Anaerobic Dissolution Rates of U(IV)-Oxide by Abiotic and Nitrate-Dependent Bacterial Pathways

The long-term stability of U(IV) solid phases in anaerobic aquifers depends upon their reactivity in the presence of oxidizing chemical species and microbial catalysts. We performed flow-through column experiments under anaerobic conditions to investigate the mechanisms and dissolution rates of biogenic, noncrystalline UO₂(s) by chemical oxidants (nitrate and/or nitrite) or by Thiobacillus denitrificans, a widespread, denitrifying, chemolithoautotrophic model bacterium. Dissolution rates of UO₂(s) with dissolved nitrite were approximately 5 to 10 times greater than with nitrate alone. In the presence of wild-type T. denitrificans and nitrate, UO₂(s) dissolution rates were similar to those of abiotic experiments with nitrite (from 1.15 × 10^-14 to 4.94 × 10^-13 mol m^-2 s^-1). Experiments with a T. dentrificans mutant strain defective in U(IV) oxidation supported microbially mediated U(IV) oxidation. X-ray absorption spectroscopy (XAS) analysis of post-reaction solids showed the presence of mononuclear U(VI) species rather than a solid U(VI) phase. At steady-state U release, kinetic and spectroscopic results suggest detachment of oxidized U(VI) from the UO₂(s) surface as the rate-determining step rather than electron transfer or ion diffusion. Under anaerobic conditions, production of nitrite by nitrate-reducing microorganisms and enzymatically catalyzed, nitrate-dependent U(IV) oxidation are likely dual processes by which reduced U solids may be oxidized and mobilized in the aqueous phase.

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter

Soil microbial biomass can reach its annual maximum pool size beneath the winter snowpack and is known to decline abruptly following snowmelt in seasonally snow-covered ecosystems. Observed differences in winter versus summer microbial taxonomic composition also suggests that phylogenetically conserved traits may permit winter- versus summer-adapted microorganisms to occupy distinct niches. In this study, we sought to identify archaea, bacteria, and fungi that are associated with the soil microbial bloom overwinter and the subsequent biomass collapse following snowmelt at a high-altitude watershed in central Colorado, United States. Archaea, bacteria, and fungi were categorized into three life strategies (Winter-Adapted, Snowmelt-Specialist, Spring-Adapted) based upon changes in abundance during winter, the snowmelt period, and after snowmelt in spring. We calculated indices of phylogenetic relatedness (archaea and bacteria) or assigned functional attributes (fungi) to organisms within life strategies to infer whether phylogenetically conserved traits differentiate Winter-Adapted, Snowmelt-Specialist, and Spring-Adapted groups. We observed that the soil microbial bloom was correlated in time with a pulse of snowmelt infiltration, which commenced 65 days prior to soils becoming snow-free. A pulse of nitrogen (N, as nitrate) occurred after snowmelt, along with a collapse in the microbial biomass pool size, and an increased abundance of nitrifying archaea and bacteria (e.g., Thaumarchaeota, Nitrospirae). Winter- and Spring-Adapted archaea and bacteria were phylogenetically clustered, suggesting that phylogenetically conserved traits allow Winter- and Spring-Adapted archaea and bacteria to occupy distinct niches. In contrast, Snowmelt-Specialist archaea and bacteria were phylogenetically overdispersed, suggesting that the key mechanism(s) of the microbial biomass crash are likely to be density-dependent (e.g., trophic interactions, competitive exclusion) and affect organisms across a broad phylogenetic spectrum. Saprotrophic fungi were the dominant functional group across fungal life strategies, however, ectomycorrhizal fungi experienced a large increase in abundance in spring. If well-coupled plant-mycorrhizal phenology currently buffers ecosystem N losses in spring, then changes in snowmelt timing may alter ecosystem N retention potential. Overall, we observed that snowmelt separates three distinct soil niches that are occupied by ecologically distinct groups of microorganisms. This ecological differentiation is of biogeochemical importance, particularly with respect to the mobilization of nitrogen during winter, before and after snowmelt.

Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme

We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting the formidable demands on PhdB for catalysis of this reaction. Evidence that PhdB was able to bind α,α-difluorophenylacetate but was unable to catalyze its decarboxylation supported the enzyme's abstraction of a methylene H atom. Diminished activity of H327A and Y691F mutants was consistent with proposed proton donor roles for His327 and Tyr691. Collectively, these and other data most strongly support PhdB attack at the methylene carbon.

Use of carbon stable isotopes to monitor biostimulation and electron donor fate in chromium-contaminated groundwater

Hexavalent chromium Cr(VI) is a common inorganic contaminant in industrial areas and represents a serious threat to human health due its toxicity. Here we report experimental results from a field-scale investigation of Cr(VI) bio-immobilization at Hanford 100H reservation, a U.S Department of Energy facility (Washington State, USA). Microbial Cr(VI) reduction was stimulated via injection of a¹³C-labeled sodium lactate solution into the high-permeability aquifer consisting of gravel and coarse sand sediments. Concentrations and carbon isotope ratios of metabolites, including dissolved inorganic carbon and total organic carbon, and compound-specific analysis of acetate and propionate, together with phospholipid fatty acids (biomass) have been analyzed to help provide an understanding of the predominant redox processes accompanying Cr(VI) reduction. Results of our study indicate that the injection of an electron donor caused a sharp decrease of Cr(VI) concentration from ∼32 to ∼10 nM. Cr(VI) reduction was associated with a decrease in the concentration of carboxylic acids, such as lactate (∼6 mM to undetectable), propionate (∼9 mM to undetectable), and acetate (∼6 mM to undetectable), as well as dissolved inorganic carbon (30-10 mM C). Carbon isotope data indicate carbon transfers from the original substrate to organic byproducts and mineralized carbon. Concentrations of metabolites and stable isotope data as well as carbon isotope mass balance calculations were used to monitor biologically mediated reduction of Cr(VI).

