Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization

Successes in biocatalytic polyester recycling have raised the possibility of deconstructing alternative polymers enzymatically, with polyamide (PA) being a logical target due to the array of amide-cleaving enzymes present in nature. Here, we screen 40 potential natural and engineered nylon-hydrolyzing enzymes (nylonases), using mass spectrometry to quantify eight compounds resulting from enzymatic nylon-6 (PA6) hydrolysis. Comparative time-course reactions incubated at 40-70 °C showcase enzyme-dependent variations in product distributions and extent of PA6 film depolymerization, with significant nylon deconstruction activity appearing rare. The most active nylonase, a NylCK variant we rationally thermostabilized (an N-terminal nucleophile (Ntn) hydrolase, NylCK-TS, Tm = 87.4 °C, 16.4 °C higher than the wild-type), hydrolyzes 0.67 wt% of a PA6 film. Reactions fail to restart after fresh enzyme addition, indicating that substrate-based limitations, such as restricted enzyme access to hydrolysable bonds, prohibit more extensive deconstruction. Overall, this study expands our understanding of nylonase activity distribution, indicates that Ntn hydrolases may have the greatest potential for further development, and identifies key targets for progressing PA6 enzymatic depolymerization, including improving enzyme activity, product selectivity, and enhancing polymer accessibility.

Integrated Advanced Molecular Tools Predict In Situ cVOC Degradation Rates: Field Demonstration

Chlorinated volatile organic compound (cVOC) degradation rate constants are crucial information for site management. Conventional approaches generate rate estimates from the monitoring and modeling of cVOC concentrations. This requires time series data collected along the flow path of the plume. The estimates of rate constants are often plagued by confounding issues, making predictions cumbersome and unreliable. Laboratory data suggest that targeted quantitative analysis of Dehalococcoides mccartyi (Dhc) biomarker genes (qPCR) and proteins (qProt) can be directly correlated with reductive dechlorination activity. To assess the potential of qPCR and qProt measurements to predict rates, we collected data from cVOC-contaminated aquifers. At the benchmark study site, the rate constant for degradation of cis-dichloroethene (cDCE) extracted from monitoring data was 11.0 ± 3.4 yr-1, and the rate constant predicted from the abundance of TceA peptides was 6.9 yr-1. The rate constant for degradation of vinyl chloride (VC) from monitoring data was 8.4 ± 5.7 yr-1, and the rate constant predicted from the abundance of TceA peptides was 5.2 yr-1. At the other study sites, the rate constants for cDCE degradation predicted from qPCR and qProt measurements agreed within a factor of 4. Under the right circumstances, qPCR and qProt measurements can be useful to rapidly predict rates of cDCE and VC biodegradation, providing a major advance in effective site management.

Application of a multiple lines of evidence approach to document natural attenuation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in groundwater

This study utilized innovative analyses to develop multiple lines of evidence for natural attenuation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in groundwater at the U.S. Department of Energy's Pantex Plant. RDX, as well as the degradation product 4-nitro-2,4-diazabutanal (NDAB; produced by aerobic biodegradation or alkaline hydrolysis) were detected in a large portion of the plume, with lower concentrations of the nitroso-containing metabolites produced during anaerobic biodegradation. 16S metagenomic sequencing detected the presence of bacteria known to aerobically degrade RDX (e.g., Gordonia, Rhodococcus) and NDAB (Methylobacterium), as well as the known anoxic RDX degrader Pseudomonas fluorescens I-C. Proteomic analysis detected both the aerobic RDX degradative enzyme XplA, and the anoxic RDX degradative enzyme XenB. Groundwater enrichment cultures supplied with low concentrations of labile carbon confirmed the potential of the extant groundwater community to aerobically degrade RDX and produce NDAB. Compound-specific isotope analysis (CSIA) of RDX collected at the site showed fractionation of nitrogen isotopes with δ¹⁵N values ranging from approximately -5‰ to +9‰, providing additional evidence of RDX degradation. Taken together, these results provide evidence of in situ RDX degradation in the Pantex Plant groundwater. Furthermore, they demonstrate the benefit of multiple lines of evidence in supporting natural attenuation assessments, especially with the application of innovative isotopic and -omic technologies.

