Rice University logo
Top blue bar image
Pedro Alvarez

Alvarez Lab

General Background

The Alvarez Lab integrates expertise in environmental biotechnology, microbiology and nanotechnology to conduct multidisciplinary and globally-relevant research on water treatment and reuse (e.g., advanced photo-oxidation processes and nanomaterial-enabled microbial control), bioremediation of contaminated aquifers, fate and transport of toxic chemicals, antibiotic resistance propagation and control, water footprint of biofuels, microbial-plant interactions, and environmental implications of nanotechnology. Whereas our research topics and methods are quite diverse (involving molecular biology, microbial ecology, contaminant hydrogeology, materials science, biogeochemistry, photochemistry, and water resources management), there are two unifying trends. First is a commitment to enhance water resources sustainability through policy-relevant research.  Second is a tendency to work on the leading edge of discovery rather than on the side of refinement.  We also collaborate with numerous colleagues in Latin America, China and Europe, to offer students opportunities for international integrative experiences beyond the technical core. Current funding sources include NSF, SERDP, API, and several private industries and foundations. Applications from interested exceptional students are welcome.

Examples of Past Research Contributions

The Alvarez lab has made various significant contributions to the practice and pedagogy of groundwater bioremediation. Past award-wining research contributions include (a) the discovery that substrate interactions between target pollutants can significantly affect the rate and extent of biodegradation, including the development of mathematical models that describe interactions such as metabolic flux dilution and catabolite repression to assess the natural attenuation of contaminant mixtures; (b) the groundwater quality implications of the presence of biofuels in gasoline spills, such as the preferential degradation of ethanol plus the accelerated depletion of electron acceptors and the transient accumulation of acetate (a common anaerobic metabolite) that thermodynamically inhibits hydrocarbon biodegradation and natural attenuation, resulting in longer hydrocarbon plumes and a greater risk of exposure; (c) the exploitation of biogeochemical niches in permeable reactive zero-valent iron (ZVI) barriers (e.g., coupling generation of cathodic hydrogen during iron corrosion with anaerobic reductive biotransformations) to enhance the treatment of oxidized pollutants; (d) the discovery that some sewage treatment plants can serve as breeding grounds and point sources of multidrug-resistant bacteria; and (e) the development of biomarkers to quantify aerobic biodegradation of 1,4-dioxane in support of bioremediation forensics and natural attenuation performance assessment.

The Alvarez lab has also conducted pioneering research on the potential environmental impacts of nanotechnology. The widespread production of engineered nanomaterials and their rapid incorporation into a variety of consumer products and applications is outpacing the development of appropriate regulations to mitigate potential risks associated with their release to the environment. Past contributions include (a) discerning how nanomaterials interact with bacteria (which are the basis of all known ecosystems) and influence microbial ecosystem services (e.g., nutrient cycling, waste biodegradation, primary productivity), and elucidating their mode of action; (b) developing novel and greener (solar-based) nano-enabled disinfection approaches that purify water without the need for electricity and without creating harmful disinfection byproducts; (c) discovering that some fullerene nanoparticles can cause teratogenic effects in fish that can be mitigated by administering anti-oxidants; (d) discerning that natural organic matter can coat nanoparticles and decrease their bioavailability and toxicity; (e) discerning unintended consequences such as biofilm promotion by sublethal concentrations of bactericidal silver nanoparticles; and (e) illustrating the potential for nanoparticle bioaccumulation and transport through food webs. Collectively, these contributions represent a timely and proactive effort towards the development of appropriate guidelines and conceptual models to steward the sustainable design, use and disposal of engineered nanomaterials.

More recently, the Alvarez lab has focused on nanotechnology water treatment (NEWT), such as enhancing the efficiency and selectivity of photocatalysis for viral and bacterial disinfection and detoxification of pharmaceuticals under solar irradiation (thus obviating the need for electricity), and development of water filtration membranes that incorporate antimicrobial nanoparticles exhibit superior biofouling resistance.  Research in this area seeks to contribute to the development of modular, multifunctional and high-efficiency processes enabled by nanotechnology, which have great potential to both retrofit ageing water infrastructure and develop high performance, low maintenance decentralized treatment and reuse systems including point-of-use devices.