Methyl Ketones from Municipal Solid Waste Blends by One-Pot Ionic-Liquid Pretreatment, Saccharification, and Fermentation

The conversion of municipal solid waste (MSW) and lignocellulosic biomass blends to methyl ketones (MKs) was investigated by using bioderived ionic liquid (bionic liquid)-based hydrolysates followed by fermentation with an engineered Escherichia coli strain. The hydrolysates were produced by a one-pot process using six types of MSW-biomass blends, choline-based bionic liquids, and commercial enzymes. Based on the sugar yields, one blend (corn stover/MSW=95:5, w/w) and two bionic liquids {cholinium lysinate ([Ch][Lys]) and cholinium aspartate ([Ch]₂ [Asp])} were selected for scale-up studies. Maximum yields of 82.3 % glucose and 54.4 % xylose were obtained from the selected blend in the scale-up studies (6 L), which was comparable with 83.6 % glucose and 52.8 % xylose obtained at a smaller scale (0.2 L). Comparable or higher yields of medium-chain (C₁₁ -C₁₇ ) MKs were achieved by using the MSW-biomass blend-derived hydrolysates, relative to the sugar controls (glucose and xylose) with similar sugar feeding concentrations. Up to 1145 mg L^-1 of MKs was produced by using MSW-biomass-derived hydrolysates, and the MK titer decreased to 300 mg L^-1 when the bionic-liquid concentration in the hydrolysate increased from 1 to 2 %, indicative of bionic-liquid inhibition. Technoeconomic analysis was conducted to investigate the economic potential of using the selected MSW-biomass blend as a feedstock to produce MKs.

Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning

The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids

Plants are an attractive sourceof renewable carbon for conversion to biofuels and bio-based chemicals. Conversion strategies often use a fraction of the biomass, focusing on sugars from cellulose and hemicellulose. Strategies that use plant components, such as aromatics and amino acids, may improve the efficiency of biomass conversion. Pseudomonas putida is a promising host for its ability to metabolize a wide variety of organic compounds. P. putida was engineered to produce methyl ketones, which are promising diesel blendstocks and potential platform chemicals, from glucose and lignin-related aromatics. Unexpectedly, P. putida methyl ketone production using Arabidopsis thaliana hydrolysates was enhanced 2-5-fold compared with sugar controls derived from engineered plants that overproduce lignin-related aromatics. This enhancement was more pronounced (~seven-fold increase) with hydrolysates from nonengineered switchgrass. Proteomic analysis of the methyl ketone-producing P. putida suggested that plant-derived amino acids may be the source of this enhancement. Mass spectrometry-based measurements of plant-derived amino acids demonstrated a high correlation between methyl ketone production and amino acid concentration in plant hydrolysates. Amendment of glucose-containing minimal media with a defined mixture of amino acids similar to those found in the hydrolysates studied led to a nine-fold increase in methyl ketone titer (1.1 g/L).

Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG

We previously engineered Escherichia coli to overproduce medium- to long-chain saturated and monounsaturated methyl ketones, which could potentially be applied as diesel fuel blending agents or in the flavor and fragrance industry. Recent efforts at strain optimization have focused on cofactor balance, as fatty acid-derived pathways face the systematic metabolic challenge of net NADPH consumption (in large part, resulting from the key fatty acid biosynthetic enzyme FabG [β-ketoacyl-ACP reductase]) and net NADH production. In this study, we attempted to mitigate cofactor imbalance by heterologously expressing NADH-dependent, rather than NADPH-dependent, versions of FabG identified in previous studies. Of the four NADH-dependent versions of FabG tested in our previously best-reported methyl ketone-producing strain (EGS1895), the version from Acholeplasma laidlawii (Al_FabG) showed the greatest increase in methyl ketone yield in shake flasks (35-75% higher than for an RFP negative-control strain, depending on sugar loading). An improved strain (EGS2920) attained methyl ketone titers during fed-batch fermentation of 5.4 ± 0.5 g/L, which were, on average, ca. 40% greater than those for the base strain (EGS1895) under fermentation conditions optimized in this study. Shotgun proteomic data for strains EGS2920 and EGS1895 during fed-batch fermentation were consistent with the goal of alleviating NADPH limitation through expression of Al_FabG. For example, relative to strain EGS1895, strain EGS2920 significantly upregulated glucose-6-phosphate isomerase (directing flux into glycolysis rather than the NADPH-producing pentose phosphate pathway) and downregulated MaeB (a NADP⁺ -dependent malate dehydrogenase). Overall, the results suggest that heterologous expression of NADH-dependent FabG in E. coli may improve sustained production of fatty acid-derived renewable fuels and chemicals.

Engineering E. coli for simultaneous glucose-xylose utilization during methyl ketone production

Background

We previously developed an E. coli strain that overproduces medium-chain methyl ketones for potential use as diesel fuel blending agents or as flavors and fragrances. To date, the strain’s performance has been optimized during growth with glucose. However, lignocellulosic biomass hydrolysates also contain a substantial portion of hemicellulose-derived xylose, which is typically the second most abundant sugar after glucose. Commercialization of the methyl ketone-producing technology would benefit from the increased efficiency resulting from simultaneous, rather than the native sequential (diauxic), utilization of glucose and xylose.

Results

In this study, genetic manipulations were performed to alleviate carbon catabolite repression in our most efficient methyl ketone-producing strain. A strain engineered for constitutive expression of xylF and xylA (involved in xylose transport and metabolism) showed synchronized glucose and xylose consumption rates. However, this newly acquired capability came at the expense of methyl ketone titer, which decreased fivefold. Further efforts were made to improve methyl ketone production in this strain, and we found that two strategies were effective at enhancing methyl ketone titer: (1) chromosomal deletion of pgi (glucose-6-phosphate isomerase) to increase intracellular NADPH supply and (2) downregulation of CRP (cAMP receptor protein) expression by replacement of the native RBS with an RBS chosen based upon mutant library screening results. Combining these strategies resulted in the most favorable overall phenotypes for simultaneous glucose–xylose consumption without compromising methyl ketone titer at both 1 and 2% total sugar concentrations in shake flasks.

Conclusions

This work demonstrated a strategy for engineering simultaneous utilization of C₆ and C₅ sugars in E. coli without sacrificing production of fatty acid-derived compounds.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0862-6) contains supplementary material, which is available to authorized users.

