R-3 Repository :: Browsing by Author "Alvarez, Pedro J.J."

Browsing by Author "Alvarez, Pedro J.J."

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1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes
(Wiley, 2017) He, Ya; Mathieu, Jacques; da Silva, Marcio L.B.; Li, Mengyan; Alvarez, Pedro J.J.
Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4-dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g-dioxane per g-protein per day) were comparable to those of two dioxane-metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH-06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di-iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l−1) below detectable levels (5 μg l−1) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane-degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.
A New Frontier in Texas: Managing and Regulating Brackish Groundwater
(James A. Baker III Institute for Public Policy, 2015) Buono, Regina M.; Zodrow, Katherine R.; Alvarez, Pedro J.J.; Li, Qilin; James A. Baker III Institute for Public Policy
Providing access to clean water is a grand challenge in engineering, and supplying sufficient, clean water is a problem around the globe. This challenge is visible in Texas, where drought coincides with population growth and increases in water demand. The 2012 Texas State Water Plan reports a 2,700 million cubic meters (MCM) gap between fresh water supply and demand in 2010, a number predicted to grow to 3,100 MCM by 2060 if new sources of water are not developed or substantial decreases in demand are not obtained. Due to the inherent political difficulty of decreasing water demand, policy makers and water providers are evaluating new water sources, including wastewater for direct or indirect reuse and brackish groundwater for desalination or direct use. It has been estimated that Texas aquifers contain more than 3,300,000 MCM of brackish groundwater, which, if converted to freshwater, could meet current consumption needs for 150 years, albeit at a greater water treatment cost. Using Texas as a case study, this article addresses which policies are desirable to best manage the supply of brackish groundwater. We review the geological, technical, and legal contexts of groundwater in Texas and situate brackish groundwater within those constructs. We consider efforts by other U.S. states to regulate brackish groundwater and identify desirable goals for its management, including facilitating access to and incentivizing use of brackish groundwater and protecting fresh water aquifers from potential saline intrusion related to brackish groundwater production. Various brackish groundwater policies are examined, and policy recommendations regarding use of the resource are offered.
Bacterial Endospores as Phage Genome Carriers and Protective Shells
(American Society for Microbiology, 2018) Gabiatti, Naiana; Yu, Pingfeng; Mathieu, Jacques; Lu, Grant W.; Wang, Xifan; Zhang, Hangjun; Soares, Hugo M.; Alvarez, Pedro J.J.
Bacterial endospores can serve as phage genome protection shells against various environmental stresses to enhance microbial control applications. The genomes of polyvalent lytic Bacillus phages PBSC1 and PBSC2, which infect both B. subtilis subsp. subtilis and B. cereusNRS 248, were incorporated into B. subtilis endospores (without integration into the host chromosome). When PBSC1 and PBSC2 were released from germinating endospores, they significantly inhibited the growth of the targeted opportunistic pathogen B. cereus Optimal endospore entrapment was achieved when phages were introduced to the fast-sporulating prespores at a multiplicity of infection of 1. Longer endospore maturation (48 h versus 24 h) increased both spore yield and efficiency of entrapment. Compared with free phages, spore-protected phage genomes showed significantly higher resistance toward high temperatures (60 to 80°C), extreme pH (pH 2 or pH 12), and copper ions (0.1 to 10 mg/liter). Endospore germination is inducible by low concentrations of l-alanine or by a germinant mixture (l-asparagine, d-glucose, d-fructose, and K+) to trigger the expression, assembly, and consequent release of phage particles within 60 to 90 min. Overall, the superior resiliency of polyvalent phages protected by endospores might enable nonrefrigerated phage storage and enhance phage applications after exposure to adverse environmental conditions.IMPORTANCE: Bacteriophages are being considered for the control of multidrug-resistant and other problematic bacteria in environmental systems. However, the efficacy of phage-based microbial control is limited by infectivity loss during phage delivery and/or storage. Here, we exploit the pseudolysogenic state of phages, which involves incorporation of their genome into bacterial endospores (without integration into the host chromosome), to enhance survival in unfavorable environments. We isolated polyvalent (broad-host-range) phages that efficiently infect both benign and opportunistically pathogenic Bacillusstrains and encapsulated the phage genomes in B. subtilis endospores to significantly improve resistance to various environmental stressors. Encapsulation by spores also significantly enhanced phage genome viability during storage. We also show that endospore germination can be induced on demand with nutrient germinants that trigger the release of active phages. Overall, we demonstrate that encapsulation of polyvalent phage genomes into benign endospores holds great promise for broadening the scope and efficacy of phage biocontrol.
