Calibration of a high spectral resolution lidar using a Michelson interferometer, with data examples from ORACLES.

The NASA Langley airborne second-generation High Spectral Resolution Lidar (HSRL-2) uses a density-tuned field-widened Michelson interferometer to implement the HSRL technique at 355 nm. The Michelson interferometer optically separates the received backscattered light between two channels, one of which is dominated by molecular backscattering, while the other contains most of the light backscattered by particles. This interferometer achieves high and stable contrast ratio, defined as the ratio of particulate backscatter signal received by the two channels. We show that a high and stable contrast ratio is critical for precise and accurate backscatter and extinction retrievals. Here, we present retrieval equations that take into account the incomplete separation of particulate and molecular backscatter in the measurement channels. We also show how the accuracy of the contrast ratio assessment propagates to error in the optical properties. For both backscattering and extinction, larger errors are produced by underestimates of the contrast ratio (compared to overestimates), more extreme aerosol loading, and-most critically-smaller true contrast ratios. We show example results from HSRL-2 aboard the NASA ER-2 aircraft from the 2016 ORACLES field campaign in the southeast Atlantic, off the coast of Africa, during the biomass burning season. We include a case study where smoke aerosol in two adjacent altitude layers showed opposite differences in extinction- and backscatter-related Ångström exponents and a reversal of the lidar ratio spectral dependence, signatures which are shown to be consistent with a relatively modest difference in smoke particle size.

The distinctive isotopic signature of plant-derived chloromethane: possible application in constraining the atmospheric chloromethane budget.

Chloromethane (CH(3)Cl) is the most abundant halocarbon in the atmosphere. Although largely of natural origin it is responsible for around 17% of chlorine-catalysed ozone destruction. Sources identified to date include biomass burning, oceanic emissions, wood-rotting fungi, higher plants and most recently tropical ferns. Current estimates reveal a shortfall of around 2 million ty(-1) in sources versus sinks for the halocarbon. It is possible that emissions from green plants have been substantially underestimated. A potentially valuable tool for validating emission flux estimates is comparison of the delta13C value of atmospheric CH(3)Cl with those of CH(3)Cl from the various sources. Here we report delta13C values for CH(3)Cl released by two species of tropical ferns and show that the isotopic signature of CH(3)Cl from pteridophytes like that of CH(3)Cl from higher plants is quite different from that of CH(3)Cl produced by biomass burning, fungi and industry. delta13C values for CH(3)Cl produced by Cyathea smithii and Angiopteris evecta were respectively -72.7 per thousand and -69.3 per thousand representing depletions relative to plant biomass of 42.3 per thousand and 43.4 per thousand. The characteristic isotopic signature of CH(3)Cl released by green plants should help constrain their contribution to the atmospheric burden when reliable delta13C values for all other major sources of CH(3)Cl are obtained and a globally averaged delta13C value for atmospheric CH(3)Cl is available.

Do vesicle cells of the red alga Asparagopsis (Falkenbergia stage) play a role in bromocarbon production?

The Rhodophyceae (red algae) are an established source of volatile halocarbons in the marine environment. Some species in the Bonnemaisoniaceae have been reported to contain large amounts of halogens in structures referred to as vesicle cells, suggesting involvement of these specialised cells in the production of halocarbons. We have investigated the role of vesicle cells in the accumulation and metabolism of bromide in an isolate of the red macroalga Asparagopsis (Falkenbergia stage), a species known to release bromocarbons. Studies of laboratory-cultivated alga, using light microscopy, revealed a requirement of bromide for both the maintenance and formation of vesicle cells. Incubation of the alga in culture media with bromide concentrations below 64 mgl(-1) (the concentration of Br(-) in seawater) resulted in a decrease in the proportion of vesicle cells to pericentral cells. The abundance of vesicle cells was correlated with bromide concentration below this level. Induction of vesicle cell formation in cultures of Falkenbergia occurred at concentrations as low as 8 mgl(-1), with the abundance of vesicle cells increasing with bromide concentration up to around 100 mgl(-1). Further studies revealed a positive correlation between the abundance of vesicle cells and dibromomethane and bromoform production. Interestingly, however, whilst dibromomethane production was stimulated by the presence of bromide in the culture media, bromoform release remained unaffected suggesting that the two compounds are formed by different mechanisms.

Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria.

The largest biological fractionations of stable carbon isotopes observed in nature occur during production of methane by methanogenic archaea. These fractionations result in substantial (as much as approximately 70 per thousand) shifts in delta(13)C relative to the initial substrate. We now report that a stable carbon isotopic fractionation of comparable magnitude (up to 70 per thousand) occurs during oxidation of methyl halides by methylotrophic bacteria. We have demonstrated biological fractionation with whole cells of three methylotrophs (strain IMB-1, strain CC495, and strain MB2) and, to a lesser extent, with the purified cobalamin-dependent methyltransferase enzyme obtained from strain CC495. Thus, the genetic similarities recently reported between methylotrophs, and methanogens with respect to their pathways for C(1)-unit metabolism are also reflected in the carbon isotopic fractionations achieved by these organisms. We found that only part of the observed fractionation of carbon isotopes could be accounted for by the activity of the corrinoid methyltransferase enzyme, suggesting fractionation by enzymes further along the degradation pathway. These observations are of potential biogeochemical significance in the application of stable carbon isotope ratios to constrain the tropospheric budgets for the ozone-depleting halocarbons, methyl bromide and methyl chloride.

Continuous flow stable isotope methods for study of delta(13)C fractionation during halomethane production and degradation.

Gas chromatography/mass spectrometry/isotope ratio mass spectrometry (GC/MS/IRMS) methods for delta(13)C measurement of the halomethanes CH(3)Cl, CH(3)Br, CH(3)I and methanethiol (CH(3)SH) during studies of their biological production, biological degradation, and abiotic reactions are presented. Optimisation of gas chromatographic parameters allowed the identification and quantification of CO(2), O(2), CH(3)Cl, CH(3)Br, CH(3)I and CH(3)SH from a single sample, and also the concurrent measurement of delta(13)C for each of the halomethanes and methanethiol. Precision of delta(13)C measurements for halomethane standards decreased (+/-0.3, +/-0.5 and +/-1.3 per thousand) with increasing mass (CH(3)Cl, CH(3)Br, CH(3)I, respectively). Given that carbon isotope effects during biological production, biological degradation and some chemical (abiotic) reactions can be as much as 100 per thousand, stable isotope analysis offers a precise method to study the global sources and sinks of these halogenated compounds that are of considerable importance to our understanding of stratospheric ozone destruction.

Carbon isotope ratios for chloromethane of biological origin: potential tool in determining biological emissions.

Chloromethane (CH3Cl) with a global atmospheric burden of 5.3 million t is the most abundant halocarbon in the atmosphere. However, the origin of ca. 50% of the estimated annual global input of 4 million t of the gas to the atmosphere has yet to be determined. As the oceanic contribution to the global CH3Cl flux is now tightly constrained, an important terrestrial source is either underestimated or unrecognized. It has recently been proposed that higher plants may represent a CH3Cl source of sufficient magnitude to resolve the global budget imbalance. A potentially useful tool in validating CH3Cl emission flux estimates is comparison of the carbon isotope ratio of atmospheric CH3Cl with those of CH3Cl originating from various sources. Here we report the first measurements of delta13C for CH3Cl produced biologically. The CH3Cl released by the higher plant species Batis maritima and Solanum tuberosum was dramatically depleted in 13C with respect to plant tissue (delta13C = -36.8/1000 and -34.5/1000, respectively); CH3Cl released by the fungus Phellinus pomaceus also showed significant 13C depletion with respect to the wood growth substrate (delta13C = -17.9/1000). When reliable delta13C values for the other major sources of atmospheric CH3Cl become available, the distinctive isotopic signature of plant-derived CH3Cl should help constrain the contribution to the atmospheric burden from this source.

Halomethane:bisulfide/halide ion methyltransferase, an unusual corrinoid enzyme of environmental significance isolated from an aerobic methylotroph using chloromethane as the sole carbon source.