Reoxidation of Chromium(III) Products Formed under Different Biogeochemical Regimes

Hexavalent chromium, Cr(VI), is a widespread and toxic groundwater contaminant. Reductive immobilization to Cr(III) is a treatment option, but its success depends on the long-term potential for reduced chromium precipitates to remain immobilized under oxidizing conditions. In this unique long-term study, aquifer sediments subjected to reductive Cr(VI) immobilization under different biogeochemical regimes were tested for their susceptibility to reoxidation. After reductive treatment for 1 year, sediments were exposed to oxygenated conditions for another 2 years in flow-through, laboratory columns. Under oxidizing conditions, immobilized chromium reduced under predominantly denitrifying conditions was mobilized at low concentrations (≪1 μM Cr(VI); ∼ 3% of Cr(III) deposited) that declined over time. A conceptual model of a limited pool of more soluble Cr(III), and a larger pool of relatively insoluble Cr(III), is proposed. In contrast, almost no chromium was mobilized from columns reduced under predominantly fermentative conditions, and where reducing conditions persisted for several months after introduction of oxidizing conditions, presumably due to the presence of a reservoir of reduced species generated during reductive treatment. The results from this 3-year study demonstrate that biogeochemical conditions present during reductive treatment, and the potential for buildup of reducing species, will impact the long-term sustainability of the remediation effort.

Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain

Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling, based on published and newly generated data, is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain. In this system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs (e.g., oxidizing Fe(II), S compounds, and ammonium) is linked to the presence of DO, which has higher concentrations near the water table.

Monoterpene 'thermometer' of tropical forest-atmosphere response to climate warming

Tropical forests absorb large amounts of atmospheric CO₂ through photosynthesis but elevated temperatures suppress this absorption and promote monoterpene emissions. Using ¹³ CO₂ labeling, here we show that monoterpene emissions from tropical leaves derive from recent photosynthesis and demonstrate distinct temperature optima for five groups (Groups 1-5), potentially corresponding to different enzymatic temperature-dependent reaction mechanisms within β-ocimene synthases. As diurnal and seasonal leaf temperatures increased during the Amazonian 2015 El Niño event, leaf and landscape monoterpene emissions showed strong linear enrichments of β-ocimenes (+4.4% °C^-1 ) at the expense of other monoterpene isomers. The observed inverse temperature response of α-pinene (-0.8% °C^-1 ), typically assumed to be the dominant monoterpene with moderate reactivity, was not accurately simulated by current global emission models. Given that β-ocimenes are highly reactive with respect to both atmospheric and biological oxidants, the results suggest that highly reactive β-ocimenes may play important roles in the thermotolerance of photosynthesis by functioning as effective antioxidants within plants and as efficient atmospheric precursors of secondary organic aerosols. Thus, monoterpene composition may represent a new sensitive 'thermometer' of leaf oxidative stress and atmospheric reactivity, and therefore a new tool in future studies of warming impacts on tropical biosphere-atmosphere carbon-cycle feedbacks.

Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer

Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with an initial N₂ headspace and were sampled every 5 days for metagenome and metatranscriptome profiles in combination with biogeochemical measurements. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO₂ during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after 2 weeks. A pulse of methanogenesis co-occurred with acetogenesis, but only accounted for a small fraction of carbon flux. The depletion of DOM over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO₂ fixation, H₂ oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates (numerous lesser expressed cell-wall-associated hydrolases targeted peptidoglycan). Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Enhanced fatty acid production in engineered chemolithoautotrophic bacteria using reduced sulfur compounds as energy sources

Chemolithoautotrophic bacteria that oxidize reduced sulfur compounds, such as H₂S, while fixing CO₂ are an untapped source of renewable bioproducts from sulfide-laden waste, such as municipal wastewater. In this study, we report engineering of the chemolithoautotrophic bacterium Thiobacillus denitrificans to produce up to 52-fold more fatty acids than the wild-type strain when grown with thiosulfate and CO₂. A modified thioesterase gene from E. coli (‘tesA) was integrated into the T. denitrificans chromosome under the control of P_kan or one of two native T. denitrificans promoters. The relative strength of the two native promoters as assessed by fatty acid production in engineered strains was very similar to that assessed by expression of the cognate genes in the wild-type strain. This proof-of-principle study suggests that engineering sulfide-oxidizing chemolithoautotrophic bacteria to overproduce fatty acid-derived products merits consideration as a technology that could simultaneously produce renewable fuels/chemicals as well as cost-effectively remediate sulfide-contaminated wastewater.

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Reduced S compounds and CO₂ can be feedstocks for biobased chemicals and biofuels.

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Fatty acids increased 52-fold in Thiobacillus denitrificans with E. coli ‘tesA.

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Native T. denitrificans promoters driving ‘tesA predictably enhanced fatty acids.

Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli

Ladderanes are hydrocarbon chains with three or five linearly concatenated cyclobutane rings that are uniquely produced as membrane lipid components by anammox (anaerobic ammonia-oxidizing) bacteria. By virtue of their angle and torsional strain, ladderanes are unusually energetic compounds, and if produced biochemically by engineered microbes, could serve as renewable, high-energy-density jet fuel components. The biochemistry and genetics underlying the ladderane biosynthetic pathway are unknown, however, previous studies have identified a pool of 34 candidate genes from the anammox bacterium, Kuenenia stuttgartiensis, some or all of which may be involved with ladderane fatty acid biosynthesis. The goal of the present study was to establish a systematic means of testing the candidate genes from K. stuttgartiensis for involvement in ladderane biosynthesis through heterologous expression in E. coli under anaerobic conditions. This study describes an efficient means of assembly of synthesized, codon-optimized candidate ladderane biosynthesis genes in synthetic operons that allows for changes to regulatory element sequences, as well as modular assembly of multiple operons for simultaneous heterologous expression in E. coli (or potentially other microbial hosts). We also describe in vivo functional tests of putative anammox homologs of the phytoene desaturase CrtI, which plays an important role in the hypothesized ladderane pathway, and a method for soluble purification of one of these enzymes. This study is, to our knowledge, the first experimental effort focusing on the role of specific anammox genes in the production of ladderanes, and lays the foundation for future efforts toward determination of the ladderane biosynthetic pathway. Our substantial, but far from comprehensive, efforts at elucidating the ladderane biosynthetic pathway were not successful. We invite the scientific community to take advantage of the considerable synthetic biology resources and experimental results developed in this study to elucidate the biosynthetic pathway that produces unique and intriguing ladderane lipids.

Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids

Although natural products are best known for their use in medicine and agriculture, a number of fatty acid-derived and isoprenoid natural products are being developed for use as renewable biofuels and bio-based chemicals. This review summarizes recent work on fatty acid-derived compounds (fatty acid alkyl esters, fatty alcohols, medium- and short-chain methyl ketones, alkanes, α-olefins, and long-chain internal alkenes) and isoprenoids, including hemiterpenes (e.g., isoprene and isopentanol), monoterpenes (e.g., limonene), and sesquiterpenes (e.g., farnesene and bisabolene).

