Denitrifiers in a pH-neutral fen
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ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR690362.fastq.gz | Fastqsanger.gz | |||
| ERR690363.fastq.gz | Fastqsanger.gz | |||
| ERR690364.fastq.gz | Fastqsanger.gz | |||
| ERR690365.fastq.gz | Fastqsanger.gz | |||
| ERR690366.fastq.gz | Fastqsanger.gz |
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Project description:Peatlands are invaluable but threatened ecosystems that store huge amounts of organic carbon globally and emit the greenhouse gasses carbon dioxide (CO2) and methane (CH4). Trophic interactions of microbial groups essential for methanogenesis are poorly understood in such systems, despite their importance. Thus, the present study aimed at unraveling trophic interactions between fermenters and methanogens in a nitrogen-limited, subarctic, pH-neutral fen. In situ CH4 emission measurements indicated that the fen is a source of CH4, and that CH4 emissions were higher in plots supplemented with ammonium compared to unsupplemented plots. The amino sugar N-acetylglucosamine was chosen as model substrate for peat fermenters since it can serve as organic carbon and nitrogen source and is a monomer of chitin and peptidoglycan, two abundant biopolymers in the fen. Supplemental N-acetylglucosamine was fermented to acetate, ethanol, formate, and CO2 during the initial incubation of anoxic peat soil microcosms without preincubation. Subsequently, ethanol and formate were converted to acetate and CH4. When methanogenesis was inhibited by bromoethanesulfonate, acetate and propionate accumulated. Long-term preincubation considerably increased CH4 production in unsupplemented microcosms and microcosms supplemented with methanogenic substrates. Supplemental H2-CO2 and formate stimulated methanogenesis the most, whereas acetate had an intermediary and methanol a minor stimulatory effect on methane production in preincubated microcosms. Activity of acetogens was suggested by net acetate production in microcosms supplemented with H2-CO2, formate, and methanol. Microbial community analysis of field fresh soil indicated the presence of many physiologically unresolved bacterial taxa, but also known primary and secondary fermenters, acetogens, iron reducers, sulfate reducers, and hydrogenotrophic methanogens (predominately Methanocellaceae and Methanoregulaceae). Aceticlastic methanogens were either not abundant (Methanosarcinaceae) or could not be detected due to limited coverage of the used primers (Methanotrichaceae). The collective results indicate a complex interplay of synergy and competition between fermenters, methanogens, acetogens, and potentially iron as well as sulfate reducers. While acetate derived from fermentation or acetogenesis in this pH-neutral fen likely plays a crucial role as carbon source for the predominant hydrogenotrophic methanogens, it remains to be resolved whether acetate is also converted to CH4 via aceticlastic methanogenesis and/or syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis.
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Project description:Wetlands are sources of denitrification-derived nitrous oxide (N2O). Thus, the denitrifier community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitrifiers approximated 10(11) cells x g(DW)(-1) (where DW is dry weight) and 10(8) cells x g(DW)(-1), respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (v(max)) values for denitrification in anoxic microcosms ranged from 1 to 24 and -19 to -105 nmol N2O h(-1) x g(DW)(-1), with maximal values occurring in the upper soil layers. Denitrification was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitrification. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomic units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifier diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifier community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifier communities capable of complete denitrification and consumption of atmospheric N2O at in situ pH.
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Project description:We proposed that DNA recombination/repair processes play a role in memory formation. Here, we used microarray analysis of rat amygdala genes to identify possible DNA recombination/repair factors involved in memory consolidation of conditioned taste aversion (CTA). Among the genes that showed statistically significant differential expression, we identified fen-1, encoding a flap-structure specific DNA endonuclease. Amygdalar fen-1 mRNA induction was associated to the illness component of CTA, since it could be observed by the pairing of a flavor and gastrointestinal illness, by the illness itself, but not by the presentation of the flavor alone. No CTA related induction of fen-1 expression was observed in the insular cortex. Importantly, functional validation studies demonstrated that amygdalar suppression of fen-1 expression impaired memory consolidation of CTA. Overall, our studies helped identify a new DNA recombination/repair candidate factor involved in memory formation of aversive experiences.
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Project description:We report here the discovery and development of boron-assisted oxime formation as a powerful connective reaction for chemical biology. Oximes proximal to boronic acids form in neutral aqueous buffer with rate constants of more than 104 M-1 s-1, the largest to date for any oxime condensation. Boron's dynamic coordination chemistry confers an adaptability that seems to aid a number of elementary steps in the oxime condensation. In addition to applications in bioconjugation, the emerging importance of boronic acids in chemical biology as carbohydrate receptors or peroxide probes, and the growing list of drugs and drug candidates containing boronic acids suggest many potential applications.
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Project description:PurposeTo test the effects of acidic vs. neutral pH glycyrrhizin (GLY) on the unwounded and wounded normal mouse cornea and after infection with Pseudomonas aeruginosa isolates KEI 1025 and multidrug-resistant MDR9.MethodsAcidic or neutral GLY vs. phosphate-buffered saline (PBS) was topically applied to normal or wounded corneas of C57BL/6 mice. In unwounded corneas, goblet cells and corneal nerves were stained and quantitated. After wounding, corneas were fluorescein stained and photographed using a slit lamp. Mice also were infected with KEI 1025 or MDR9 and the protective effects of GLY pH evaluated comparatively.ResultsIn the unwounded cornea, application of acidic or neutral GLY vs. PBS reduced the number of bulbar conjunctival goblet cells but did not alter corneal nerve density. Similar application of GLY to scarified corneas delayed wound closure. After KEI 1025 infection, none of the GLY vs. PBS-treated corneas perforated; GLY treatment also decreased plate count (neutral pH more effective) and reduced MPO and several cytokines. Similarly, for MDR9, GLY at either pH was protective and also enhanced the effects of moxifloxacin to which MDR9 is resistant.ConclusionAcidic or neutral pH GLY decreased goblet cell number but had no effect on nerve density. After corneal wounding, GLY at either pH (1) delayed wound closure and, (2) after infection, decreased keratitis when used alone or in combination with moxifloxacin. Neutral pH did not alter the therapeutic effect of GLY and would be preferred if used clinically.
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