A novel dehalogenating/transhalogenating enzyme, halomethane:bisulfide/halide ion methyltransferase, has been isolated from the facultatively methylotrophic bacterium strain CC495, which uses chloromethane (CH(3)Cl) as the sole carbon source. Purification of the enzyme to homogeneity was achieved in high yield by anion-exchange chromatography and gel filtration. The methyltransferase was composed of a 67-kDa protein with a corrinoid-bound cobalt atom. The purified enzyme was inactive but was activated by preincubation with 5 mM dithiothreitol and 0.5 mM CH(3)Cl; then it catalyzed methyl transfer from CH(3)Cl, CH(3)Br, or CH(3)I to the following acceptor ions (in order of decreasing efficacy): I(-), HS(-), Cl(-), Br(-), NO(2)(-), CN(-), and SCN(-). Spectral analysis indicated that cobalt in the native enzyme existed as cob(II)alamin, which upon activation was reduced to the cob(I)alamin state and then was oxidized to methyl cob(III)alamin. During catalysis, the enzyme shuttles between the methyl cob(III)alamin and cob(I)alamin states, being alternately demethylated by the acceptor ion and remethylated by halomethane. Mechanistically the methyltransferase shows features in common with cobalamin-dependent methionine synthase from Escherichia coli. However, the failure of specific inhibitors of methionine synthase such as propyl iodide, N(2)O, and Hg(2+) to affect the methyltransferase suggests significant differences. During CH(3)Cl degradation by strain CC495, the physiological acceptor ion for the enzyme is probably HS(-), a hypothesis supported by the detection in cell extracts of methanethiol oxidase and formaldehyde dehydrogenase activities which provide a metabolic route to formate. 16S rRNA sequence analysis indicated that strain CC495 clusters with Rhizobium spp. in the alpha subdivision of the Proteobacteria and is closely related to strain IMB-1, a recently isolated CH(3)Br-degrading bacterium (T. L. Connell Hancock, A. M. Costello, M. E. Lidstrom, and R. S. Oremland, Appl. Environ. Microbiol. 64:2899-2905, 1998). The presence of this methyltransferase in bacterial populations in soil and sediments, if widespread, has important environmental implications.

Comparison of the Efficacies of Chloromethane, Methionine, and S-Adenosylmethionine as Methyl Precursors in the Biosynthesis of Veratryl Alcohol and Related Compounds in Phanerochaete chrysosporium.

The effect on veratryl alcohol production of supplementing cultures of the lignin-degrading fungus Phanerochaete chrysosporium with different methyl-(sup2)H(inf3)-labelled methyl precursors has been investigated. Both chloromethane (CH(inf3)Cl) and l-methionine caused earlier initiation of veratryl alcohol biosynthesis, but S-adenosyl-l-methionine (SAM) retarded the formation of the compound. A high level of C(sup2)H(inf3) incorporation into both the 3- and 4-O-methyl groups of veratryl alcohol occurred when either l-[methyl-(sup2)H(inf3)]methionine or C(sup2)H(inf3)Cl was present, but no significant labelling was detected when S-adenosyl-l-[methyl-(sup2)H(inf3)]methionine was added. Incorporation of C(sup2)H(inf3) from C(sup2)H(inf3)Cl was strongly antagonized by the presence of unlabelled l-methionine; conversely, incorporation of C(sup2)H(inf3) from l-[methyl-(sup2)H(inf3)]methionine was reduced by CH(inf3)Cl. These results suggest that l-methionine is converted either directly or via an intermediate to CH(inf3)Cl, which is utilized as a methyl donor in veratryl alcohol biosynthesis. SAM is not an intermediate in the conversion of l-methionine to CH(inf3)Cl. In an attempt to identify the substrates for O methylation in the metabolic transformation of benzoic acid to veratryl alcohol, the relative activities of the SAM- and CH(inf3)Cl-dependent methylating systems on several possible intermediates were compared in whole mycelia by using isotopic techniques. 4-Hydroxybenzoic acid was a much better substrate for the CH(inf3)Cl-dependent methylation system than for the SAM-dependent system. The CH(inf3)Cl-dependent system also had significantly increased activities toward both isovanillic acid and vanillyl alcohol compared with the SAM-dependent system. On the basis of these results, it is proposed that the conversion of benzoic acid to veratryl alcohol involves para hydroxylation, methylation of 4-hydroxybenzoic acid, meta hydroxylation of 4-methoxybenzoic acid to form isovanillic acid, and methylation of isovanillic acid to yield veratric acid.

