macrophages. Coupled with reduced secretion, these findings indicate accelerated intracellular breakdown. Differential transcription profiles identified disease-specific genes, notably including those encoding proteins involved in vesicle trafficking. Intracellular destruction of TNF was decreased by inhibitors of lysosomal function. Together, our findings suggest that in CD macrophages, an abnormal proportion of cytokines are routed to lysosomes and degraded rather than being released through the normal secretory pathway.

Reductive biotransformation of tetrachloroethene (PCE) to ethene occurred during anaerobic degradation of toluene in an enrichment culture. Ethene was detected as a dominant daughter product of PCE dechlorination with negligible accumulation of other partially chlorinated ethenes. PCE dechlorination was linked to toluene degradation, as evidenced by the findings that PCE dechlorination was limited in the absence of toluene but was restored with a spike of toluene again in the cultures. PCE was effectively dechlorinated in cultures amended with a wide range of concentrations of PCE and toluene. PCE dechlorination can be described by a Monod-like equation but followed a zero-order kinetic at high levels of PCE. In addition to toluene, benzoate and lactate were also able to be used as sole electron donors for reductive dechlorination of PCE in the cultures. In terms of dechlorination rates, lactate was the best electron donor followed by benzoate and then toluene. The kinetic characteristics of PCE dechlorination were retained in the cultures regardless of electron donors used, but the kinetic constant values were unique to each electron donor. The dechlorination rate was found to be closely correlated with the level of H2 produced during fermentation of the three organic compounds. Nitrate and sulfate were observed to be favorable electron acceptors in this culture, and their presence completely blocked electron flow to PCE. However, the presence of nitrate and sulfate did not destroy the capability of PCE dechlorination by the culture. PCE dechlorination was immediately reestablished after depletion of nitrate and sulfate in the culture. This anaerobic process provides an opportunity for concurrent remediation of chlorinated solvents and certain fuel hydrocarbons, and recognition of this process is also important in understanding the subsurface fate and transport of these contaminants under natural conditions.

The Solvent Extraction Residual Biotreatment (SERB) technology was evaluated at a former dry cleaner site in Jacksonville, FL, where an area of tetrachloroethylene (PCE) contamination was identified. The SERB technology is a treatmenttrain approach for complete site restoration, which combines an active in situ dense nonaqueous-phase liquid (DNAPL) removal technology, cosolvent extraction, with a passive enhanced in situ bioremediation technology, reductive dechlorination. During the in situ cosolvent extraction test, approximately 34 kL of 95% ethanol/5% water (v:v) was flushed through the contaminated zone, which removed approximately 60% of the estimated PCE mass. Approximately 2.72 kL of ethanol was left in the subsurface, which provided electron donorfor enhancement of biological processes in the source zone and downgradient areas. Quarterly groundwater monitoring for over 3 yr showed decreasing concentrations of PCE in the source zone from initial values of 4-350 microM to less than 150 microM during the last sampling event. Initially there was little to no daughter product formation in the source zone, but after 3 yr, measured concentrations were 242 microM for cis-dichloroethylene (cis-DCE), 13 microM for vinyl chloride, and 0.43 microM for ethene. In conjunction with the production of dissolved methane and hydrogen and the removal of sulfate, these measurements indicate that in situ biotransformations were enhanced in areas exposed to the residual ethanol. First-order rate constants calculated from concentration data for individual wells ranged from -0.63 to -2.14 yr(-1) for PCE removal and from 0.88 to 2.39 yr(-1) for cis-DCE formation. First-order rate constants based on the change in total mass estimated from contour plots of the groundwater concentration data were 0.75 yr(-1) for cis-DCE, -0.50 yr(-1) for PCE, and -0.33 yr(-1) for ethanol. Although these attenuation rate constants include additional processes, such as sorption, dispersion, and advection, they provide an indication of the overall system dynamics. Evaluation of the groundwater data from the former dry cleaner site showed that cosolvent flushing systems can be designed and utilized to aid in the enhancement of biodegradation processes at DNAPL sites.

