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Scholarly Works (5 results)

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Research Theses and Dissertations (1980)

Acid-catalyzed proton exchange in a number of primary and secondary amides has been studied by Acid-catalyzed proton exchange in a number of primary and secondary amides has been studied by NMR methods. Exchange may conceivably occur by protonation on nitrogen, or by protona­ tion on oxygen followed by N-deprotonation to the imidic-acid tautomer. These mechanisms may be distinguished experimentally, since the former pathway requires that the rate of acid-catalyzed intramolecular exchange of the diastereotopic E and Z protons be comparable to the rates of solvent exchange, whereas the latter pathway requires that the rate of acid-catalyzed intramolecular exchange be zero.

To measure rate constants in these three-site proton ex­change reactions, we have extended the NMR saturation-transfer technique of Forsen and Hoffman. The method involves the measure­ ment of intensities and spin-lattice relaxation rates in Fourier trans­form NMR spectra under conditions of selective saturation. Satura­tion-transfer experiments have been supplemented with line-broad­ening and lineshape analysis measurements where necessary.

Uncatalyzed rotation about the C-N bond in a number of amides was initially studied with the saturation-transfer method. The rate of rotation is very small for formaide, N-methylformamide, N-t-butylformamide, ethyl oxamate, malonamide, and dichloro­ acetamide, and slightly larger for acetamide, cyanoacetamide, and chloroacetamide. The rate of rotation is considerably larger in acrylamide, methacrylamide, benzamide, and salicylamide. These variations in rotation rate are rationalized in terms of the effect of substituents on the transition-state for rotation.

To confirm the reliability of the three-site saturation-transfer method, we have examined the base-catalyzed exchange in a number of primary and secondary amides, where there is no mechanistic ambiguity. In all the amides examined, there is no base-catalyzed intramolecular exchange, as expected, and the E and Z protons ex­change at different rates. The latter observation is rationalized in terms of electronic effects in the resulting imidate anions. We have additionally studied solvent effects on exchange rates, and have elucidated the role of the o-hydroxy substituent of salicylamide in providing intramolecular catalysis of proton exchange in this compound.

Water-catalyzed proton exchange in two protonated imidic esters, ethyl acetimidate and 2-iminotetrahydrofuran, has been studied by saturation-transfer, since exchange in these compounds serves as a model for the imidic-acid route. We find that HZ exchanges faster than HE in ethyl acetimidate, and slower than HE in 2-iminotetrahydrofuran. These results are consistent with the expectations that the Eap and Zsp configurations, respectively, the more stable forms of the imidic esters.

Proton exchange in fuming sulfuric acid has been examined for acetamide, 3, 5-dinitrobenzamide, and trichloroacetamide. In this solvent, where the amides are quantitatively O-protonated, exchange proceeds by proton removal from oxygen, followed by reprotonation on nitrogen, as evidenced by the observation that HE and Hz exchange at equal rates with solvent and with each other.

With a combination of saturation-transfer and lineshape analysis methods, we have elucidated the mechanism of the dilute acid-catalyzed exchange in ten primary and two secondary amides. For acetamide, acrylamide, methacrylamide, benzamide, and formamide, where the rate of acid-catalyzed intramolecular exchange of the E and Z protons is comparable to the rates of solvent exchange, it is concluded that exchange proceeds predominantly by protonation on nitrogen. Nevertheless, HE exchanges faster, and this is interpreted in terms of competition between rapid deprotona­tion of RCONH+3 and rotation about its C-N single bond. In cyano­ acetamide, ethyl oxamate, chloroacetamide, malonamide, and dichloroacetamide, intramolecular exchanges is significantly slower than solvent exchange. This result is evidence for exchange proceed­ing primarily or exclusively via the imidic-acid pathway. For all these amides except the last one, HE exchanges faster than HZ, opposite to the behavior observed in the model compound ethyl acetimidate.

In N-methylformamide, exchange occurs largely via the imidic-acid pathway, whereas in N-t-butylformamide, exchange occurs through protonation on nitrogen. In both cases, HZ exchanges faster than HE. These conclusions are supported by the observation of general-acid catalysis in N-methylformamide, and the absence of such catalysis in N-t-butylformamide.

Several additional aspects of the exchange pathways have been investigated, including the effects of solvent polarity on the relative stabilities of the isomeric imidic acids and imidate anions, the inter­ action between the -NH+3 group and solvent, and the effect of substi­ tuents on the barrier to rotation in the N-conjugate acid. Finally, the variability of mechanism in dilute acid is rationalized in terms of a polar effect of substituents, and the dominance of the N-protonation pathway in strong acid is rationalized in terms of the acidity depend­ ence of the two pathways.

    Cover page: NMR Studies of Proton Exchange in Amides
    • Article
    • Peer Reviewed
    LBL Publications (2019)
    Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.
      Cover page: Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths
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      • Peer Reviewed
      LBL Publications (2016)
      How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.
        Cover page: Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem
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        • Peer Reviewed
        UC Davis Previously Published Works (2021)

        Background

        Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.

        Results

        Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.

        Conclusions

        Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.
          Cover page: Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations
          • Article
          • Peer Reviewed
          LBL Publications (2020)

          Background

          In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed.

          Results

          The β-Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia, α-Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling.

          Conclusions

          Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated. Video Abstract.
            Cover page: Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria
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