Characterization of Chromium Bioremediation Products in Flow-Through Column Sediments Using Micro-X-ray Fluorescence and X-ray Absorption Spectroscopy

Microbially mediated reductive immobilization of chromium is a possible remediation technique for sites contaminated with Cr(VI). This study is part of a broader effort investigating the biogeochemical mechanisms for Cr(VI) reduction in Hanford 100H aquifer sediments using flow-through laboratory columns. It had previously been shown that reduced chromium in the solid phase was in the form of freshly precipitated mixed-phase Cr(III)-Fe(III) (hydr)oxides, irrespective of the biogeochemical conditions in the columns. In this study, the reduced Cr phases in the columns were investigated further using spectroscopy to understand the structure and mechanisms involved in the formation of the end products. Several samples representing potential processes that could be occurring in the columns were synthesized in the laboratory and characterized using X-ray absorption near edge structure (XANES) and X-ray scattering. The XANES of Cr(III) particles in the columns most closely resembled those from synthetic samples produced by the abiotic reaction of Cr(VI) with microbially reduced Fe(II). Microbially mediated Cr-Fe reduction products were distinct from abiotic Cr-Fe (hydr)oxides [CrFe(OH)] and organically complexed Cr(III) sorbed onto the surface of a mixed ferrihydrite-goethite mineral phase. Furthermore, analyses of the abiotically synthesized samples revealed that even the end products of purely abiotic, iron-mediated reduction of Cr(VI) are affected by factors such as the presence of excess aqueous Fe(II) and cellular matter. These results suggest that CrFe(OH) phases made under realistic subsurface conditions or in biotic cultures are structurally different from pure Cr(OH) or laboratory-synthesized CrFe(OH). The observed structural differences imply that the reactivity and stability of biogenic CrFe(OH) could potentially be different from that of abiotic CrFe(OH).

Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products

In this study of reductive chromium immobilization, we found that flow-through columns constructed with homogenized aquifer sediment and continuously infused with lactate, chromate, and various native electron acceptors diverged to have very different Cr(VI)-reducing biogeochemical regimes characterized by either denitrifying or fermentative conditions (as indicated by effluent chemical data, 16S rRNA pyrotag data, and metatranscriptome data). Despite the two dramatically different biogeochemical environments that evolved in the columns, these regimes created similar Cr(III)-Fe(III) hydroxide precipitates as the predominant Cr(VI) reduction product, as characterized by micro-X-ray fluorescence and micro-X-ray absorption near-edge structure analysis. We discuss two conflicting scenarios of microbially mediated formation of Cr(III)-Fe(III) precipitates, each of which is both supported and contradicted by different lines of evidence: (1) enzymatic reduction of Cr(VI) to Cr(III) followed by coprecipitation of Cr(III) and Fe(III) and (2) both regimes generated at least small amounts of Fe(II), which abiotically reduced Cr(VI) to form a Cr-Fe precipitate. Evidence of zones with different levels of Cr(VI) reduction suggest that local heterogeneity may have confounded interpretation of processes based on bulk measurements. This study indicates that the bulk redox status and biogeochemical regime, as categorized by the dominant electron-accepting process, do not necessarily control the final product of Cr(VI) reduction.

Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production

Background

The chemoautotrophic bacterium Ralstonia eutropha can utilize H₂/CO₂ for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO₂, little work has been done to develop genetic part libraries to enable such endeavors.

Results

We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5’ mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters P_BAD, T7, P_xyls/PM, P_lacUV5, and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts.

Conclusion

We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.

Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe(2) (+), and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c 1-cytochrome subunit of the cytochrome bc 1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. A transposon mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process.

Functionalizing bacterial cell surfaces with a phage protein

Functionalization of bacterial cell surfaces has the potential to introduce new activities by chemical modification. Here we show that a bacteriophage-receptor complex can be used to functionalize the surface of two Gram-negative proteobacteria, Escherichia coli and Ralstonia eutropha with CdSe/ZnS nanoparticles. This work highlights the potential for using microbe-phage interactions to generate new functions on living cells.

Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus

Micrococcus luteus is a Gram-positive bacterium that produces iso- and anteiso-branched alkenes by the head-to-head condensation of fatty-acid thioesters [coenzyme A (CoA) or acyl carrier protein (ACP)]; this activity is of interest for the production of advanced biofuels. In an effort to better understand the control of the formation of branched fatty acids in M. luteus, the structure of FabH (MlFabH) was determined. FabH, or β-ketoacyl-ACP synthase III, catalyzes the initial step of fatty-acid biosynthesis: the condensation of malonyl-ACP with an acyl-CoA. Analysis of the MlFabH structure provides insights into its substrate selectivity with regard to length and branching of the acyl-CoA. The most structurally divergent region of FabH is the L9 loop region located at the dimer interface, which is involved in the formation of the acyl-binding channel and thus limits the substrate-channel size. The residue Phe336, which is positioned near the catalytic triad, appears to play a major role in branched-substrate selectivity. In addition to structural studies of MlFabH, transcriptional studies of M. luteus were also performed, focusing on the increase in the ratio of anteiso:iso-branched alkenes that was observed during the transition from early to late stationary phase. Gene-expression microarray analysis identified two genes involved in leucine and isoleucine metabolism that may explain this transition.

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

Chemolithoautotrophic bacteria can be of industrial and environmental importance, but they present a challenge for systems biology studies, as their central metabolism deviates from that of model organisms and there is a much less extensive experimental basis for their gene annotation than for typical organoheterotrophs. For microbes with sequenced genomes but unconventional metabolism, the ability to create knockout mutations can be a powerful tool for functional genomics and thereby render an organism more amenable to systems biology approaches. In this chapter, we describe a genetic system for Thiobacillus denitrificans, with which insertion mutations can be introduced by homologous recombination and complemented in trans. Insertion mutations are generated by in vitro transposition, the mutated genes are amplified by the PCR, and the amplicons are introduced into T. denitrificans by electroporation. Use of a complementation vector, pTL2, based on the IncP plasmid pRR10 is also addressed.