Overall, the Alvarez lab has made lasting fundamental, practical and pedagogical contributions to water pollution control by advancing environmental biotechnology and nanotechnology, and has been proactive in raising awareness and promoting mitigation of threats to water resources associated with increased occurrence of various contaminants of emerging concern.


Current Lab Members and Research Projects

CEVE Staff NEWT Staff
Eric Jordan x4699 Ibrahim Abdallah x2048
Jennifer Mashburn x4656 Ernest Davis x6214
Andrea Torres x2353 Matt Hotze x3866
Drahomira Brejchova (ES&T) x5439 Jorge Loyo x8116
Liz Scroggins x6398


Alvarez Lab May 2018


Postdoctoral Research Fellows 

Pingfeng Yu
Postdoctoral Research Fellow

Civil and Environmental Engineering
Ph.D., 2017, Environmental Engineering, Rice University
B.S., 2011, School of Environment, Tsinghua University
My research interests include environmental microbiology/virology, environmental microbiome engineering, and antibiotic resistance. Current projects focus on:
  1. The dissemination and control of environmental antibiotic resistance;
  2. The interaction between antibiotic resistant bacteria and their phages;
  3. Application of phages and nanoparticles in microbiome engineering.



Research Scientists

Jacques Mattieu
Research Scientist

Civil and Environmental Engineering
Ph.D., 2011, Environmental Engineering, Rice University


My research interests include developing methods and technologies for microbiome engineering, bioremediation, and mitigation of antibiotic resistance.

Marcio Luis Busi da Silva
Research Scientist

Civil and Environmental Engineering
PhD University of Iowa, 1999-2004, Bioremediation.
Postdoc, 2004-2007, Bioremediation, Rice University


Recently, I have been working on strategies to enhance the removal of contaminants from groundwater. Therefore, flow though aquifer columns experiments have been constructed and set up to mimic conditions resembling aquifer systems. These columns will be used to assess the potential benefit aspects of injecting specific bacteria strains into groundwater for the removal of dioxane.



Visiting Scholars

Cong Lyu
Visiting Scholar

Civil and Environmental Engineering
Ph.D., 2011, Environmental Engineering, Jilin University


My research is focused on the application of heterogeneous catalysis for water treatment. This focuses on the development of a novel heterogeneous catalyst with high hydrophobicity, and using the novel catalyst for remediation of NAPLs and other emerging contaminants.

Huiru Zhao
Visiting Scholar

Civil and Environmental Engineering
PhD Student, 2017, Environmental Science, Nankai University


My research is focused on the toxicity of graphene oxide and bacterial resistance.

Wen Song
Visiting Scholar

Civil and Environmental Engineering
B.S., 2013, Environmental Engineering, Guangxi University


My research explores the short-time pyrolytic treatment and toxicological assessment of oil-contaminated soil.


Graduate Students 

Cory Schwarz
Laboratory Technician

Civil and Environmental Engineering
B.S., 2014, Cell & Molecular Biology, Tulane University


My work is primarily involved with monitoring and characterizing 1,4 dioxane-degrading bacteria for use in bio-remediation through benchtop scale experiments and genetic analysis of microbial communities. A secondary area of work is in polyvalent phage isolation, in addition to assisting and training students in lab techniques and on lab equipment.

Danning Zhang
Doctoral Student

Civil and Environmental Engineering
M.S 2012, Environmental Engineering, Fudan University



My research focuses on the practical application of a modified TiO2 photocatalyst for water purification and soil treatment. I work on synthesizing a highly reactive photocatalyst for the optimized contact pattern with target contaminants. The goal is to utilize the TiO2 photocatalyst to pretreat oil pollution in soil. Photocatalytic hydroxylation during pretreatment facilitates further biodegradation of these pollutants.