Biofilm control using encapsulated phages and the impact of these phage interactions on antibiotic resistance dissemination
(2022-08-05) Zuo, Pengxiao; Alvarez, Pedro J.J.
Biofilms pose a major challenge to water security because they may harbor and protect pathogens, including antibiotic resistant bacteria. Conventional chemical disinfectants are not efficient at penetrating biofilms and produce undesirable disinfection by products, hence the need for a greener chemical free biocide. Bacteriophages (phages) are one such green alternative for microbial control, however, inefficient delivery and lack of precise targeting greatly lowers their efficacy and the consequences of phage treatment on antibiotic resistance dissemination are not well understood. This dissertation provides technology with potential to improve the precision of phage treatment and mechanistic understanding of how phages affect antibiotic resistant bacteria and resistance dissemination. To enhance phage-based biofouling mitigation in water storage system, crosslinked chitosan was used to form a pH-responsive phage encapsulation that can release phages at around pH 5, but otherwise remain stable for over one month in pH neutral tap water. This encapsulation allows for controlled phage release only as needed in response to the presence of a nascent biofilm because the biofilm inner layers tend to be acidic, as shown by confocal microscopy with pH-indicator dye SNARF-4F. A facile method was developed to coat encapsulated phages onto plastic and fiberglass surfaces and demonstrated that this coating mitigates biofilm formation in tap water amended with glucose and Pseudomonas aeruginosa. Furthermore, this coating allows phages to attack biofilms from a bottom-up approach, bypassing the limitation of poor biocide penetration into the biofilm matrix. Overall, this offers a potential green alternative for biofilm mitigation and highlights the possible applications and benefits encapsulation can bring to biocides. Phages are known to control bacteria populations; yet, much is unknown about their differential effects on antibiotic resistant bacteria (ARB) proliferation. Chapter 4 shows that beta-lactam resistance may fortuitously confer phage resistance as a critical factor for enhanced ARB proliferation. Following sub-lethal exposure to amoxicillin, Escherichia coli experienced lipopolysaccharides (LPS) modifications and became cross-resistant to various phages that adsorb to receptors on LPS as the first infection step. The relevance of this phenomenon was demonstrated using activated sludge microcosms where cross-resistant E. coli experienced significantly less decay after five days than the wildtype. Furthermore, cross-resistant E. coli (but not wildtype) proliferated in Luria broth-fed microcosms. A demonstratable fitness cost associated with amoxicillin resistance exists; however, due to acquired phage resistance, cross-resistant E. coli had greater fitness than the wildtype. Overall, this demonstrates that antibiotics can alter interactions between phages and bacteria, resulting in an overlooked competitive advantage for antibiotic resistance propagation. The common co-occurrence of antibiotics and phages in both natural and engineered environments underscore the need to understand their interactions and implications for bacterial control and antibiotic resistance propagation. Chapter 5 reports that aminoglycoside antibiotics (acting as bacterial protein synthesis inhibitors) impeded replication of various phages. This hindered the efficacy of phages against bacterial growth and biofilm formation, and diminished bacterial fitness cost that suppress antibiotic resistance emergence. Therefore, this highlights an overlooked antagonistic effect of aminoglycosides on phages, which may provide an advantage to affected bacteria in the common presence of phages due to less hindrance to bacterial growth and antibiotic resistance development. Overall, encapsulation technology can improve the application of phages as self-replicating biocides by enabling controlled phage release only as needed in response to nascent biofilm formation. Furthermore, coating methods for encapsulated phages can selectively protect just the surfaces vulnerable to biofouling rather than the entire system and release phages to attack from under the biofilm, avoiding challenge of penetrating the protective biofilm matrix. However, some ARB may have fortuitous cross resistance to phages, resulting in a significant competitive advantage for ARB proliferation under selective pressure from phages. Additionally, antibiotics like aminoglycosides (acting as bacterial protein synthesis inhibitors) impeded replication of various phages, which may attenuate phage suppression of bacterial growth, biofilm formation, antibiotic tolerance, and maintenance of antibiotic resistance genes.