Complete genome sequence of Tolumonas auensis type strain (TA 4)

Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

Physiological and transcriptional studies of Cr(VI) reduction under aerobic and denitrifying conditions by an aquifer-derived pseudomonad

Cr(VI) is a widespread groundwater contaminant that is a potent toxin, mutagen, and carcinogen. In situ reductive immobilization is a favored approach for Cr(VI) bioremediation, and Cr(VI) reduction has been reported in a variety of aerobic, facultative, and anaerobic bacteria, including a number of pseudomonads. However, studies comparing Cr(VI) reduction under aerobic and denitrifying conditions in the same organism are not available. We have conducted studies with strain RCH2, a bacterium similar to Pseudomonas stutzeri that we isolated from a Cr-contaminated aquifer. Cell suspension studies with lactate demonstrated that Cr(VI) reduction could occur under either denitrifying or aerobic conditions (at comparable specific rates) and that reduction was at least 20-fold more rapid when the terminal electron acceptor (i.e., nitrate or O(2)) was present. Our results suggest that Cr(VI) reduction by strain RCH2 under either aerobic or denitrifying conditions is primarily cometabolic in the sense that the physiological electron acceptor (oxygen or nitrate) appears to be required. Under both aerobic and denitrifying conditions, the gene(s) associated with chromate reduction are not inducible by Cr. Continuous culture (chemostat) studies showed strong correlations (r(2) values >0.93) between nitrate reduction rate and the transcript copy number of either nirS (cytochrome cd(1) nitrite reductase) or narG (nitrate reductase α subunit). As our studies indicate that anaerobic Cr(VI) reduction by this pseudomonad requires active denitrification and that denitrification and chromate reduction rates are highly correlated (r(2) > 0.99), monitoring expression of such denitrification genes in biostimulated aquifers could provide valuable proxy information for in situ chromate reduction by similar bacteria even if the specific genes involved in chromate reduction have not been identified. We also report incomplete removal of reduced Cr from solution and on artifacts in the widely used diphenylcarbazide assay for Cr(VI), most notably, its complete inactivation in the presence of millimolar nitrite.

Comparative assessments of benzene, toluene, and xylene natural attenuation by quantitative polymerase chain reaction analysis of a catabolic gene, signature metabolites, and compound-specific isotope analysis

A controlled-release study conducted at Vandenberg Air Force Base involved the injection of anaerobic groundwater amended with benzene, toluene, and o-xylene (BToX; 1-3 mg/L each) in two parallel lanes: lane A injectate contained no ethanol, whereas lane B injectate contained approximately 500 mg/L ethanol. As reported previously by Mackay and co-workers, ethanol led to slower BToX disappearance in lane B. Here, we report on assessments of BToX natural attenuation by three independent and specific monitoring approaches: signature metabolites diagnostic of anaerobic TX metabolism (benzysuccinates), compound-specific isotope analysis (CSIA), and quantitative polymerase chain reaction (qPCR) analysis of a catabolic gene involved in anaerobic TX degradation (bssA). In combination, the three monitoring methods provided strong evidence of in situ TX biodegradation in both lanes A and B; however, no single method provided strong evidence for TX biodegradation in both lanes. Benzylsuccinates were detected almost exclusively in lane B, where slower TX degradation and higher residual TX concentrations led to higher metabolite concentrations. In contrast, CSIA provided evidence of TX biodegradation almost exclusively in lane A, as greater degradation rates led to more pronounced isotopic enrichment. qPCR analyses of bssA were more complex. Evidence of increases in bssA copy number (up to 200-fold) after the release started was stronger in lane A, but higher absolute bssA copy number (and bacterial abundance, based on 16S rRNA genes) was observed in lane B, where bacteria genetically capable of anaerobic TX degradation may have been growing primarily on ethanol or its metabolites rather than TX.

Development of a genetic system for the chemolithoautotrophic bacterium Thiobacillus denitrificans

Thiobacillus denitrificans is a widespread, chemolithoautotrophic bacterium with an unusual and environmentally relevant metabolic repertoire, which includes its ability to couple denitrification to sulfur compound oxidation; to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV); and to oxidize mineral electron donors. Recent analysis of its genome sequence also revealed the presence of genes encoding two [NiFe]hydrogenases, whose role in metabolism is unclear, as the sequenced strain does not appear to be able to grow on hydrogen as a sole electron donor under denitrifying conditions. In this study, we report the development of a genetic system for T. denitrificans, with which insertion mutations can be introduced by homologous recombination and complemented in trans. The antibiotic sensitivity of T. denitrificans was characterized, and a procedure for transformation with foreign DNA by electroporation was established. Insertion mutations were generated by in vitro transposition, the mutated genes were amplified by the PCR, and the amplicons were introduced into T. denitrificans by electroporation. The IncP plasmid pRR10 was found to be a useful vector for complementation. The effectiveness of the genetic system was demonstrated with the hynL gene, which encodes the large subunit of a [NiFe]hydrogenase. Interruption of hynL in a hynL::kan mutant resulted in a 75% decrease in specific hydrogenase activity relative to the wild type, whereas complementation of the hynL mutation resulted in activity that was 50% greater than that of the wild type. The availability of a genetic system in T. denitrificans will facilitate our understanding of the genetics and biochemistry underlying its unusual metabolism.

Whole-genome transcriptional analysis of chemolithoautotrophic thiosulfate oxidation by Thiobacillus denitrificans under aerobic versus denitrifying conditions

Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with key chemolithoautotrophic functions (such as sulfur compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately 10% of the genome) as differentially expressed using RMA (robust multiarray average) statistical analysis and a twofold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated, respectively, with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription-quantitative PCR analysis was used to validate these trends.

The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans

The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.

Analysis of anaerobic BTX biodegradation in a subarctic aquifer using isotopes and benzylsuccinates

In situ biodegradation of benzene, toluene, and xylenes in a petroleum hydrocarbon contaminated aquifer near Fairbanks, Alaska was assessed using carbon and hydrogen compound specific isotope analysis (CSIA) of benzene and toluene and analysis of signature metabolites for toluene (benzylsuccinate) and xylenes (methylbenzylsuccinates). Carbon and hydrogen isotope ratios of benzene were between -25.9 per thousand and -26.8 per thousand for delta13C and -119 per thousand and -136 per thousand for delta2H, suggesting that biodegradation of benzene is unlikely at this site. However, biodegradation of both xylenes and toluene were documented in this subarctic aquifer. Biodegradation of xylenes was indicated by the presence of methylbenzylsuccinates with concentrations of 17-50 microg/L in three wells. Anaerobic toluene biodegradation was also indicated by benzylsuccinate concentrations of 10-49 microg/L in the three wells with the highest toluene concentrations (1500-5000 microg/L toluene). Since benzylsuccinate typically accounts for a very small fraction of the toluene present in groundwater (generally <1 mol%), the signature metabolite approach works best at higher toluene concentrations when it is not constrained by detection limits. In wells with lower toluene concentrations (410-640 microg/L), carbon and hydrogen isotopic values were enriched by up to approximately 2 per thousand for delta13C and approximately 70 per thousand for delta2H. This evidence of isotopic fractionation verifies the effects of biodegradation in these low concentration wells where metabolites may already be below detection limits. The combined use of signature metabolite and CSIA data is particularly valuable given the challenge of verifying biodegradation in subarctic environments where degradation rates are typically much slower than in temperate environments.

