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Methane emissions, along with methanotrophs and methanogens and soil chemical properties, were investigated in a flooded rice ecosystem. Methane emission increased after rice transplantation (from 7.2 to 552 mg day(-1) m(-2) ) and was positively and significantly correlated with transcripts of pmoA and mcrA genes, transcript/gene ratios of mcrA, temperature and total organic carbon. Methane flux was negatively correlated with sulfate concentration. Methanotrophs represented only a small proportion (0.79-1.75%) of the total bacterial 16S rRNA gene reads: Methylocystis (type II methanotroph) decreased rapidly after rice transplantation, while Methylosinus and unclassified Methylocystaceae (type II) were relatively constant throughout rice cultivation. Methylocaldum, Methylobacter, Methylomonas and Methylosarcina (type I) were sparse during the early period, but they increased after 60 days, and their maximum abundances were observed at 90-120 days. Of 33 218 archaeal reads, 68.3-86.6% were classified as methanogens. Methanosaeta, Methanocella, Methanosarcina and Methanobacterium were dominant methanogens, and their maximum abundances were observed at days 60-90. Only four reads were characteristic of anaerobic methanotrophs, suggesting that anaerobic methane metabolism is negligible in this rice paddy system. After completing a multivariate canonical correspondence analysis of our integrated data set, we found normalized mcrA/pmoA transcript ratios to be a promising parameter for predicting net methane fluxes emitted from rice paddy soils., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)

Ferredoxin-NADP(+) reductase (Fpr) is known to control NADP(+)/NADPH pool in proteobacteria. There is only one fpr gene present in most proteobacteria, but Pseudomonas putida has two Fprs (FprA and FprB). We elucidated the functional relationships between the two types of Fpr and their electron transport partners [ferredoxin (Fd) and flavodoxin (Fld)] by cloning, expressing and preparing these proteins in various combinations and assessing their properties in vitro and in vivo using biochemical assays, the Far-western analysis, the yeast two-hybrid assay and structural molecular modelling. Both of the Fprs have a lower K(m) value for NADPH than for NADH in the diaphorase assays. With NADH as electron donor, FprB also has a high specific constant (k(cat)/K(m)) in the diaphorase assay. The catalytic efficiency of FprA is higher when Fld is present as its redox partner, compared to the kinetics observed with other electron transport partners in a NADPH-dependent cytochrome c reduction assay. The highest specific constant (k(cat)/K(m)) of FprB was observed in the presence of FdA. FprB's K(m) value and catalytic activity (k(cat)) with NADH were significant in cytochrome c reduction assays. Strong kinetic interactions of Fprs with their redox partners were also demonstrated by homology modelling, the Far-western analysis and the in vivo yeast two-hybrid system. This study demonstrates for the first time that Fprs in P. putida function as diaphorase, Fd/Fld reductases and determines their preferred redox partner in vivo and in vitro.

Objective: To investigate the effects of: I) short- (8 weeks), II) long-term (3 years) weight loss, and III) the degree of weight loss on circulating levels of adiponectin, high sensitive-C reactive protein (hs-CRP), and fibrinogen in obese subjects. Moreover, to evaluate the effect of the lipase inhibitor, orlistat, on these parameters., Design: Weight loss induced in 93 obese subjects (mean weight: 108.9+/-15.8 kg) through 8-week very-low-energy diet (VLED, 800 kcal/day) followed by randomization to orlistat or placebo together with lifestyle intervention for further 3 years. Adiponectin and hs-CRP were measured at baseline, after 8 weeks of VLED and 6, 12, and 36 months after the VLED by flowmetric xMAP technology (Luminex Multi-Analyte Profiling System, Luminex Corp., Austin, TX, USA). Fibrinogen was measured in a coagulation assay., Results: Weight loss after VLED treatment was 14.3+/-4.5 kg and after 3 years 7.7+/-8.7 kg. Orlistat-treated subjects regained 3.9 kg less than placebo-treated from the end of the VLED to 3 years (P=0.01). No differences were detected between the two groups regarding changes in adiponectin, hs-CRP, or fibrinogen. Accordingly, the groups were combined for further analyses. Serum adiponectin increased by 22% (P<0.05) after the VLED but returned to baseline after 3 years. Both short- and long-term weight losses needed to be in excess of 10% (approximately 12 kg) in order to increase adiponectin levels significantly. Weight loss was associated with a significant decrease in hs-CRP. Fibrinogen decreased by 12% (P<0.05) after 3 years., Conclusions: In obese subjects, weight loss was associated with an increase in serum adiponectin and a decrease in hs-CRP and plasma fibrinogen. Long-term weight loss (3 years) must exceed 10% to induce a combined significant improvement in these inflammatory markers.

NahR, a LysR-type transcriptional regulator, is required for expression of naphthalene catabolic operons. However, detailed mechanisms of transcriptional activation by NahR are poorly understood. Many transcriptional activators make direct contact with RNA polymerase (RNAP) to initiate transcription. We investigated the hypothesis that direct contact between NahR and the alpha subunit of RNAP (alphaRNAP) may be involved in expression of the naphthalene catabolic operons in Pseudomonas putida NCIB 9816-4. Interactions between the NahR and alphaRNAP in P. putida NCIB 9816-4 were analyzed using the yeast two-hybrid system. The results obtained indicate that protein-protein interactions occur between alphaRNAP and the NahR. Gene activation by NahR is consistent with the general transcriptional mechanism of class I transcription factors, which function by contacting alphaRNAP.

