OH and HO₂ radicals chemistry at a suburban site during the EXPLORE-YRD campaign in 2018

The first OH and HO2 radical observation in Yangtze River Delta, one of the four major urban agglomerations in China, was carried out at a suburban site Taizhou in summer 2018 from May to June, aiming to elucidate the atmospheric oxidation capacity in this region. The maximum diurnal averaged OH and HO2 concentrations were 1.0 × 107 cm−3 and 1.1 × 109 cm−3, respectively, which were the second highest HOx (sum of OH and HO2) radical concentrations observed in China. HONO photolysis was the dominant radical primary source, accounting for 42 % of the total radical initiation rate. Other contributions were from carbonyl photolysis (including HCHO, 24 %), O3 photolysis (17 %), alkenes ozonolysis (14 %), and NO3 oxidation (3 %). A chemical box model based on RACM2-LIM1 mechanism could generally reproduce the observed HOx radicals, but systematic discrepancy remained in the afternoon for OH radical, when NO mixing ratio was less than 0.3 ppb. Additional recycling mechanism equivalent to 100 ppt NO was capable to fill the gap. The sum of monoterpenes was on average up to 0.4 ppb during daytime, which was allocated all to α-pinene in the base model. Sensitivity test without monoterpene input showed the modelled OH and HO2 concentrations would increase by 7 % and 4 %, respectively, but modelled RO2 concentration would significantly decrease by 23 %, indicating that monoterpene was an important precursor of RO2 radicals in this study. Consequently, the daily integrated net ozone production would reduce by 6.3 ppb if without monoterpene input, proving the significant role of monoterpene on the photochemical O3 production in this study. Besides, the generally good agreement between observed and modelled HOx concentrations suggested no significant HO2 heterogeneous uptake process during this campaign. Incorporation of HO2 heterogeneous uptake process would worsen the agreement between HOx radical observation and simulation, and the discrepancy would be beyond the measurement-model combined uncertainties using an effective uptake coefficient of 0.2. Finally, the ozone production efficiency (OPE) was only 1.7 in this study, a few folds lower than other studies in (sub)urban environments. The low OPE indicated slow radical propagation rate and short chain length. As a consequence, ozone formation was suppressed by the low NO concentration in this study.

Biosynthesis of Poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from CO2 by a Recombinant Cupriavidus necator

The copolyester of 3-hydroxybutyrate (3HB) and 3-hydoxyhexanoate (3HHx), PHBHHx, is one of the most practical kind of bacterial polyhydroxyalkanoates due to its high flexibility and marine biodegradability. PHBHHx is usually produced from vegetable oils or fatty acids through b-oxidation, whereas biosynthesis from sugars has been achieved by recombinant strains of hydrogen-oxidizing bacterium Cupriavidus necator. This study investigated the biosynthesis of PHBHHx from CO2 as the sole carbon source by engineered C. necator strains. The recombinant strains capable of synthesizing PHBHHx from fructose were cultivated in a flask using complete mineral medium and a substrate gas mixture (H2/O2/CO2 = 8:1:1). The results of GC and 1H NMR analyses indicated that the recombinants of C. necator synthesized PHBHHx from CO2 with high cellular content. When 1.0 g/L (NH4)2SO4 was used as a nitrogen source, the 3HHx composition of PHBHHx in the strain MF01∆B1/pBBP-ccrMeJ4a-emd was 47.7 ± 6.2 mol%. Further investigation demonstrated that the PHA composition can be regulated by using (R)-enoyl-CoA hydratase (PhaJ) with different substrate specificity. The composition of 3HHx in PHBHHx was controlled to about 11 mol%, suitable for practical applications, and high cellular content was kept in the strains transformed with pBPP-ccrMeJAc-emd harboring short-chain-length-specific PhaJ.

Direct copolymerization of ethylene with protic comonomers enabled by multinuclear Ni catalysts

Ethylene/polar monomer coordination copolymerization offers an attractive way of making functionalized polyolefins. However, ethylene copolymerization with industrially relevant short chain length alkenoic acid remain a big challenge. Here we report the efficient direct copolymerization of ethylene with vinyl acetic acid by tetranuclear nickel complexes. The protic monomer can be extended to acrylic acid, allylacetic acid, ω-alkenoic acid, allyl alcohol, and homoallyl alcohol. Based on X-ray analysis of precatalysts, control experiments, solvent-assisted electrospray ionization-mass spectrometry detection of key catalytic intermediates, and density functional theory studies, we propose a possible mechanistic scenario that involves a distinctive vinyl acetic acid enchainment enabled by Ni···Ni synergistic effects. Inspired by the mechanistic insights, binuclear nickel catalysts are designed and proved much more efficient for the copolymerization of ethylene with vinyl acetic acid or acrylic acid, achieving the highest turnover frequencies so far for both ethylene and polar monomers simultaneously.