Metabolites detected during biodegradation of 13C6-benzene in nitrate-reducing and methanogenic enrichment cultures

The mechanism for anaerobic metabolism of benzene remains unknown. To date, there have been only a few studies reporting metabolites of anaerobic benzene biodegradation, in part because anaerobic benzene-degrading enrichment cultures are not very common and only two isolates have been characterized to date. Phenol and benzoate, metabolites consistent with benzene hydroxylation or benzene carboxylation, have been identified previously in mixed cultures, and more recently benzene methylation to toluene has been proposed as another possible mechanism for anaerobic benzene degradation. In this study, 13C6-benzene was added to nitrate-reducing and methanogenic enrichment cultures and specific 13C-labeled metabolites were monitored over time. The putative metabolites were detected by gas chromatography/mass spectrometry in ether extracts of 100-mL samples of culture taken at each time point. This method of analysis provided the sensitivity required to accurately quantify low concentrations of these compounds. In addition, benzoate trapping was used in an attemptto increase concentrations of upstream metabolites. In both cultures, in the presence and absence of unlabeled benzoate (trap), [ring-13C]-toluene and [ring-13C]benzoate were detected transiently during degradation. The data strongly support initial methylation of benzene to toluene, followed bytransformation to benzoate. Although benzene methylation has been proposed previously, this is the first direct evidence to supportthis pathway. In the methanogenic culture only, 13C6-phenol was also detected. The transient appearance of phenol, which appeared to be further transformed to benzoate, suggests that a pathway involving hydroxylation to phenol, as proposed in other studies, was also operative.

Anaerobic, nitrate-dependent oxidation of U(IV) oxide minerals by the chemolithoautotrophic bacterium Thiobacillus denitrificans

Under anaerobic conditions and at circumneutral pH, cells of the widely distributed, obligate chemolithoautotrophic bacterium Thiobacillus denitrificans oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated with nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium.

Biochemical and genetic evidence of benzylsuccinate synthase in toluene-degrading, ferric iron-reducing Geobacter metallireducens

In vitro assays demonstrated that toluene-grown cells of Geobacter metallireducens catalyzed the addition of toluene to fumarate to form benzylsuccinate under anaerobic conditions. The specific in vitro rate of benzylsuccinate formation was ca. 45% of the specific in vivo rate of toluene consumption. In addition, bssA and bssB, which code for the alpha and beta subunits of benzylsuccinate synthase (BSS), respectively, were found to have sequences in G. metallireducens similar to the only sequences heretofore available (for three denitrifying strains). This is the first report of the presence of BSS in a ferric iron-reducing bacterium; BSS activity has previously been reported in denitrifying, sulfate-reducing, and anoxygenic phototrophic toluene degraders, as well as in a highly enriched methanogenic, toluene-degrading culture.

In situ transformation of deuterated toluene and xylene to benzylsuccinic acid analogues in BTEX-contaminated aquifers

Techniques for detecting and quantifying anaerobic transformations of benzene, toluene, ethylbenzene, and xylene (BTEX) are needed to assess the feasibility of using in situ bioremediation to treat BTEX-contaminated groundwater aquifers. Deuterated surrogates of toluene (toluene-d8) and xylene (o-xylene-d10) were injected into BTEX-contaminated aquifers during single-well push-pull tests to monitor for the in situ formation of deuterated benzylsuccinic acid (BSA-d8) and o-methyl-BSA-d10. Test solutions (250 L) containing toluene-d8 (9-22 microM) and o-xylene-d10 (4-9 microM) along with a conservative bromide tracer (1.3 mM) and nitrate (4 mM) as an electron acceptor were injected into four wells at two sites. Detection of BSA-d8 and o-methyl-BSA-d10 in groundwater samples collected from the same wells following injection unequivocally demonstrated anaerobic in situ toluene-d8 and o-xylene-d10 transformation with calculated zero-order formation rates ranging from 1.0 to 7.4 nM/day. Concurrent utilization of co-injected nitrate was rapid in all tests at both sites, with zero-order rates ranging from 13 to 39 microM/h. The field tests conducted in this study represent the first reported use of deuterated aromatic hydrocarbons to detect and quantify anaerobic BTEX transformation product formation in the subsurface.

A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene

We have developed a real-time polymerase chain reaction (PCR) method that can quantify hydrocarbon-degrading bacteria in sediment samples based on a catabolic gene associated with the first step of anaerobic toluene and xylene degradation. The target gene, bssA, codes for the alpha-subunit of benzylsuccinate synthase. The primer-probe set for real-time PCR was based on consensus regions of bssA from four denitrifying bacterial strains; bssA sequences for two of these strains were determined during this study. The method proved to be sensitive (detection limit ca. 5 gene copies) and had a linear range of >7 orders of magnitude. We used the method to investigate how gasohol releases from leaking underground storage tanks could affect indigenous toluene-degrading bacteria. Microcosms inoculated with aquifer sediments from four different sites were incubated anaerobically with BTEX (benzene, toluene, ethylbenzene, and xylenes) and nitrate in the presence and absence of ethanol. Overall, population trends were consistent with observed toluene degradation activity: the microcosms with the most rapid toluene degradation also had the largest numbers of bssA copies. In the microcosms with the most rapid toluene degradation, numbers of bssA copies increased 100-to 1000-fold over the first 4 days of incubation, during which time most of the toluene had been consumed. These results were supported by slot blot analyses with unamplified DNA and by cloning and sequencing of putative bssA amplicons, which confirmed the real-time PCR method's specificity for bssA. Use of a companion real-time PCR method for estimating total eubacterial populations (based on 16S rDNA) indicated that, in some cases, ethanol disproportionately supported the growth of bacteria that did not contain bssA. The real-time PCR method for bssA could be a powerful tool for monitored natural attenuation of BTEX in fuel-contaminated groundwater. To our knowledge, this is the first reported molecular method that targets anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene.