Brackish Groundwater: Current Status and Potential Benefits for Water Management
(James A. Baker III Institute for Public Policy, 2016) Buono, Regina M.; Zodrow, Katherine R.; Alvarez, Pedro J.J.; Li, Qilin; James A. Baker III Institute for Public Policy
Critical Uncertainties and Gaps in the Environmental- and Social-Impact Assessment of the Proposed Interoceanic Canal through Nicaragua
(Oxford University Press, 2016) Huete-Pérez, Jorge A.; Ortega-Hegg, Manuel; Urquhart, Gerald R.; Covich, Alan P.; Vammen, Katherine; Rittmann, Bruce E.; Miranda, Julio C.; Espinoza-Corriols, Sergio; Acevedo, Adolfo; Acosta, María L.; Gómez, Juan P.; Brett, Michael T.; Hanemann, Michael; Härer, Andreas; Incer-Barquero, Jaime; Joyce, Frank J.; Lauer, J. Wesley; Maes, Jean Michel; Tomson, Mason B.; Meyer, Axel; Montenegro-Guillén, Salvador; Whitlow, W. Lindsay; Schnoor, Jerald L.; Alvarez, Pedro J.J.
The proposed interoceanic canal will connect the Caribbean Sea with the Pacific Ocean, traversing Lake Nicaragua, the major freshwater reservoir in Central America. If completed, the canal would be the largest infrastructure-related excavation project on Earth. In November 2015, the Nicaraguan government approved an environmental and social impact assessment (ESIA) for the canal. A group of international experts participated in a workshop organized by the Academy of Sciences of Nicaragua to review this ESIA. The group concluded that the ESIA does not meet international standards; essential information is lacking regarding the potential impacts on the lake, freshwater and marine environments, and biodiversity. The ESIA presents an inadequate assessment of natural hazards and socioeconomic disruptions. The panel recommends that work on the canal project be suspended until an appropriate ESIA is completed. The project should be resumed only if it is demonstrated to be economically feasible, environmentally acceptable, and socially beneficial.
Development of a Predictive and Mechanistic Model for Capacitive Deionization
(2015-10-22) Heldenbrand, Amy M; Li, Qilin; Alvarez, Pedro J.J.; Tomson, Mason B
The objective of this research was to develop a mechanistic and predictive model for capacitive deionization (CDI). The commonly-known Gouy Chapman Stern (GCS) model was modified to account for finite ion size and pore geometry by including the Carnahan-Starling (CS) equation of state and considering boundary conditions resulting from difference in pore shape and size and the subsequent impact on potential and concentration profiles. This GCS-CS model with pore geometry was applied to six model activated carbons (MACs) of uniform pore size to analyze the effect of influent salt concentration, pore size and geometry, and applied voltage on ion removal. The general trends found in modeling results were consistent with data presented in the literature. These findings were then compared with the commonly used CDI models, which could not replicate them. This indicates the complexity present in this new model is necessary for accurate representation of ion adsorption in CDI.