Hassan Javed
Doctoral Student

M.A., 2017, Chemistry, Rice University.
B.S., 2015, Chemistry, Lahore University of Management Sciences (LUMS)



My research involves exploring photocatalytic and adsorption based technologies for environmental remediation.

Jordin Metz
Doctoral Student

B.S. 2016, Chemistry, Tufts University


My research is about using nanoparticles to capture waste heat for use in water treatment.

Pengxiao Zuo
Doctoral Student

Civil and Environmental Engineering
B.S., 2015 Biology, McGill University
M.S., 2016 Bioresource Engineering, McGill University


Currently I am researching the use of polyvalent phages to control problematic bacteria such as sulfate reducing bacteria. I am looking to improve the efficiency of phages as bio-control agents through selection and engineering processes. I also want to develop methods to use phages for gene delivery to target antibiotic resistance genes.

Ruonan Sun
Doctoral Student

Civil and Environmental Engineering
B.S., 2017, Environmental Science, Peking University


1,4-Dioxane is a synthetic organic chemical and has become a contaminant of emerging concern in water systems.My research focuses on the biodegradation of 1,4-dioxane. I am trying to figure out the feasibility of plasmid bioaugmentation, exploring whether the plasmid that contains the 1,4-dioxane degradation gene can be horizontally transferred to other strains, and identify strains that can anaerobically degrade 1,4-dioxane as pure culture.

Ya He
Doctoral Student

Civil and Environmental Engineering
B.S., 2014, Environmental Engineering, Tsinghua University


My research is about the bioremediation of 1,4-dioxane (dioxane) in groundwater, mainly focusing on the following aspects:

  • Using conventional enrichment and dilution methods or novel isolation methods to isolate bacteria that can degrade dioxane metabolically
  • Using molecular methods to study the dioxane degradation mechanisms or find the gene encoding enzymes needed for the degradation of dioxane

Optimizing the operational conditions for bacterial bioaugmentation of dioxane based on bench scale study for some dioxane impacted sites or studying the possibility of gene bioaugmentation with our revised understanding of the genetic bases of degradation of dioxane.


Undergraduate Students 

Sabrina Bisaga
Undergraduate Student

Chemical and Biomolecular Engineering
Degree in progress
I work with Cory Schwarz on the bioremediation of 1,4-dioxane. We research bacteria strains to naturally decompose 1,4-dioxane.





Final Magazine

Alvarez started his academic career in 1993 at the University of Iowa, where he also served as Associate Director for the Center for Bioprocessing and Biocatalysis.  During his tenure at Iowa, he pioneered research on the groundwater quality impacts associated with ethanol-blend releases. He discovered that the preferential degradation of ethanol and the accelerated depletion of nutrients and electron acceptors hinders hydrocarbon degradation and results in longer hydrocarbon plumes that pose a greater risk of exposure. He also characterized potential aesthetic impacts such as taste and odor produced by butyric acid and other byproducts of ethanol fermentation. His more recent finding that ethanol preferentialy migrates through the capillary fringe and undergoes phase separation (leaving behind a hydrocarbon non-aqueous phase) has important implications for site assessment and remediation of fuel ethanol releases.  Alvarez’s research on the potential groundwater impacts of fuel ethanol earned him the Malcom Pirnie-AEESP Frontiers in Research Award in 2008, and provided guidelines for many states (e.g., California, Iowa and Maine) and the EPA on the remediation and natural attenuation of groundwater impacted by leaking underground storage tanks.


Monitoring and Remediation MagazineAfter moving to Rice University in 2003, Alvarez continued to contribute to the practice and pedagogy of hazardous waste remediation. He wrote two bioremediation textbooks (including the only one written in Spanish and one published by Wiley & Sons). In collaboration with Herb Ward and Joe Hughes in a pilot-scale study, Alvarez’s students demonstrated that chlorinated solvent DNAPLs commonly present in source zones can be effectively treated by bioaugmentation with dehalorespiring bacteria.  This approach can significantly cut down remediation cost, and is being increasingly used by remediation companies at sites impacted by chlorinated solvents. This project received the WEF McKee Medal for Groundwater Restoration or Sustainable Use. Recently, Alvarez developed catabolic gene biomarkers to quantify the presence and expression of anaerobic degradation of monoaromatic hydrocarbons.  This contribution has significant potential to support site-specific decisions to select or reject natural attenuation as a remedial approach, and to enhance the performance assessment and forensic analysis of bioremediation. For instance, it can help to reliably estimate biodegradation rates (and cleanup time) at a small fraction of the cost of traditional flux transects or mass balance approaches.