In Vivo Characterization and Application of the PHA Synthase from Azotobacter vinelandii for the Biosynthesis of Polyhydroxyalkanoate Containing 4-Hydroxybutyrate

Polyhydroxyalkanoate (PHA) is a biodegradable thermoplastic naturally synthesized by many microorganisms, and the PHA synthase (PhaC) is known to be the key enzyme involved in determining the material properties and monomer composition of the produced PHA. The ability to exploit widely distributed, commonly found soil microorganisms such as Azotobacter vinelandii to synthesize PHA containing the lipase-degradable 4-hydroxybutyrate (4HB) monomer will allow for convenient production of biocompatible and flexible PHA. Comparisons between the A. vinelandii wild type and mutant strains, with and without a surface layer (S-layer), respectively, in terms of gene or amino acid sequences, synthase activity, granule morphology, and PHA productivity, revealed that the S-layer is the sole factor affecting PHA biosynthesis by A. vinelandii. Based on PHA biosynthesis using different carbon sources, the PhaC of A. vinelandii showed specificity for short-chain-length PHA monomers, making it a member of the Class I PHA synthases. In addition, it was proven that the PhaC of A. vinelandii has the inherent ability to polymerize 4-hydroxybutyrate (4HB) and the mediated accumulation of PHA with 4HB fractions ranging from 10 mol% to as high as 22 mol%. The synthesis of biocompatible PHA containing tailorable amounts of 4HB with an expanded range of elasticity and lipase-degradability will enable a wider range of applications in the biomedical field.

Fructose-Based Production of Short-Chain-Length and Medium-Chain-Length Polyhydroxyalkanoate Copolymer by Arctic Pseudomonas sp. B14-6

Arctic bacteria employ various mechanisms to survive harsh conditions, one of which is to accumulate carbon and energy inside the cell in the form of polyhydroxyalkanoate (PHA). Whole-genome sequencing of a new Arctic soil bacterium Pseudomonas sp. B14-6 revealed two PHA-production-related gene clusters containing four PHA synthase genes (phaC). Pseudomonas sp. B14-6 produced poly(6% 3-hydroxybutyrate-co-94% 3-hydroxyalkanoate) from various carbon sources, containing short-chain-length PHA (scl-PHA) and medium-chain-length PHA (mcl-PHA) composed of various monomers analyzed by GC-MS, such as 3-hydroxybutyrate, 3-hydroxyhexanoate, 3-hydroxyoctanoate, 3-hydroxydecanoate, 3-hydroxydodecenoic acid, 3-hydroxydodecanoic acid, and 3-hydroxytetradecanoic acid. By optimizing the PHA production media, we achieved 34.6% PHA content using 5% fructose, and 23.7% PHA content using 5% fructose syrup. Differential scanning calorimetry of the scl-co-mcl PHA determined a glass transition temperature (Tg) of 15.3 °C, melting temperature of 112.8 °C, crystallization temperature of 86.8 °C, and 3.82% crystallinity. In addition, gel permeation chromatography revealed a number average molecular weight of 3.6 × 104, weight average molecular weight of 9.1 × 104, and polydispersity index value of 2.5. Overall, the novel Pseudomonas sp. B14-6 produced a polymer with high medium-chain-length content, low Tg, and low crystallinity, indicating its potential use in medical applications.