Spatially-distinct redox conditions and degradation rates following field-scale bioaugmentation for RDX-contaminated groundwater remediation

In situ bioaugmentation for cleanup of an hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)-contaminated groundwater plume was recently demonstrated. Results of a forced-gradient, field-scale cell transport test with Gordonia sp. KTR9 and Pseudomonas fluorescens strain I-C cells (henceforth "KTR9" and "Strain I-C") showed these strains were transported 13 m downgradient over 1 month. Abundances of xplA and xenB genes, respective indicators of KTR9 and Strain I-C, approached injection well cell densities at 6 m downgradient, whereas gene abundances (and conservative tracer) had begun to increase at 13 m downgradient at test conclusion. In situ push-pull tests were subsequently completed to measure RDX degradation rates in the bioaugmented wells under ambient gradient conditions. Time-series monitoring of RDX, RDX end-products, conservative tracer, xplA and xenB gene copy numbers and XplA and XenB protein abundance were used to assess the efficacy of bioaugmentation and to estimate the apparent first-order RDX degradation rates during each test. A collective evaluation of redox conditions, RDX end-products, varied RDX degradation kinetics, and biomarkers indicated that Strain I-C and KTR9 rapidly degraded RDX. Results showed bioaugmentation is a viable technology for accelerating RDX cleanup in the demonstration site aquifer and may be applicable to other sites. Full-scale implementation considerations are discussed.

Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with ¹³C-/¹⁵N-labeled peptides determined 1.8 × 10³ TceA and 1.2 × 10² VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.

Use of omic tools to assess methyl tert-butyl ether (MTBE) degradation in groundwater

This study employed innovative technologies to evaluate multiple lines of evidence for natural attenuation (NA) of methyl tertiary-butyl ether (MTBE) in groundwater at the 22 Area of Marine Corps Base (MCB) Camp Pendleton after decommissioning of a biobarrier system. For comparison, data from the 13 Area Gas Station where active treatment of MTBE is occurring was used to evaluate the effectiveness of omic techniques in assessing biodegradation. Overall, the 22 Area Gas Station appeared to be anoxic. MTBE was detected in large portion of the plume. In comparison, concentrations of MTBE at the 13 Area Gas Station were much higher (42,000 μg/L to 2800 μg/L); however, none of the oxygenates were detected. Metagenomic analysis of the indigenous groundwater microbial community revealed the presence of bacterial strains known to aerobically and anaerobically degrade MTBE at both sites. While proteomic analysis at the 22 Area Gas Station showed the presence of proteins of MTBE degrading microorganisms, the MTBE degradative proteins were only found at the 13 Area Gas Station. Taken together, these results provide evidence for previous NA of MTBE in the groundwater at 22 Area Gas Station and demonstrate the effectiveness of innovative-omic technologies to assist monitored NA assessments.

Enhanced biodegradation of sediment-bound heavily weathered crude oil with ligninolytic enzymes encapsulated in calcium-alginate beads

The degradation of crude and weathered crude oil following the application of crude and calcium-alginate encapsulated ligninolytic enzymes was studied using in situ microcosms. Changes in the chemical composition of the oil were monitored in crude enzyme extracts, as well as a sediment matrix, for as long as 70 days. Compound-specific effects of ligninolytic enzymes applied to the sediments were observed over time through changes in concentration of total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAHs) and fractions of saturates, aromatics, resins and asphaltenes (SARA). As the oil weathered, most TPH and PAH fractions showed a rapid decrease in concentration. As sediment oil concentrations decreased following treatment with ligninolytic enzymes, the microbial population was enriched with hydrocarbon-degrading species. This trend demonstrates that the oil fractions initially not bioavailable for microbial degradation, were subsequently released to the sediment via catalytic conversion with laccase and manganese peroxidase, and the oil continues to be biodegraded by microbial populations.