Engineered nanomaterials and plant interactions: uptake, translocation, transformation and physiological effects
(2014-11-12) Wang, Jing; Alvarez, Pedro J.J.; Schnoor, Jerald L.; Braam, Janet; Li, Qilin
The increasing likelihood of engineered nanomaterial (ENM) releases to the environment and their potential applications in agriculture highlight the importance of understanding ENM interactions with plants, which are cornerstone of most ecosystems. This study investigated how silver nanoparticles (Ag NPs) of different sizes affect plant growth over a wide range of concentrations and how coating charge affects quantum dots (QDs) uptake, translocation and transformation within woody plants. Even though both Ag NPs (5, 10, and 25 nm) and silver ion (Ag+) were phytotoxic to poplars and Arabidopsis above a specific concentration, a stimulatory effect was observed on root elongation, fresh weight and evapotranspiration of both plants at a narrow range of sub-lethal concentrations. Plants were most susceptible to the toxic effects of Ag+, but Ag NPs also showed some toxicity at higher concentrations and this susceptibility increased with decreasing Ag NP size. Both poplars and Arabidopsis accumulated silver, but silver distribution in shoot organs varied between plant species. Arabidopsis accumulated silver primarily in leaves (at ten-fold higher concentrations than in the stem or flower tissues), whereas poplars accumulated silver at similar concentrations in leaves and stems. Uptake of cationic QDs by poplar was faster than anionic QDs, possibly due to electrostatic attraction of cationic QDs to the negatively charged root cell wall. QDs aggregated upon root uptake, and their translocation to poplar shoots was likely limited by the endodermis. After 2-day exposure, both cationic and anionic coatings were likely degraded from the internalized QDs inside the plant, leading to the aggregation of the metallic cores and a “red-shift” of fluorescence. The fluorescence of cationic QD aggregates inside roots was stable through the 11-day exposure period, while that of the anionic QD aggregates was quenched probably due to destabilization of the coating inside the plant, even though these QDs were more stable in the hydroponic solution. Overall, the phyto-stimulatory effect observed in this study precludes the generalization of the phytotoxicity of Ag NPs. The QDs study highlights the importance of coating properties in the rate and extent to which NPs are assimilated by plants and potentially introduced into food webs.
Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress
(Springer Nature, 2021) Huang, Dan; Yu, Pingfeng; Ye, Mao; Schwarz, Cory; Jiang, Xin; Alvarez, Pedro J.J.
Background: Microbe–virus interactions have broad implications on the composition, function, and evolution of microbiomes. Elucidating the effects of environmental stresses on these interactions is critical to identify the ecological function of viral communities and understand microbiome environmental adaptation. Heavy metal-contaminated soils represent a relevant ecosystem to study the interplay between microbes, viruses, and environmental stressors. Results: Metagenomic analysis revealed that Cr pollution adversely altered the abundance, diversity, and composition of viral and bacterial communities. Host–phage linkage based on CRISPR indicated that, in soils with high Cr contamination, the abundance of phages associated with heavy metal-tolerant hosts increased, as did the relative abundance of phages with broad host ranges (identified as host–phage linkages across genera), which would facilitate transfection and broader distribution of heavy metal resistance genes in the bacterial community. Examining variations along the pollutant gradient, enhanced mutualistic phage–bacterium interactions were observed in the face of greater environmental stresses. Specifically, the fractions of lysogens in bacterial communities (identified by integrase genes within bacterial genomes and prophage induction assay by mitomycin-C) were positively correlated with Cr contamination levels. Furthermore, viral genomic analysis demonstrated that lysogenic phages under higher Cr-induced stresses carried more auxiliary metabolic genes regulating microbial heavy metal detoxification. Conclusion: With the intensification of Cr-induced environmental stresses, the composition, replication strategy, and ecological function of the phage community all evolve alongside the bacterial community to adapt to extreme habitats. These result in a transformation of the phage–bacterium interaction from parasitism to mutualism in extreme environments and underscore the influential role of phages in bacterial adaptation to pollution-related stress and in related biogeochemical processes.
Fullerene compositions and methods for photochemical purification
(2014-03-25) Alvarez, Pedro J.J.; Lee, Jaesang; Wilson, Lon J.; Mackeyev, Yuri; Kim, Jaehong; Rice University; Georgia Tech Research Corporation; United States Patent and Trademark Office
In various embodiments, the present disclosure describes fullerene derivatives that are capable of photocatalytically generating reactive oxygen species in the presence of ultraviolet and/or visible light. In some embodiments, the fullerene derivatives are aminofullerenes containing a plurality of amine-terminated moieties covalently bonded to the fullerene cage. The fullerene derivatives may optionally be covalently bonded to a substrate surface for use in photocatalytic disinfection systems for removing various contaminants including, for example, bacteria, viruses, protozoa and chemical pollutants. Methods using the present fullerene and aminofullerene derivatives in various purification processes are also described herein.