Microbial Polyhydroxyalkanoates Granules: An Approach Targeting Biopolymer for Medical Applications and Developing Bone Scaffolds

Microbial polyhydroxyalkanoates (PHA) are proteinaceous storage granules ranging from 100 nm to 500 nm. Bacillus sp. serve as unique bioplastic sources of short-chain length and medium-chain length PHA showcasing properties such as biodegradability, thermostability, and appreciable mechanical strength. The PHA can be enhanced by adding functional groups to make it a more industrially useful biomaterial. PHA blends with hydroxyapatite to form nanocomposites with desirable features of compressibility. The reinforced matrices result in nanocomposites that possess significantly improved mechanical and thermal properties both in solid and melt states along with enhanced gas barrier properties compared to conventional filler composites. These superior qualities extend the polymeric composites’ applications to aggressive environments where the neat polymers are likely to fail. This nanocomposite can be used in different industries as nanofillers, drug carriers for packaging essential hormones and microcapsules, etc. For fabricating a bone scaffold, electrospun nanofibrils made from biocomposite of hydroxyapatite and polyhydroxy butyrate, a form of PHA, can be incorporated with the targeted tissue. The other methods for making a polymer scaffold, includes gas foaming, lyophilization, sol–gel, and solvent casting method. In this review, PHA as a sustainable eco-friendly NextGen biomaterial from bacterial sources especially Bacillus cereus, and its application for fabricating bone scaffold using different strategies for bone regeneration have been discussed.

Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes

ABSTRACT Ammonia monooxygenase (AMO) is a key nitrogen-transforming enzyme belonging to the same copper-dependent membrane monooxygenase family (CuMMO) as the particulate methane monooxygenase (pMMO). The AMO from ammonia-oxidizing archaea (AOA) is very divergent from both the AMO of ammonia-oxidizing bacteria (AOB) and the pMMO from methanotrophs, and little is known about the structure or substrate range of the archaeal AMO. This study compares inhibition by C2 to C8 linear 1-alkynes of AMO from two phylogenetically distinct strains of AOA, “Candidatus Nitrosocosmicus franklandus” C13 and “Candidatus Nitrosotalea sinensis” Nd2, with AMO from Nitrosomonas europaea and pMMO from Methylococcus capsulatus (Bath). An increased sensitivity of the archaeal AMO to short-chain-length alkynes (≤C5) appeared to be conserved across AOA lineages. Similarities in C2 to C8 alkyne inhibition profiles between AMO from AOA and pMMO from M. capsulatus suggested that the archaeal AMO has a narrower substrate range than N. europaea AMO. Inhibition of AMO from “Ca. Nitrosocosmicus franklandus” and N. europaea by the aromatic alkyne phenylacetylene was also investigated. Kinetic data revealed that the mechanisms by which phenylacetylene inhibits “Ca. Nitrosocosmicus franklandus” and N. europaea are different, indicating differences in the AMO active site between AOA and AOB. Phenylacetylene was found to be a specific and irreversible inhibitor of AMO from “Ca. Nitrosocosmicus franklandus,” and it does not compete with NH3 for binding at the active site. IMPORTANCE Archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) initiate nitrification by oxidizing ammonia to hydroxylamine, a reaction catalyzed by ammonia monooxygenase (AMO). AMO enzyme is difficult to purify in its active form, and its structure and biochemistry remain largely unexplored. The bacterial AMO and the closely related particulate methane monooxygenase (pMMO) have a broad range of hydrocarbon cooxidation substrates. This study provides insights into the AMO of previously unstudied archaeal genera, by comparing the response of the archaeal AMO, a bacterial AMO, and pMMO to inhibition by linear 1-alkynes and the aromatic alkyne, phenylacetylene. Reduced sensitivity to inhibition by larger alkynes suggests that the archaeal AMO has a narrower hydrocarbon substrate range than the bacterial AMO, as previously reported for other genera of AOA. Phenylacetylene inhibited the archaeal and bacterial AMOs at different thresholds and by different mechanisms of inhibition, highlighting structural differences between the two forms of monooxygenase.

Prophage induction mediated by quorum sensing signals alters soil bacterial community structure

Recent findings have revealed a role for bacterial quorum sensing communication in bacteriophage (phage) reproduction decisions. However quorum sensing based phage-host interactions remain largely unknown, with the mechanistic details revealed for only a few phage-host pairs and a dearth of information available at the microbial community level. Here we report on the specific action of individual quorum-sensing signals (acyl-homoserine lactones; AHLs varying in acyl-chain length from four to 14 carbon atoms) on prophage induction in soil microbial communities. AHL treatment significantly decreased the bacterial diversity (Shannon Index) but did not significantly impact species richness. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs. Each AHL targeted a different subset of bacterial taxa. Our observations demonstrate that individual AHLs trigger prophage induction in different bacterial taxa leading to changes in microbial community structure.