Novel treatment technologies for PFAS compounds: A critical review

Perfluorinated compounds such as perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) have recently drawn great attention due to their wide distribution in aquatic environments. The understanding of the physicochemical properties and fate and transport of PFAs in groundwater is still limited. Preliminary studies indicate that these compounds can readily bioaccumulate and pose human and animal health concerns. Due to their physicochemical properties, PFOS and PFOA are water soluble, nonvolatile and persistent in the environment, which is a cause of concern related to their treatment with conventional remediation technologies. Extraction with inefficient carbon adsorption is one of the most common treatment technologies for remediation of PFOS- or PFOA-impacted groundwater. Several other innovative and promising technologies, including sonochemistry, bioremediation and photolysis, have been tested for their effectiveness in removal of perfluorinated compounds. This paper provides a baseline for understanding research needs to better develop treatment technologies for PFOA and PFOS in groundwater. Frontiers for improving the state of practice for PFOA and PFOS treatment include the development of more cost-effective ex situ treatment methods and the development and demonstration of promising in situ treatment technologies at the pilot and full scale.

Physiological Peculiarities of Lignin-Modifying Enzyme Production by the White-Rot Basidiomycete Coriolopsis gallica Strain BCC 142

Sixteen white-rot Basidiomycota isolates were screened for production of lignin-modifying enzymes (LME) in glycerol- and mandarin peel-containing media. In the synthetic medium, Cerrena unicolor strains were the only high laccase (Lac) (3.2–9.4 U/mL) and manganese peroxidase (MnP) (0.56–1.64 U/mL) producers while one isolate Coriolopsis gallica was the only lignin peroxidase (LiP) (0.07 U/mL) producer. Addition of mandarin peels to the synthetic medium promoted Lac production either due to an increase in fungal biomass (Funalia trogii, Trametes hirsuta, and T. versicolor) or enhancement of enzyme production (C. unicolor, Merulius tremellosus, Phlebia radiata, Trametes ochracea). Mandarin peels favored enhanced MnP and LiP secretion by the majority of the tested fungi. The ability of LiP activity production by C. gallica, C. unicolor, F. trogii, T. ochracea, and T. zonatus in the medium containing mandarin-peels was reported for the first time. Several factors, such as supplementation of the nutrient medium with a variety of lignocellulosic materials, nitrogen source or surfactant (Tween 80, Triton X-100) significantly influenced production of LME by a novel strain of C. gallica. Moreover, C. gallica was found to be a promising LME producer with a potential for an easy scale up cultivation in a bioreactor and high enzyme yields (Lac-9.4 U/mL, MnP-0.31 U/mL, LiP-0.45 U/mL).

Relative contributions of mercury bioavailability and microbial growth rate on net methylmercury production by anaerobic mixed cultures

Monomethylmercury (MeHg) is produced in many aquatic environments by anaerobic microorganisms that take up and methylate inorganic forms of Hg(II). Net methylation of Hg(II) appears to be correlated with factors that affect the activity of the anaerobic microbial community and factors that increase the bioavailability of Hg(II) to these organisms. However, the relative importance of one versus the other is difficult to elucidate even though this information can greatly assist remediation efforts and risk assessments. Here, we investigated the effects of Hg speciation (dissolved Hg and nanoparticulate HgS) and microbial activity on the net production of MeHg using two mixed microbial cultures that were enriched from marine sediments under sulfate reducing conditions. The cultures were amended with dissolved Hg (added as a dissolved nitrate salt) and nanoparticulate HgS, and grown under different carbon substrate concentrations. The results indicated that net mercury methylation was the highest for cultures incubated in the greatest carbon substrate concentration (60 mM) compared to incubations with less carbon (0.6 and 6 mM), regardless of the form of mercury amended. Net MeHg production in cultures exposed to HgS nanoparticles was significantly slower than in cultures exposed to dissolved Hg; however, the difference diminished with slower growing cultures with low carbon addition (0.6 mM). The net Hg methylation rate was found to correlate with sulfate reduction rate in cultures exposed to dissolved Hg, while methylation rate was roughly constant for cultures exposed to nanoparticulate HgS. These results indicated a potential threshold of microbial productivity: below this point net MeHg production was limited by microbial activity, regardless of Hg bioavailability. Above this threshold of productivity, Hg speciation became a contributing factor towards net MeHg production.