Fundamentals of a Sustainable U.S. Biofuels Policy
(James A. Baker III Institute for Public Policy, 2010) Alvarez, Pedro J.J.; Burken, Joel G.; Coan, James D.; de Oliveira, Marcelo E. Dias; Dominguez-Faus, Rosa; Gomez, Diego E.; Jaffe, Amy Myers; Medlock, Kenneth B. III; Powers, Susan E.; Soligo, Ronald; Smulcer, Lauren A.; James A. Baker III Institute for Public Policy
Genotoxicity and Cytotoxicity of Cadmium Sulfide Nanomaterials to Mice: Comparison Between Nanorods and Nanodots
(Mary Ann Liebert, Inc., 2014) Liu, Lu; Sun, Meiqing; Li, Qingzhao; Zhang, Hongmei; Alvarez, Pedro J.J.; Liu, Huajie; Chen, Wei
Cadmium sulfide (CdS) nanomaterials (such as CdS nanodots or nanorods) are widely used in optical, electronic, and biological applications. Large-scale production and use of these materials will likely result in accidental and incidental releases, which raise concerns about their potential environmental and human-health impacts. Most studies on toxicity of Cd-containing nanomaterials have focused on nanodots, and the relative toxicity of Cd containing nanorods is not well understood. Here, we compared genotoxicity and cytotoxicity of CdS nanorods (30-50nm diameter, 500-1100 nm length) and cubic CdS nanodots (3-5 nm) in mice by examining total cadmium accumulation in organs, acute toxicity, DNA damage, spermatozoon viability and abnormality, kidney and liver damage, and oxidative stress. Compared with (smaller) nanodots, nanorods resulted in relatively low bioaccumulation, acute toxicity, and damage to spermatozoa and the tested organs. Differences in toxicity between CdS nanodots and nanorods could not be fully explained by differences in their metal ion (Cd2 + ) release patterns, based on control tests with mice gavaged with dissolved CdCl2 at equivalent concentrations. This underscores that toxicity of metallic nanomaterials could not be solely predicted based either on their elemental composition or on the amount of ions released before receptor intake. Particle morphology (including size) may also need to be considered.
Inhibition of biofouling on reverse osmosis membrane surfaces by germicidal ultraviolet light side-emitting optical fibers
(Elsevier, 2022) Rho, Hojung; Yu, Pingfeng; Zhao, Zhe; Lee, Chung-Seop; Chon, Kangmin; Perreault, François; Alvarez, Pedro J.J.; Amy, Gary; Westerhoff, Paul; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment
Biofouling of membrane surfaces poses significant operational challenges and costs for desalination and wastewater reuse applications. Ultraviolet (UV) light can control biofilms while reducing chemical usage and disinfection by-products, but light deliveries to membrane surfaces in spiral wound geometries has been a daunting challenge. Thin and flexible nano-enabled side-emitting optical fibers (SEOFs) are novel light delivery devices that enable disinfection or photocatalytic oxidation by radiating UV light from light-emitting diodes (LEDs). We envision SEOFs as an active membrane spacer to mitigate biofilm formation on reverse osmosis (RO) membranes. A lab-scale RO membrane apparatus equipped with SEOFs allowed comparison of UV-A (photocatalysis-enabled) versus UV-C (direct photolysis disinfection). Compared against systems without any light exposure, systems with UV-C light formed thinner—but denser—biofilms, prevented permeate flux declines due to biofouling, and maintained the highest salt rejection. Results were corroborated by in-situ optical coherence tomography and ex-situ measurements of biofilm growth on the membranes. Transcriptomic analysis showed that UV-C SEOFs down-regulated quorum sensing and surface attachment genes. In contrast, UV-A SEOFs upregulated quorum sensing, surface attachment, and oxidative stress genes, resulting in higher extracellular polymeric substances (EPS) accumulation on membrane surfaces. Overall, SEOFs that deliver a low fluence of UV-C light onto membrane surfaces are a promising non-chemical approach for mitigating biofouling formation on RO membranes.