Haloalkane degradation and assimilation by Rhodococcus rhodochrous NCIMB 13064.

The bacterium Rhodococcus rhodochrous NCIMB 13064, isolated from an industrial site, could use a wide range of 1-haloalkanes as sole carbon source but apparently utilized several different mechanisms simultaneously for assimilation of substrate. Catabolism of 1-chlorobutane occurred mainly by attack at the C-1 atom by a hydrolytic dehalogenase with the formation of butanol which was metabolized via butyric acid. The detection of small amounts of gamma-butyrolactone in the medium suggested that some oxygenase attack at C-4 also occurred, leading to the formation of 4-chlorobutyric acid which subsequently lactonized chemically to gamma-butyrolactone. Although 1-chlorobutane-grown cells exhibited little dehalogenase activity on 1-chloroalkanes with chain lengths above C10, the organism utilized such compounds as growth substrates with the release of chloride. Concomitantly, gamma-butyrolactone accumulated to 1 mM in the culture medium with 1-chlorohexadecane as substrate. Traces of 4-hydroxybutyric acid were also detected. It is suggested that attack on the long-chain chloroalkane is initiated by an oxygenase at the non-halogenated end of the molecule leading to the formation of an omega-chlorofatty acid. This is degraded by beta-oxidation to 4-chlorobutyric acid which is chemically lactonized to gamma-butyrolactone which is only slowly further catabolized via 4-hydroxybutyric acid and succinic acid. However, release of chloride into the medium during growth on long-chain chloroalkanes was insufficient to account for all the halogen present in the substrate. Analysis of the fatty acid composition of 1-chlorohexadecane-grown cells indicated that chlorofatty acids comprised 75% of the total fatty acid content with C14:0, C16:0, C16:1 and C18:1 acids predominating. Thus the incorporation of 16-chlorohexadecanoic acid, the product of oxygenase attack directly into cellular lipid represents a third route of chloroalkane assimilation. This pathway accounts at least in part for the incomplete mineralization of long-chain chloroalkane substrates. This is the first report of the coexistence of a dehalogenase and the ability to incorporate long-chain haloalkanes into the lipid fraction within a single organism and raises important questions regarding the biological treatment of haloalkane containing effluents.

Evidence for the existence of independent chloromethane- and S-adenosylmethionine-utilizing systems for methylation in Phanerochaete chrysosporium.

O methylation of acetovanillone at 4 position by C2H3Cl and S-adenosyl[methyl-2H3]methionine was monitored in whole mycelia of Phanerochaete chrysosporium in the presence and absence of S-adenosylhomocysteine. Both the amount of the methylation product, 3,4-dimethoxyacetophenone, and the percent C2H3 incorporation into the 4-methoxyl group of the compound were determined. The results strongly suggest the presence of biochemically distinct systems for O methylation of acetovanillone utilizing S-adenosylmethionine and chloromethane, respectively, as the methyl donor. The S-adenosylmethionine-dependent enzyme is induced early in the growth cycle, with activity attaining an initial maximum after 55 h of incubation. Methylation by this enzyme is totally suppressed by 1 mM S-adenosylhomocysteine over almost the entire growth cycle. S-Adenosylmethionine-dependent O-methyltransferase activity is detectable in cell extracts, and the purification and characterization of the enzyme are described elsewhere (C. Coulter, J. T. Kennedy, W. C. McRoberts, and D. B. Harper, Appl. Environ. Microbiol. 59:706-711, 1993). The chloromethane-utilizing methylation system is absent in early growth but attains peak activity in the mid-growth phase after 72 h of incubation. The system is not significantly inhibited by S-adenosylhomocysteine at any stage of growth. No chloromethane-dependent O-methyltransferase activity is detectable in cell extract, suggesting that the enzyme is membrane bound and/or part of a multienzyme complex. Although the biochemical role of the chloromethane-dependent methylation system in metabolism is not known, one possible function could be the regeneration of veratryl alcohol degraded by the attack of lignin peroxidase.

Purification and Properties of an S-Adenosylmethionine: 2,4-Disubstituted Phenol O-Methyltransferase from Phanerochaete chrysosporium.