Thiol-Based Selective Extraction Assay to Comparatively Assess Bioavailable Mercury in Sediments

Bioaccumulation of methylmercury in the aquatic food web is governed in part by the methylation of inorganic divalent mercury (Hg(II)) by anaerobic microorganisms. In sulfidic settings, a small fraction of total Hg(II) is typically bioavailable to methylating microorganisms. Quantification of this fraction is difficult due to uncertainties in the speciation of Hg(II) and the mechanisms of uptake by methylating microbes. However, recent studies have shown that the bioavailable fraction is likely to include a portion of Hg(II) associated with solid phases, that is, nanostructured mercuric sulfides. Moreover, addition of thiols to suspensions of methylating cultures coincides with increased uptake into cells and methylmercury production. Here, we present a thiol-based selective extraction assay to provide information on the bioavailable Hg fraction in sediments. In the procedure, sediment samples were exposed to a nitrogen-purged solution of glutathione (GSH) for 30 min and the amount of GSH-leachable mercury was quantified. In nine sediment samples from a marine location, the relative GSH-leachable mercury concentration was strongly correlated to the relative amount of methylmercury in the sediments (r²=0.91, p<0.0001) across an order of magnitude of methylmercury concentration values. The approach was further applied to anaerobic sediment slurry microcosm experiments in which sediments were cultured under the same microbial growth conditions but were amended with multiple forms of Hg with a known spectrum of bioavailability. GSH-leachable Hg concentrations increased with observed methylmercury concentrations in the microcosms, matching the trend of species bioavailability in our previous work. Results suggest that a thiol-based selective leaching approach is an improvement compared with other proposed methods to assess Hg bioavailability in sediment and that this approach could provide a basis for comparison of sites where Hg methylation is a concern.

Net methylation of mercury in estuarine sediment microcosms amended with dissolved, nanoparticulate, and microparticulate mercuric sulfides

The production of methylmercury (MeHg) by anaerobic microorganisms depends in part on the speciation and bioavailability of inorganic mercury to these organisms. Our previous work with pure cultures of methylating bacteria has demonstrated that the methylation potential of mercury decreased during the aging of mercuric sulfides (from dissolved to nanoparticulate and microcrystalline HgS). The objective of this study was to understand the relationship between mercury sulfide speciation and methylation potential in experiments that more closely simulate the complexity of sediment settings. The study involved sediment slurry microcosms that represented a spectrum of salinities in an estuary and were each amended with different forms of mercuric sulfides: dissolved Hg and sulfide, nanoparticulate HgS (3-4 nm in diameter), and microparticulate HgS (>500 nm). The results indicated that net MeHg production was influenced by both the activity of sulfate-reducing microorganisms (roughly represented by the rate of sulfate loss) and the bioavailability of mercury. In the presence of abundant sulfate and carbon sources (supporting relatively high microbial activity), net MeHg production in the slurries amended with dissolved Hg was greater than in slurries amended with nano-HgS, similar to previous experiments with pure bacterial cultures. In microcosms with minimal microbial activity (indicated by low rates of sulfate loss), the addition of either dissolved Hg or nano-HgS resulted in similar amounts of net MeHg production. For all slurries receiving micro-HgS, MeHg production did not exceed abiotic controls. In slurries amended with dissolved and nano-HgS, mercury was mainly partitioned to bulk-scale mineral particles and colloids, indicating that Hg bioavailability was not simply related to dissolved Hg concentration or speciation. Overall, the results suggest that models for mercury methylation potential in the environment will need to balance the relative contributions of mercury speciation and activity of methylating microorganisms.