Mechanism for selective binding of aromatic compounds on oxygen-rich graphene nanosheets based on molecule size/polarity matching
(AAAS, 2022) Fu, Heyun; Wang, Bingyu; Zhu, Dongqiang; Zhou, Zhicheng; Bao, Shidong; Qu, Xiaolei; Guo, Yong; Ling, Lan; Zheng, Shourong; Duan, Pu; Mao, Jingdong; Schmidt-Rohr, Klaus; Tao, Shu; Alvarez, Pedro J.J.
Selective binding of organic compounds is the cornerstone of many important industrial and pharmaceutical applications. Here, we achieved highly selective binding of aromatic compounds in aqueous solution and gas phase by oxygen-enriched graphene oxide (GO) nanosheets via a previously unknown mechanism based on size matching and polarity matching. Oxygen-containing functional groups (predominately epoxies and hydroxyls) on the nongraphitized aliphatic carbons of the basal plane of GO formed highly polar regions that encompass graphitic regions slightly larger than the benzene ring. This facilitated size match–based interactions between small apolar compounds and the isolated aromatic region of GO, resulting in high binding selectivity relative to larger apolar compounds. The interactions between the functional group(s) of polar aromatics and the epoxy/hydroxyl groups around the isolated aromatic region of GO enhanced binding selectivity relative to similar-sized apolar aromatics. These findings provide opportunities for precision separations and molecular recognition enabled by size/polarity match–based selectivity.
Municipal Solid Waste as a Viable Alternative Fuel in the U.S.A.
(2014-11-25) McPhail, Ana; Griffin, Robert; Alvarez, Pedro J.J.; El-Halwagi, Mahmoud; Medlock, Kenneth; Lin, Cynthia
This thesis work evaluates whether municipal solid waste (MSW) may be a viable alternative and renewable fuel source within the United States. The framework for achieving this objective is split into two large, distinct studies. The first study discerns the relationship between MSW composition (including varying moisture), air pollutant concentrations and associated heating values. Models included AspenPlus® software for the deterministic simulation modeling of thermodynamic and pollution information, and U.S. EPA models WAR and WARM to determine the potential environmental impacts (PEI) and greenhouse gas emission equivalencies, respectively, for each MSW scenario. An economic profitability analysis was also conducted. This study focused on five high impact air combustion products: SO2, CO, CO2, NO and NO2. Results show that flue gas concentrations (and therefore PEI) depend on the composition and moisture of the MSW, in addition to the MSW to coal ratio. The recycled paper and composted organics scenario gave the lowest heating value (8,251 MBtu/lb). Approximate ranges for the WAR results (PEI/hr) are 7,410 to 7,663 for NO, 4 to 8 for NO2, 18 to 105 for CO, 30 to 46 for CO2, and 89 to 2,152 for SO2. WARM results show lower net CO2 emission equivalents to landfill MSW with reduced paper and organics, while combustion is preferred for MSW with paper, organics, or plastics reduction. Reduction in pollutant concentrations yielded a reduction in profit between ~20-30%. There were savings associated with emission costs by using MSW in lieu of coal: up to ~3.3% for NO, ~20-47% for NO2, and ~95% for SO2. In summary, the measurable impact MSW composition and moisture had on pollutant concentration, heating value, and economic parameters were important. The second study is used to link the information gathered in the first study with legislative actions locally and abroad. In this study, four unique scenarios and one aggregate scenario varied subsidies, health impacts, fines, energy credits and fiscal policy data and distributions using Monte Carlo analysis to evaluate and foster policy initiatives while determining the economic feasibility of MSW as a renewable fuel for municipalities. Results show the supply stack for electricity generation uses the cheapest fuel (coal), then the second cheapest (natural gas) until demand is met or more fuels are needed. The social marginal cost (SMC) without considering further policy changes yields costs of $0.165/kWh for coal, $0.209/kWh for NG and $0.349/kWh for MSW. Implementing policy changes for internalizing the health impacts currently paid for by the community and the aggregate impact of all scenarios would level the economic playing field for MSW, providing lower SMC’s of $0.327/kWh for MSW in both cases, and higher SMC’s for coal and NG in other scenarios such that the order of the supply stack changes. This work advances the fundamental understanding of the economic limitations and advantages, and the policies needed to foster further proliferation of MSW as a fuel.