Geochemical and microbiological factors that control long-term performance of subsurface permeable reactive barriers were evaluated at the Elizabeth City, North Carolina, and the Denver Federal Center, Colorado, sites. These ground water treatment systems use zero-valent iron filings (Peerless Metal Powders Inc.) to intercept and remediate chlorinated hydrocarbon compounds at the Denver Federal Center (funnel-and-gate system) and overlapping plumes of hexavalent chromium and chlorinated hydrocarbons at Elizabeth City (continuous wall system). Zero-valent iron at both sites is a long-term sink for carbon, sulfur, calcium, silicon, nitrogen, and magnesium. After about four years of operation, the average rates of inorganic carbon (IC) and sulfur (S) accumulation are 0.09 and 0.02 kg/m2/year, respectively, at Elizabeth City where upgradient waters contain <400 mg/L of total dissolved solids (TDS). At the Denver Federal Center site, upgradient ground water contains 1000 to 1200 mg/L TDS and rates of IC and S accumulation are as high as 2.16 and 0.80 kg/m2/year, respectively. At both sites, consistent patterns of spatially variable mineral precipitation and microbial activity are observed. Mineral precipitates and microbial biomass accumulate the fastest near the upgradient aquifer-Fe0 interface. Maximum net reductions in porosity due to the accumulation of sulfur and inorganic carbon precipitates range from 0.032 at Elizabeth City to 0.062 at the Denver Federal Center (gate 2) after about four years. Although pore space has been lost due the accumulation of authigenic components, neither site shows evidence of pervasive pore clogging after four years of operation.

Water quality in five marinas on Lake Texoma, located on the Oklahoma and Texas border, was monitored between June 1999 and November 2000. Focus was to evaluate lake water associated with marinas for methyl tert-butyl ether (MTBE). Lake water was collected at locations identified as marina entrance, gasoline filling station, and boat dock. Occurrence of MTBE showed a direct seasonal trend with recreational boating activity at marina areas. There was a positive correlation with powerboat usage ratio, which was directly related to the gallons of gasoline sold. Sampling before and after the high boat use holiday weekends determined the apparent influence of powerboat activity on MTBE contamination. Boat dock locations were the most sensitive sites to MTBE contamination, possibly due to gasoline spillage during engine startup. The most common compound of the BTEX series found with MTBE was toluene and co-occurrence was most frequent at gasoline filling stations.

This paper investigated an improved electrochemical approach that is able to provide hydrogen for anaerobic bioremediation of chloroethenes in subsurface. Hydrogen is the ultimate electron donor of biodechlorination processes. In experiments, iron wire was used as electrodes, an anaerobic bacteria enrichment collected from a site contaminated with chloroethenes as test microbes, perchloroethylene (PCE) as model chloroethene. Experiments were conducted by switching the polarities of electrodes periodically and supplying electrical power in an intermittent way. The results showed that an electrochemical bioreactor that was switched 1 time/10 min and operated only 8 h a day was able to produce more hydrogen than that operated 24h a day at 0.4V without polarity switching, stimulating microbial growth more effectively. The intermittent operation also resulted in periodical release of overpotentials that built up on electrode surfaces, thus prevented charged ions and particles from attaching on electrodes. The hydrogen produced was available for microbial growth and PCE dechlorination. It is suggested that the improved electrochemical process developed in this study has significant implications to anaerobic bioremediation.

This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% beta- and gamma-Proteobacteria (B+G), 31 to 35% alpha-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the FC aquifer community. These studies demonstrated that alterations in aquifer microbial communities resulting from specific anthropogenic perturbances can be inferred from microcosm studies integrating chemical and phylogenetic probe analysis and in the case of hydrocarbon contamination may facilitate the identification of organisms important for in situ biodegradation processes. Further work integrating and coordinating microcosm and field experiments is needed to explore how differences in scale, substrate complexity, and other hydrogeological conditions may affect patterns observed in these systems.

A mixed culture of Bacillus sp. K1 and Sphingomonas paucimobilis EPA 505 was exposed to chromate and naphthalene. Batch experiments showed that chromate was reduced and naphthalene was degraded by the mixed culture. Chromate reduction occurred initially at a high rate followed by a decrease in rate until chromate reduction ceased. Chromate reduction decreased in the mixed culture when a lower ratio of S. paucimobilis EPA 505 to Bacillus sp. K1 was utilized. A kinetic model incoporating a term for the cell density ratio is proposed to describe chromate reduction in the mixed culture under both chromate limited and electron donor limited conditions. The validity of the model, and its parameter values, was verified by experimental data generated under a variety of initial population compositions and a broad range of chromate concentrations. The consistent result of experimental data with model predictions implies that the model is useful for evaluating the interactions and the use of mixed culture for chromate removal. (c) 1996 John Wiley & Sons, Inc.

The effect of the addition of common fermentation products on the dehalogenation of tetrachloroethene was studied in methanogenic slurries made with aquifer solids. Lactate, propionate, crotonate, butyrate, and ethanol stimulated dehalogenation activity, while acetate, methanol, and isopropanol did not.

A reversed-phase liquid chromatographic column-switching system was used for the determination of phenol, benzoic acid and cresol (PBC) in the presence of toluene in ground water microcosm. A precolumn was connected in series with an analytical column via a column-switching valve. After the injection, as soon as PBC were eluted from the precolumn to the analytical column, the valve was switched so that the precolumn was between the analytical column and the UV detector. Toluene and other non-polar compounds were eluted from the precolumn in a very short time and detected along with the solvent front. Subsequently, PBC were separated on the analytical column and passed through the precolumn one more time before being detected by the UV detector. The total analysis time was 15 min. This technique facilitated the study of the basic mechanism and path way of anaerobic degradation of toluene in ground water aquifer.