This study explored the geochemistry and microbial diversity of a Superfund site containing trichloroethene (TCE) and an unusual co-pollutant, tetrakis(2-ethylbutoxy)silane. Geochemical analysis of contaminated groundwater indicated subsurface anaerobiosis, reductive dechlorination of TCE to predominantly cis-1,2-dichloroethene, and (transient) accumulation of 2-ethylbutanol and 2-ethylbutyrate as a result of tetrakis(2-ethylbutoxy)silane breakdown. Comparative analysis of 106 16S rDNA and 61 16S-23S rDNA intergenic spacer region sequences - obtained from pristine and contaminated groundwater via DNA extraction, PCR amplification, cloning and sequencing - revealed that the contaminated groundwater featured (i) a distinct microbial community, (ii) reduced species diversity, (iii) various anaerobes, and (iv) bacteria closely related to the TCE-dechlorinating, dichloroethene-accumulating genus Dehalobacter, whereas (v) the TCE-dechlorinating, ethene-producing species Dehalococcoides ethenogenes was not detectable. Thus, geochemical and molecular biological results were in excellent agreement in this first ecological field study linking in situ reductive dechlorination of TCE to metabolism of tetraalkoxysilanes.

An industrial site contaminated with a mixture of volatile organic compounds in its subsurface differed from previously reported locations in that the contamination consisted of a mixture of chlorinated, brominated, and non-halogenated aromatic and aliphatic solvents in an alluvial aquifer. The source area was adjacent to a river. Of the contaminants present in the aquifer, benzene, toluene, and chlorobenzene (BTC) were of primary concern. Studies of the physical, chemical, and microbiological characteristics of site groundwater were conducted. The studies concentrated on BTC, but also addressed the fate of the other aquifer VOCs. Gas chromatographic analyses performed on laboratory microcosms demonstrated that subsurface microorganisms were capable of BTC degradation. Mineralization of BTC was demonstrated by the release of 14CO2 from radiolabelled BTC. In the field, distribution patterns of nutrients and electron acceptors were consistent with expression of in situ microbial metabolic activity: methane, conductivity, salinity and o-phosphate concentrations were all positively correlated with contaminant concentration; while oxidation-reduction potential, nitrate, dissolved oxygen and sulfate concentrations were negatively correlated. Total aerobes, aerotolerant anaerobes, BTC-specific degraders, and acridine orange direct microscopic microorganism counts were strongly and positively correlated with field contaminant concentrations. The relative concentrations of benzene and toluene were lower away from the core of the plume compared to the less readily metabolized compound, chlorobenzene. Hydrodynamic modeling of electron-acceptor depletion conservatively estimated that 450 kg of contaminant have been removed from the subsurface yearly. Models lacking a biodegradation term predicted that 360 kg of contaminant would reach the river annually, which would result in measurable contaminant concentrations. River surveillance, however, has only rarely detected these compounds in the sediment and then only at trace concentrations. Thus, the combination of field modeling, laboratory studies, and site surveillance data confirm that significant in situ biodegradation of the contaminants has occurred. These studies establish the presence of intrinsic bioremediation of groundwater contaminants in this unusual industrial site subsurface habitat.

We have previously found that histamine (HA) is involved in the mediation of restraint- and ether stress-induced release of the POMC-derived peptides ACTH and beta-endorphin (beta-END). In the present study we investigated the possible involvement of hypothalamic histaminergic neurons in the mediation of insulin/hypoglycemia-induced release of ACTH and beta-END in conscious male rats. To do so, hypoglycemia stress was performed during 1) inhibition of HA synthesis, 2) activation of inhibitory presynaptic HA H3-auto-receptors, or 3) blockade of postsynaptic HA H1- or H2-receptors. Hypoglycemia (plasma glucose, 2.2 +/- 0.3 nmol) induced by insulin (3 IU/kg, ip) caused a 3- to 5-fold increase in the plasma concentrations of ACTH and beta-END. A negative exponential correlation was found between the plasma glucose concentration and the ACTH and beta-END levels. Pretreatment of the animals with the HA synthesis inhibitor alpha-fluoromethylhistidine (1.0 mumol) intracerebroventricularly (icv) in a lateral ventricle, inhibited the ACTH and beta-END responses to insulin/hypoglycemia by 60%. When administered ip (100 mumol/kg), the synthesis inhibitor decreased the beta-END response 50%, but did not affect ACTH secretion significantly. Pretreatment of the rats with the H3-receptor agonist R(alpha)methylhistamine (50 mumol/kg, ip, twice) inhibited the secretory responses of ACTH and beta-END to insulin/hypoglycemia by 60-80%. This inhibitory effect of R(alpha)methylhistamine was reversed by prior administration of the specific H3-receptor antagonist thioperamide. Administration of the H1-antagonists mepyramine and cetirizine dose-dependently inhibited the ACTH and beta-END responses to insulin/hypoglycemia, with the highest dose (mepyramine, 350 nmol, icv; cetirizine, 40 mumol/kg, ip) inhibiting the response by 80-100%. The H1-antagonist SKF-93944 (226 nmol, icv) inhibited the ACTH response, but had no effect on the beta-END response. Administration of the H2-antagonists cimetidine (400 nmol, icv) and ranitidine (400 nmol, icv) inhibited the ACTH and beta-END responses to insulin/hypoglycemia by 50-80%. We conclude that histaminergic neurons are involved in the mediation of the insulin/hypoglycemia-induced release of ACTH and beta-END and that the effect is mediated via activation of primarily postsynaptic H1-receptors and, to a lesser extent, H2-receptors.