Other Magazine

Alvarez has led various international collaborative field studies. With Henry Corseuil at the Universidade Federal de Santa Catarina, Brazil, they conducted a comprehensive long-term (10-year) study of an ethanol blend release, and showed that the transient accumulation of acetate (a common anaerobic metabolite) thermodynamically inhibitis anaerobic benzene biodegradation. Thus, some state agencies and the EPA are beginning to request acetate analysis as part of the regular site characterization process for ethanol blend releases. In collaboration with Nankai University, Alvarez directed a 100-mile survey of the Haihe River and showed that antibiotic resistance genes draining from animal farms are an emerging class of pollutants, and discerned environmental factors that contribute to their environmental amplification or attenuation.




Another Magazine

Alvarez has applied his expertise in environmental microbiology to advance our understanding of the microbial response, adaptation, and impact due to nanomaterials exposure.  This is an important subject because microorganisms are the basis of all known ecosystems, serving as primary agents of biogeochemical cycling and supporting food webs.  Recent discoveries include that (a) buckminsterfullerene stable water suspensions (nC60) are strongly bactericidal and their mode of action involves oxidation of cell membrane proteins and interruption of energy transduction upon direct contact; (b) nC60 is also teratogenic and delays zebrafish embryo and larva development and causes pericardial edema, which can be mitigated by antioxidants (this was the first developmental toxicity study of any type of nanomaterial and showed the importance of mitigating oxidative stress); (c) C60 bioaccumulates in earthworms to a much lower extent than predicted by its hydrophobicity (which showed that traditional fugacity models do not apply to nanoparticles); (d) the antibacterial mechanism of silver nanoparticles is exclusively due to silver ion release, whose bioavailability and toxicity can be significantly mitigated by common ligands in water; and (e) quantum dots are easily weathered and release toxic metals that, at sublethal concentrations, can stimulate nitrogen cycling.  These findings are important not only to understand and mitigate potential impacts to microbial ecosystem services, but also to develop greener disinfection, anti-fouling and anti-corrosion applications based on nanotechnology.  Contributions to such applications include findings that (f) aminofullerene photocatalysts exhibit high efficiency for viral disinfection and detoxification of pharmaceuticals under solar irradiation (thus obviating the need for electricity), and (g) water filtration membranes that incorporate antimicrobial nanoparticles exhibit superior biofouling resistance.

So Many Magazines

Alvarez has also made several international contributions to water resources protection and associated policy. When he was a Ph.D. student, acting as an independent consultant, he helped formulate policies for the sustainable development of water resources in the Commonwealth of Dominica, and designed and implemented the groundwater monitoring plan for the City of Ann Arbor landfill.  Later as a professor, he served as advisor to two Presidents of Nicaragua (Violeta Chamorro and Enrique Bolaños) on matters ranging from the remediation of Lake Nicaragua to hydroelectric power development. As a member of the board of directors of the Nicaraguan National Agency for Water Supply and Wastewater Treatment (ENACAL), he oversaw the design concept and bidding process for a $30-million wastewater treatment plant (the first one) in Managua.  He also helped formulate groundwater remediation policy for the Mexican Petroleum Institute (IMP) as a scientific advisory board member.  More recently, he increased public awareness about the large water footprint of fuel ethanol (e.g., driving one mile on ethanol is the equivalent of consuming 50 gallons of water – a drink or drive issue) with the help of the Leopold Leadership Foundation. Alvarez was also a Founding Member of the Nicaraguan Academy of Sciences in 2008, and promoted the adoption of sustainable water management as a core value.