An enzyme catalyzing the O-methylation of acetovanillone (3-methoxy-4-hydroxyacetophenone) by S-adeno-sylmethionine was isolated from Phanerochaete chrysosporium and purified 270-fold by ultrafiltration, anion-exchange chromatography, and gel filtration. The enzyme exhibited a pH optimum between 7 and 9 and was rapidly denatured at temperatures above 55 degrees C. The K(m) values for acetovanillone and S-adenosylmethionine were 34 and 99 muM, respectively. S-Adenosylhomocysteine acted as a powerful competitive inhibitor of S-adenosylmethionine, with a K(i) of 41 muM. The enzyme was also susceptible to inhibition by thiol reagents and low concentrations of heavy metal ions. Gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the enzyme was monomeric and had a molecular weight of approximately 53,000. Substrate specificity studies showed that 3-methoxy- and 3,5-dimethoxy-substituted 4-hydroxy-benzaldehydes, -benzoic acids, and -acetophenones were the preferred substrates for the enzyme. The corresponding 3,4-dihydroxy compounds were methylated relatively slowly, while the 3-hydroxy-4-methoxy compounds were almost inactive as substrates. Substituents in both the 2 and 4 positions relative to the hydroxyl group appeared to be essential for significant enzyme attack of a substrate. Provided that certain steric criteria were satisfied, the nature of the substituent was not critical. Hence, xenobiotic compounds such as 2,4-dichlorophenol and 2,4-dibromophenol were methylated almost as readily as acetovanillone. However, an extended side chain in the 4 position was not compatible with activity as a substrate, and neither homovanillic, caffeic, nor ferulic acid was methylated. The substrate range of the O-methyltransferase tends to imply a role in the catabolism or detoxification of lignin degradation products such as vanillic and syringic acids.

Carbon-phosphorus bond cleavage activity in cell-free extracts of Enterobacter aerogenes ATCC 15038 and Pseudomonas sp. 4ASW.

Carbon-phosphorus bond cleavage activity was investigated in cell-free extracts of Enterobacter aerogenes ATCC 15038 (IFO 12010) and Pseudomonas sp. 4ASW, strains known to utilize a range of phosphonates as sole phosphorus source. In vitro phosphonatase activity was detected in extracts of both organisms; however extensive analysis failed to detect any organic product from phosphonates other than phosphonoacetal dehyde. Non-specific liberation of phosphate was observed in Pseudomonas sp. 4ASW, associated with a single fraction of FPLC-purified extract, and is believed to result from the activity of cellular phosphatases.

Chloromethane, Methyl Donor in Veratryl Alcohol Biosynthesis in Phanerochaete chrysosporium and Other Lignin-Degrading Fungi.

Chloromethane, a gaseous natural product implicated in methylation processes in Phellinus pomaceus, has been shown to act as methyl donor in veratryl alcohol biosynthesis in the lignin-degrading fungi Phanerochaete chrysosporium, Phlebia radiata, and Coriolus versicolor, none of which released detectable amounts of CH(3)Cl during growth. When P. chrysosporium was grown in a medium containing CH(3)Cl, levels of CH(3) incorporation into the 3- and 4-O-methyl groups of veratryl alcohol were very high and initially similar to those observed when the medium was supplemented with l-[methyl-H(3)]methionine. When CH(3)Cl was added to cultures actively synthesizing veratryl alcohol, incorporation of CH(3) was very rapid, with 81% of veratryl alcohol labeled after 12 h. By contrast, incorporation of CH(3) from l-[methyl-H(3)]methionine was comparatively slow, attaining 10% after 12 h. It is proposed that these lignin-degrading fungi possess a tightly channeled multienzyme system in which CH(3)Cl biosynthesis is closely coupled to CH(3)Cl utilization for methylation of veratryl alcohol precursors.

Purification and properties of S-adenosylmethionine: aldoxime O-methyltransferase from Pseudomonas sp. N.C.I.B. 11652.