Mechanisms regulating mercury bioavailability for methylating microorganisms in the aquatic environment: a critical review

Mercury is a potent neurotoxin for humans, particularly if the metal is in the form of methylmercury. Mercury is widely distributed in aquatic ecosystems as a result of anthropogenic activities and natural earth processes. A first step toward bioaccumulation of methylmercury in aquatic food webs is the methylation of inorganic forms of the metal, a process that is primarily mediated by anaerobic bacteria. In this Review, we evaluate the current state of knowledge regarding the mechanisms regulating microbial mercury methylation, including the speciation of mercury in environments where methylation occurs and the processes that control mercury bioavailability to these organisms. Methylmercury production rates are generally related to the presence and productivity of methylating bacteria and also the uptake of inorganic mercury to these microorganisms. Our understanding of the mechanisms behind methylation is limited due to fundamental questions related to the geochemical forms of mercury that persist in anoxic settings, the mode of uptake by methylating bacteria, and the biochemical pathway by which these microorganisms produce and degrade methylmercury. In anoxic sediments and water, the geochemical forms of mercury (and subsequent bioavailability) are largely governed by reactions between Hg(II), inorganic sulfides, and natural organic matter. These interactions result in a mixture of dissolved, nanoparticulate, and larger crystalline particles that cannot be adequately represented by conventional chemical equilibrium models for Hg bioavailability. We discuss recent advances in nanogeochemistry and environmental microbiology that can provide new tools and unique perspectives to help us solve the question of how microorganisms methylate mercury. An understanding of the factors that cause the production and degradation of methylmercury in the environment is ultimately needed to inform policy makers and develop long-term strategies for controlling mercury contamination.

Fungal laccase, manganese peroxidase and lignin peroxidase: gene expression and regulation

Extensive research efforts have been dedicated to characterizing expression of laccases and peroxidases and their regulation in numerous fungal species. Much attention has been brought to these enzymes broad substrate specificity resulting in oxidation of a variety of organic compounds which brings about possibilities of their utilization in biotechnological and environmental applications. Research attempts have resulted in increased production of both laccases and peroxidases by the aid of heterologous and homologous expression. Through analysis of promoter regions, protein expression patterns and culture conditions manipulations it was possible to compare and identify common pathways of these enzymes' production and secretion. Although laccase and peroxidase proteins have been crystallized and thoroughly analyzed, there are still a lot of questions remaining about their evolutionary origin and the physiological functions. This review describes the present understanding of promoter sequences and correlation between the observed regulatory effects on laccase, manganese peroxidase and lignin peroxidase genes transcript levels and the presence of specific response elements.

Maximizing microbial degradation of perchlorate using a genetic algorithm: Media optimization

Microbial communities are under constant influence of physical and chemical components in ecosystems. Shifts in conditions such as pH, temperature or carbon source concentration can translate into shifts in overall ecosystem functioning. These conditions can be manipulated in a laboratory setup using evolutionary computation methods such as genetic algorithms (GAs). In work described here, a GA methodology was successfully applied to define sets of environmental conditions for microbial enrichments and pure cultures to achieve maximum rates of perchlorate degradation. Over the course of 11 generations of optimization using a GA, we saw a statistically significant 16.45 and 16.76-fold increases in average perchlorate degradation rates by Dechlorosoma sp. strain KJ and Dechloromonas sp. strain Miss R, respectively. For two bacterial consortia, Pl6 and Cw3, 5.79 and 5.75-fold increases in average perchlorate degradation were noted. Comparison of zero-order kinetic rate constants for environmental conditions in GA-determined first and last generations of all bacterial cultures additionally showed marked increases.

Development of drinking water standards for perchlorate in the United States

Perchlorate, an anion that originates as a contaminant in ground and surface waters, is both naturally occurring and manmade. Because of its toxicity, there has been increased interest in setting drinking water safety standards and in health effects when perchlorate is present at low (parts per billion (ppb)) levels. In January 2009, the EPA issued a heath advisory to assist state and local officials in addressing local contamination of perchlorate in drinking water. The interim health advisory level of 15 micrograms per liter (microg/L), or ppb, is based on the reference dose recommended by the National Research Council (NRC) of the National Academy of Sciences (NAS). This paper describes scope and extent of contaminant issues and a legal process of setting standards for perchlorate concentration in drinking water in the United States of America.