A rapid method for the simultaneous quantification of non-volatile and volatile fatty acids in aqueous sample by ion-exclusion chromatography is described. The sample is directly injected into the column and detected by a chemically suppressed conductivity detector, connected in tandem with an UV detector at 210 nm. The method allows detection of fatty acid as low as 1 ppm with a linear dynamic range up to 1000 ppm. At least 13 fatty acids can be determined within 50 min. This technique has been used to monitor the common fermentation products (lactate, acetate, propionate and butyrate) of the reductive dehalogenation of tetrachloroethene by anaerobic bacteria.

The genes encoding essential enzymes of the fermentative pathway for ethanol production in Zymomonas mobilis, an obligately ethanologenic bacterium, were inserted into Escherichia coli under the control of a common promoter. Alcohol dehydrogenase II and pyruvate decarboxylase from Z. mobilis were expressed at high levels in E. coli, resulting in increased cell growth and the production of ethanol as the principal fermentation product from glucose. These results demonstrate that it is possible to change the fermentation products of an organism, such as E. coli, by the addition of genes encoding appropriate enzymes which form an alternative system for the regeneration of NAD+.

The gene encoding the principal Butyrivibrio fibrisolvens xylosidase (xylB) has been cloned and expressed in Escherichia coli under the control of the lac promoter. The coding region for this gene was localized within a 3.2-kilobase B. fibrisolvens DNA fragment in pUC18. A new protein band was observed in recombinant E. coli containing xylB. This protein (approximately 60,000 molecular weight) was presumed to be the xylosidase monomer. The optimal pH (5.5) and substrate range for the recombinant and native xylosidases appeared identical. Both enzymes hydrolyzed xylo-oligosaccharides with chain lengths of 2 to 5 and both were inactive on xylan.

Six new xylanolytic bacterial strains have been isolated from a Napier grass-fed anaerobic digester. These strains were identified as Butyrivibrio fibrisolvens and were similar in many respects to ruminal isolates described previously. The new isolates exhibited a high degree of DNA homology with several ruminal strains of B. fibrisolvens. Xylan or xylose was required to induce the production of enzymes for xylan degradation, xylanase and xylosidase. Production of these enzymes was repressed in the presence of glucose. Xylanase activity was predominantly extracellular, while that of xylosidases was cell associated. The new isolates of B. fibrisolvens grew well in defined medium containing xylan as the sole carbon source and did not produce obvious slime or capsular layers. These strains may be useful for future genetic investigations.

The gene encoding glyceraldehyde-3-phosphate dehydrogenase was isolated from a library of Zymomonas mobilis DNA fragments by complementing a deficient strain of Escherichia coli. It contained tandem promoters which were recognized by E. coli but appeared to function less efficiently than the enteric lac promoter in E. coli. The open reading frame for this gene encoded 337 amino acids with an aggregate molecular weight of 36,099 (including the N-terminal methionine). The primary amino acid sequence for this gene had considerable functional homology and amino acid identity with other eucaryotic and bacterial genes. Based on this comparison, the gap gene from Z. mobilis appeared to be most closely related to that of the thermophilic bacteria and to the chloroplast isozymes. Comparison of this gene with other glycolytic enzymes from Z. mobilis revealed a conserved pattern of codon bias and several common features of gene structure. A tentative transcriptional consensus sequence is proposed for Z. mobilis based on comparison of the five known promoters for three glycolytic enzymes.

The gene which encodes alcohol dehydrogenase II (adhB) from Zymomonas mobilis was cloned in Escherichia coli as a 1.4-kilobase DNA fragment by using a novel indicator plate which directly detects the expression of this activity by recombinant colonies. The DNA sequence for this clone contained an open reading frame encoding a polypeptide of 383 amino acids, with a molecular weight of 40,141. Although this protein exhibited very little homology with other known alcohol dehydrogenases, the predicted amino acid composition was in excellent agreement with that reported for the purified alcohol dehydrogenase II protein from Z. mobilis. In Z. mobilis, the adhB gene was transcribed from tandem promoters which were separated by 100 base pairs and ended with a transcriptional terminator (13-base-pair palindrome). In Escherichia coli, only one of the Z. mobilis promoters was used, despite apparent similarity to the enteric consensus promoter. The adhB gene was transcribed at low levels in E. coli from the P2 promoter of Z. mobilis but was expressed well in E. coli under control of the lac promoter (approximately 0.25% of the total cell protein).