Pyro-Catalytic Treatment of Crude-oil Contaminated Soils Amended with Metal Ion-Exchanged Clays
(2022-08-12) Denison, Sara Beth; Alvarez, Pedro J.J.
Terrestrial oil spills significantly outnumber marine oil spills every year. Exposure to crude oil spills is detrimental to human and environmental health and needs fast remediation. Pyrolytic treatment of crude-oil contaminated soils offers great potential for rapid remediation without destroying soil fertility, with lower energy requirements and costs than other thermal treatments (i.e. incineration). This study incorporated clays impregnated with non-toxic transition metals (iron or copper) as an amendment to decrease the required pyrolytic treatment time and temperature. We found that amending a weathered crude-oil contaminated soil with 10% (by weight) of bentonite, which had been modified via ion-exchange with either Fe or Cu, achieved significant TPH removal at pyrolysis temperature of 370°C and, unprecedentedly, at 300°C with 15-min contact time. The catalytic role of the metal ion-exchanged clays was validated using thermogravimetric analysis coupled with mass spectrometry, which revealed markers of pyrolytic degradation products of crude oil at lower temperatures than those observed for unamended soil. This work shows proof of concept that metal-impregnated clays can enhance rapid pyro-catalytic treatment of crude-oil contaminated soils, and encourages further work to understand the detailed reaction mechanisms to inform process design.
Rapid Metabolism of 1,4-Dioxane to below Health Advisory Levels by Thiamine-Amended Rhodococcus ruber Strain 219
(American Chemical Society, 2021) Simmer, Reid A.; Richards, Patrick M.; Ewald, Jessica M.; Schwarz, Cory; da Silva, Marcio L.B.; Mathieu, Jacques; Alvarez, Pedro J.J.; Schnoor, Jerald L.
Bioremediation is a promising treatment technology for 1,4-dioxane-contaminated groundwater. However, metabolic dioxane-degrading bacteria identified to date are limited by their slow kinetics and inability to sustain growth at low dioxane concentrations (<100 μg/L). Furthermore, strains may underperform because of missing growth factors, such as amino acids or vitamins. In this work, we reevaluate Rhodococcus ruber strain 219 as a dioxane-degrading strain with bioaugmentation potential. We report rapid growth and metabolic dioxane degradation by R. ruber 219 when supplemented with thiamine (vitamin B1). We also discern that the strain lacks a complete de novo thiamine synthesis pathway, indicating that R. ruber 219 is a probable thiamine auxotroph. However, when supplemented with thiamine, the strain’s Monod kinetics (Ks = 0.015 ± 0.03 μg/L) and exceedingly low Smin (0.49 ± 1.16 μg/L) suggest this strain can maintain growth at very low dioxane concentrations (<100 μg/L). Accordingly, we demonstrate that thiamine-grown R. ruber 219 sustains degradation of dilute dioxane (<100 μg/L) to below health advisory levels. This is the first study to report sustained metabolic dioxane biodegradation to below health advisory levels of 0.35 μg/L. Overall, our findings solidify R. ruber 219 as a promising candidate for bioremediation of dioxane-contaminated groundwater.
Recombination-assisted megaprimer (RAM) cloning
(Elsevier, 2014) Mathieu, Jacques; Alvarez, Emilia; Alvarez, Pedro J.J.