Analysis of benzylsuccinates in groundwater by liquid chromatography/tandem mass spectrometry and its use for monitoring in situ BTEX biodegradaton

Benzylsuccinic acid (BS) and methylbenzylsuccinic acid (MeBS) isomers have been proposed as distinctive indicators of anaerobic toluene and xylene metabolism in fuel-contaminated aquifers; however, labor-intensive analytical procedures have limited their analysis at field sites. In this article, a rapid electrospray LC/MS/MS (liquid chromatography/mass spectrometry/mass spectrometry) method for benzylsuccinates is described that involves selected reaction monitoring, internal standard quantification with [ring-2H5]BS, small sample size (<1 mL), and no extraction/concentration steps. The highly selective LC/MS/ MS method was shown to be sensitive (detection limits ca. 0.3 microg/L), accurate, and precise. The method was used to characterize geographic and temporal distributions of BS and MeBS isomers in an anaerobic, hydrocarbon-contaminated aquifer. BS was never detected, and MeBS isomers were detected in the three wells with the highest concentrations of BTEX (benzene, toluene, ethylbenzene, and xylenes); MeBS concentrations ranged from <0.3 to 205 microg/L. A strong linear correlation (r2 = 0.94; n = 12) was found between concentrations of total MeBS isomers and their parent compounds, xylenes, which suggests that anaerobic xylene metabolism at this site was probably first-order rather than zero-order. The novel LC/MS/MS method for BS and MeBS isomers is a promising technique for rapid and reliable monitoring of in situ bioremediation of gasoline-contaminated groundwater.

Anaerobic biotransformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) by aquifer bacteria using hydrogen as the sole electron donor

RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) is a nitramine explosive that has contaminated soil and groundwater at military installations throughout the US. Although anaerobic RDX metabolism has been reported, the process is not well understood, as past studies have typically involved complex, undefined media with multiple potential electron donors and acceptors. In this study, bacteria enriched from RDX-contaminated aquifer sediments consumed RDX in a defined, bicarbonate-buffered, anaerobic medium containing hydrogen as the sole electron donor and RDX as a potential electron acceptor and sole nitrogen source. RDX was not consumed in live controls that did not contain hydrogen. Transient formation of mononitroso- and dinitroso-RDX metabolites (hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine and hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine, respectively) was documented by liquid chromatography-mass spectrometry. However, studies with 14C-labeled RDX suggested that mineralization to carbon dioxide was negligible (<2%), which is consistent with cometabolic transformation. Several lines of evidence suggest that the RDX-transforming bacteria under study were homoacetogens, including correlations between RDX consumption and acetate production. Methanogens were unlikely to be responsible for RDX metabolism, as the presence of 2-bromoethanesulfonate, an inhibitor of methanogenesis, did not appear to affect RDX metabolism. The presence of nitrate reversibly halted RDX metabolism, whereas ammonium had no discernible effect, which implies that: (i) nitrate, which commonly occurs in RDX-contaminated groundwater, may inhibit in situ RDX metabolism, and (ii) although RDX may act as both a nitrogen source and cometabolic electron sink, the latter role predominates, as RDX reduction will proceed regardless of whether or not a more favorable nitrogen source is present.

Use of liquid chromatography/tandem mass spectrometry to detect distinctive indicators of in situ RDX transformation in contaminated groundwater

An important element of monitored natural attenuation is the detection in groundwater of distinctive products of pollutant degradation or transformation. In this study, three distinctive products of the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) were detected in contaminated groundwater from the Iowa Army Ammunition Plant; the products were MNX (hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine), DNX (hexahydro-1,3-dinitroso-5-nitro-1,3,5-triazine), and TNX (hexahydro-1,3,5-trinitroso-1,3,5-triazine). These compounds are powerful indicators of RDX transformation for several reasons: (a) they have unique chemical features that reveal their origin as RDX daughter products, (b) they have no known commercial, industrial, or natural sources, and (c) they are well documented as anaerobic RDX metabolites in laboratory studies. The products were analyzed by LC/MS/MS (liquid chromatography/mass spectrometry/mass spectrometry) with selected reaction monitoring and internal standard quantification using [ring-U-15N]RDX. Validation tests showed the novel LC/MS/MS method to be of favorable sensitivity (detection limits ca. 0.1 microg/L), accuracy, and precision. The products, which were detected in all groundwater samples with RDX concentrations of > ca. 1 microg/L (25 out of 55 samples analyzed), were present at concentrations ranging from near the detection limit to 430 microg/L. MNX was the typically the most abundant of the three nitroso-substituted products; concentrations of the products seldom exceeded 4 mol % of the RDX concentration, although they ranged as high as 26 mol % (TNX). Geographic and temporal distributions of RDX, MNX, DNX, and TNX were assessed. A degradation product resulting from RDX ring cleavage, methylenedinitramine, was not detected by LC/MS/MS in any sample (detection limit ca. 0.6-4 microg/L). This extensive field characterization of MNX, DNX, and TNX distributions in groundwater by a highly selective analytical method (LC/MS/MS) is significant because very little is known about the occurrence of intrinsic RDX transformation in contaminated aquifers.

Aerobic biodegradation of methyl tert-butyl ether by aquifer bacteria from leaking underground storage tank sites

The potential for aerobic methyl tert-butyl ether (MTBE) degradation was investigated with microcosms containing aquifer sediment and groundwater from four MTBE-contaminated sites characterized by oxygen-limited in situ conditions. MTBE depletion was observed for sediments from two sites (e.g., 4.5 mg/liter degraded in 15 days after a 4-day lag period), whereas no consumption of MTBE was observed for sediments from the other sites after 75 days. For sediments in which MTBE was consumed, 43 to 54% of added [U-(14)C]MTBE was mineralized to (14)CO(2). Molecular phylogenetic analyses of these sediments indicated the enrichment of species closely related to a known MTBE-degrading bacterium, strain PM1. At only one site, the presence of water-soluble gasoline components significantly inhibited MTBE degradation and led to a more pronounced accumulation of the metabolite tert-butyl alcohol. Overall, these results suggest that the effects of oxygen and water-soluble gasoline components on in situ MTBE degradation will vary from site to site and that phylogenetic analysis may be a promising predictor of MTBE biodegradation potential.