An enzyme catalysing the O-methylation of isobutyraldoxime by S-adenosyl-L-methionine was isolated from Pseudomonas sp. N.C.I.B. 11652. The enzyme was purified 220-fold by DEAE-cellulose chromatography, (NH4)2SO4 fractionation, gel filtration on Sephadex G-100 and chromatography on calcium phosphate gel. Homogeneity of the enzyme preparation was confirmed by isoelectric focusing on polyacrylamide gel and sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. The enzyme showed a narrow pH optimum at 10.25, required thiol-protecting agents for activity and was rapidly denatured at temperatures above 35 degrees C. The Km values for isobutyraldoxime and S-adenosyl-L-methionine were respectively 0.24 mM and 0.15 mM. Studies on substrate specificity indicated that attack was mainly restricted to oximes of C4-C6 aldehydes, with preference being shown for those with branching in the 2- or 3-position. Ketoximes were not substrates for the enzyme. Gel filtration on Sephadex G-100 gave an Mr of 84 000 for the intact enzyme, and sodium dodecyl sulphate/polyacrylamide-gel electrophoresis indicated an Mr of 37 500, suggesting the presence of two subunits in the intact enzyme. S-Adenosylhomocysteine was a powerful competitive inhibitor of S-adenosylmethionine, with a Ki of 0.027 mM. The enzyme was also susceptible to inhibition by thiol-blocking reagents and heavy-metal ions. Mg2+ was not required for maximum activity.

Characterization of a nitrilase from Nocardia sp. (Rhodochrous group) N.C.I.B. 11215, using p-hydroxybenzonitrile as sole carbon source.

The purification and properties of an enzyme from Nocardia sp. which catalyses the conversion of p-hydroxybenzonitrile to p-hydroxybenzoic acid and ammonia without intermediate formation of the amide is described. The enzyme displayed a broad pH optimum between 7.0 and 9.5 and exhibited Michaelis-Menten kinetics with Km of 1.27 mM for p-hydroxybenzonitrile. The 12-unit multimeric enzyme possessed a mol. wt of 560,000 and was sensitive to thiol-specific reagents. Although aliphatic nitriles were not substrates for the enzyme a broad range of substituted aromatic nitriles were attacked with a general preference being shown for those with meta substitution.

The bacterial biogenesis of isobutyraldoxime O-methyl ether, a novel volatile secondary metabolite.

Production of the volatile metabolite, isobutyraldoxime O-methyl ether (IBME) by a Moraxella-like organism NCIB 11650 was investigated under a variety of environmental conditions using gas chromatography. Under aerobic conditions up to 10 micrograms IBME ml-1 was produced on mineral salts media containing 0.5% (w/v) glucose or succinate as sole C source with 0.1% (w/v) NH4Cl as sole N source. Exogenous L-valine further stimulated IBME formation up to 25 micrograms ml-1 but supplementation of the medium with D-isomer or other amino acids had little effect on IBME production and did not lead to the appearance of analogues of IBME. Trapping experiments using [14C]valine confirmed that IBME was derived from this amino acid. Several other bacterial species examined, e.g. Alcaligenes sp. NCIB 11652, another Moraxella-like organism NCIB 11651 and Pseudomonas sp. NCIB 11653 also produced IBME under similar conditions. The Alcaligenes strain synthesized up to 20 micrograms ml-1 in the absence of valine and up to 90 micrograms ml-1 in its presence. The product of IBME exhibited many features characteristic of the formation of a secondary metabolite. Thus biosynthesis was confined to a narrower range of temperature than cell division, was almost completely suppressed by 300 mM-phosphate and was inhibited by high concentrations of readily utilizable C sources. Although IBME synthesis in the Moraxella-like organism NCIB 11650 appeared to be growth-related, its formation by both the Alcaligenes sp. and the Moraxella-like organism NCIB 11651 was delayed until the late-exponential and early-stationary phases of growth. The biological significance of this novel class of secondary metabolite is discussed and a possible biosynthetic route proposed.

Identification of isobutyronitrile and isobutyraldoxime O-methyl ether as volatile microbial catabolites of valine.

G.l.c.--mass-spectral analysis of headspace above cultures of Aeromonas and Moraxella spp. indicates the presence of isobutyronitrile, isobutyraldoxime O-methyl ether, methacrylonitrile and possibly methacrylaldoxime O-methyl ether. Accumulation of these catabolites is maximal under low oxygen concentrations and is enhanced by enrichment of the medium with valine. Isobutyraldoxime O-methyl ether is established as the compound observed but not identified in previous studies with other bacterial species involved in spoilage of meat and chicken.