No molecular cloning technique is considered universally reliable, and many suffer from being too laborious, complex, or expensive. Restriction-free cloning is among the simplest, most rapid, and cost-effective methods, but does not always provide successful results. We modified this method to enhance its success rate through the use of exponential amplification coupled with homologous end-joining. This new method, recombination-assisted megaprimer (RAM) cloning, significantly extends the application of restriction-free cloning, and allows efficient vector construction with much less time and effort when restriction-free cloning fails to provide satisfactory results. The following modifications were made to the protocol: 1) Limited number of PCR cycles for both megaprimer synthesis and the cloning reaction to reduce error propagation; 2) Elimination of phosphorylation and ligation steps previously reported for cloning methods that used exponential amplification, through the inclusion of a reverse primer in the cloning reaction with a 20 base pair region of homology to the forward primer; 3) The inclusion of 1 M betaine to enhance both reaction specificity and yield.
Redistribution of intracellular and extracellular free & adsorbed antibiotic resistance genes through a wastewater treatment plant by an enhanced extracellular DNA extraction method with magnetic beads
(Elsevier, 2019) Yuan, Qing-Bin; Huang, Ya-Meng; Wu, Wen-Bin; Zuo, Pengxiao; Hu, Nan; Zhou, Yong-Zhang; Alvarez, Pedro J.J.
Due to the limitations of current extraction methods, extracellular DNA (eDNA) is rarely discerned from intracellular DNA (iDNA) despite having unique contributions to antibiotic resistance genes (ARGs) propagation. Furthermore, eDNA may be free (f-eDNA) or adsorbed to or suspended solids, including cells (a-eDNA), which affects ARG persistence and transmissivity. We developed a novel method using magnetic beads to separate iDNA, a-eDNA, and f-eDNA to assess how these physical states of ARGs change across a wastewater treatment plant. This method efficiently extracted eDNA (>85.3%) with higher recovery than current methods such as alcohol precipitation, CTAB-based extraction, and DNA extraction kits (<10%). Biological treatment and UV disinfection decreased the concentration of intracellular ARGs (iARGs) and adsorbed extracellular ARGs (a-eARGs), causing an increase of released free extracellular ARGs (f-eARGs). More ARGs were discharged through the wasted biosolids than in the effluent; iARGs and a-eARGs are prevalent in wasted biosolids ((73.9 ± 22.5) % and (23.4 ± 15.3) % of total ARGs respectively), while f-eARGs were prevalent in the effluent ((90.3 ± 16.5) %). Bacterial community analysis showed significant correlations between specific genera and ARGs (e.g., Aeromonas, Pseudomonas and Acinetobacter were strongly correlated with multidrug-resistance gene blaTEM). This treatment system decreased the discharge of iARGs to receiving environments, however, increased eARG concentrations were present in the effluent, which may contribute to the environmental resistome.
Sunlight Promotes Fast Release of Hazardous Cadmium from Widely-Used Commercial Cadmium Pigment
(American Chemical Society, 2017) Liu, Huiting; Gao, Han; Long, Mingce; Fu, Heyun; Alvarez, Pedro J.J.; Li, Qilin; Zheng, Shourong; Qu, Xiaolei; Zhu, Dongqiang
Cadmium pigments are widely used in the polymer and ceramic industry. Their potential environmental risk is under debate, being the major barrier for appropriate regulation. We show that 83.0 ± 0.2% of hazardous cadmium ion (Cd2+) was released from the commercial cadmium sulfoselenide pigment (i.e., cadmium red) in aqueous suspension within 24 h under simulated sunlit conditions. This photodissolution process also generated sub-20 nm pigment nanoparticles. Cd2+ release is attributed to the reactions between photogenerated holes and the pigment lattices. The photodissolution process can be activated by both ultraviolet and visible light in the solar spectrum. Irradiation under alkaline conditions or in the presence of phosphate and carbonate species resulted in reduced charge carrier energy or the formation of insoluble and photostable cadmium precipitates on pigment surfaces, mitigating photodissolution. Tannic acid inhibited the photodissolution process by light screening and scavenging photogenerated holes. The fast release of Cd2+ from the pigment was further confirmed in river water under natural sunlight, with 38.6 ± 0.1% of the cadmium released within 4 h. Overall, this study underscores the importance to account for photochemical effects to inform risk assessments and regulations of cadmium pigments which are currently based on their low solubility.

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