Metabolic indicators for detecting in situ anaerobic alkylbenzene degradation

Monitoring programs for intrinsic bioremediation of fuel hydrocarbons require indicators that can convincingly demonstrate in situ metabolism. In this evaluation of potential indicators of in situ anaerobic alkylbenzene metabolism, laboratory and field data are reviewed for two classes of aromatic acids: (i) benzylsuccinate, E-phenylitaconate, and their methyl homologs, and (ii) benzoate, and methyl-, dimethyl-, and trimethylbenzoates. The review includes previously unpublished field data from a hydrocarbon-contaminated site in Fallon (Nevada), at which both classes of metabolites were detected in groundwater. The two classes of compounds were evaluated with respect to specificity (i.e., unique biochemical relationship to a specific alkylbenzene), stability, and generation as degradation intermediates versus dead-end products; recent developments in the biochemistry of anaerobic toluene and xylene degradation were incorporated in this evaluation. In general, benzylsuccinates/E-phenylitaconates are superior to benzoates in terms of their very high specificity to their parent hydrocarbons and their lack of commercial and industrial sources. They are also uniquely indicative of anaerobic conditions. All of the benzoates, benzylsuccinates, and E-phenylitaconates are relatively stable chemically and (with the exception of benzoate) biologically under anaerobic conditions, based on the limited data available. Although benzoate, benzylsuccinate, and E-phenylitaconate are intermediates of anaerobic toluene mineralization to carbon dioxide, their methyl homologs can be either mineralization intermediates or cometabolic dead-end products of alkylbenzenes, depending on the bacteria involved. Benzoates are far more commonly reported in field studies of hydrocarbon-contaminated aquifers than are benzylsuccinates and E-phenylitaconates, although it is not clear whether this is an accurate representation of the relative occurrence of these metabolites at contaminated sites, or whether it instead reflects the limited range of target analytes used in most field studies to date.

Anaerobic toluene activation by benzylsuccinate synthase in a highly enriched methanogenic culture

Permeabilized cells of a highly enriched, toluene-mineralizing, methanogenic culture catalyzed the addition of toluene to fumarate to form benzylsuccinate under anaerobic conditions. The specific in vitro rate of benzylsuccinate formation was >85% of the specific in vivo rate of toluene consumption. This is the first report of benzylsuccinate synthase activity in a methanogenic culture; the activity has previously been reported to occur in denitrifying, sulfate-reducing, and anoxygenic phototrophic bacteria.

Initial reactions in anaerobic oxidation of m-xylene by the denitrifying bacterium Azoarcus sp. strain T

The initial enzymatic steps in anaerobic m-xylene oxidation were studied in Azoarcus sp. strain T, a denitrifying bacterium capable of mineralizing m-xylene via 3-methylbenzoate. Permeabilized cells of m-xylene-grown Azoarcus sp. strain T catalyzed the addition of m-xylene to fumarate to form (3-methylbenzyl)succinate. In the presence of succinyl coenzyme A (CoA) and nitrate, (3-methylbenzyl)succinate was oxidized to E-(3-methylphenyl)itaconate (or a closely related isomer) and 3-methylbenzoate. Kinetic studies conducted with permeabilized cells and whole-cell suspensions of m-xylene-grown Azoarcus sp. strain T demonstrated that the specific rate of in vitro (3-methylbenzyl)succinate formation accounts for at least 15% of the specific rate of in vivo m-xylene consumption. Based on these findings, we propose that Azoarcus sp. strain T anaerobically oxidizes m-xylene to 3-methylbenzoate (or its CoA thioester) via (3-methylbenzyl)succinate and E-(3-methylphenyl)itaconate (or its CoA thioester) in a series of reactions that are analogous to those recently proposed for anaerobic toluene oxidation to benzoyl-CoA. A deuterium kinetic isotope effect was observed in the (3-methylbenzyl)succinate synthase reaction (and the benzylsuccinate synthase reaction), suggesting that a rate-determining step in this novel fumarate addition reaction involves breaking a C-H bond.

Substrate range of benzylsuccinate synthase from Azoarcus sp. strain T

Benzylsuccinate synthase, which catalyzes the anaerobic addition of the methyl carbon of toluene to fumarate, has recently been reported in several denitrifying and sulfate-reducing, toluene-degrading bacteria. In substrate range studies with partially purified benzylsuccinate synthase from denitrifying Azoarcus sp. strain T, benzylsuccinate analogs were observed as a result of fumarate addition to the following toluene surrogates: xylenes, monofluorotoluenes, benzaldehyde, and 1-methyl-1-cyclohexene (but not 4-methyl-l-cyclohexene or methylcyclohexane). Benzylsuccinate was also observed as a result of toluene addition to maleate, but no products were observed from assays with toluene and either crotonate or trans-glutaconate. Toluene-maleate addition, like toluene-fumarate addition, resulted in highly stereospecific formation of the (+)-benzylsuccinic acid enantiomer [(R)-2-benzyl-3-carboxypropionic acid]. The previously reported finding that the methyl H atom abstracted from toluene is retained in the succinyl moiety of benzylsuccinate was found to apply to several toluene surrogates. The implications of these observations for the mechanism of benzylsuccinate synthase will be discussed.

Analysis of the novel benzylsuccinate synthase reaction for anaerobic toluene activation based on structural studies of the product

Recent studies of anaerobic toluene catabolism have demonstrated a novel reaction for anaerobic hydrocarbon activation: the addition of the methyl carbon of toluene to fumarate to form benzylsuccinate. In vitro studies of the anaerobic benzylsuccinate synthase reaction indicate that the H atom abstracted from the toluene methyl group during addition to fumarate is retained in the succinyl moiety of benzylsuccinate. Based on structural studies of benzylsuccinate formed during anaerobic, in vitro assays with denitrifying, toluene-mineralizing strain T, we now report the following characteristics of the benzylsuccinate synthase reaction: (i) it is highly stereospecific, resulting in >95% formation of the (+)-benzylsuccinic acid enantiomer [(R)-2-benzyl-3-carboxypropionic acid], and (ii) active benzylsuccinate synthase does not contain an abstracted methyl H atom from toluene at the beginning or at the end of a catalytic cycle.