Criddle's research focuses on biotechnology and microbial ecology for clean water, clean energy, and healthy ecosystems.

Academic Appointments

Administrative Appointments

  • Director, William and Cloy Codiga Resource Recovery Center (2014 - Present)

Professional Education

  • PhD, Stanford University, Civil and Environmental Engineering (1990)
  • MS, Utah State University, Civil and Environmental Engineering (1984)
  • BS, Utah State University, Civil and Environmental Engineering (1982)
  • BA, Utah State University, Spanish (1982)


2014-15 Courses


All Publications

  • Optimization of Methanotrophic Growth and Production of Poly(3-Hydroxybutyrate) in a High-Throughput Microbioreactor System APPLIED AND ENVIRONMENTAL MICROBIOLOGY Sundstrom, E. R., Criddle, C. S. 2015; 81 (14): 4767-4773


    Production of poly(3-hydroxybutyrate) (P3HB) from methane has economic and environmental advantages over production by agricultural feedstock. Identification of high-productivity strains and optimal growth conditions is critical to efficient conversion of methane to polymer. Current culture conditions, including serum bottles, shake flasks, and agar plates, are labor-intensive and therefore insufficient for systematic screening and isolation. Gas chromatography, the standard method for analysis of P3HB content in bacterial biomass, is also incompatible with high-throughput screening. Growth in aerated microtiter plates coupled with a 96-well Nile red flow-cytometric assay creates an integrated microbioreactor system for high-throughput growth and analysis of P3HB-producing methanotrophic cultures, eliminating the need for individual manipulation of experimental replicates. This system was tested in practice to conduct medium optimization for P3HB production in pure cultures of Methylocystis parvus OBBP. Optimization gave insight into unexpected interactions: for example, low calcium concentrations significantly enhanced P3HB production under nitrogen-limited conditions. Optimization of calcium and copper concentrations in the growth medium increased final P3HB content from 18.1% to 49.4% and P3HB concentration from 0.69 g/liter to 3.43 g/liter while reducing doubling time from 10.6 h to 8.6 h. The ability to culture and analyze thousands of replicates with high mass transfer in completely mixed culture promises to streamline medium optimization and allow the detection and isolation of highly productive strains. Applications for this system are numerous, encompassing analysis of biofuels and other lipid inclusions, as well as analysis of heterotrophic and photosynthetic systems.

    View details for DOI 10.1128/AEM.00025-15

    View details for Web of Science ID 000356528200022

    View details for PubMedID 25956771

  • Use of low cost and easily regenerated Prussian Blue cathodes for efficient electrical energy recovery in a microbial battery ENERGY & ENVIRONMENTAL SCIENCE Xie, X., Ye, M., Liu, C., Hsu, P., Criddle, C. S., Cui, Y. 2015; 8 (2): 546-551

    View details for DOI 10.1039/c4ee03268c

    View details for Web of Science ID 000349616900012

  • Enhancing the nanomaterial bio-interface by addition of mesoscale secondary features: crinkling of carbon nanotube films to create subcellular ridges. ACS nano Xie, X., Zhao, W., Lee, H. R., Liu, C., Ye, M., Xie, W., Cui, B., Criddle, C. S., Cui, Y. 2014; 8 (12): 11958-11965


    Biological cells often interact with their local environment through subcellular structures at a scale of tens to hundreds of nanometers. This study investigated whether topographic features fabricated at a similar scale would impact cellular functions by promoting the interaction between subcellular structures and nanomaterials. Crinkling of carbon nanotube films by solvent-induced swelling and shrinkage of substrate resulted in the formation of ridge features at the subcellular scale on both flat and three-dimensional substrates. Biological cells grown upon these crinkled CNT films had enhanced activity: neuronal cells grew to higher density and displayed greater cell polarization; exoelectrogenic micro-organisms transferred electrons more efficiently. The results indicate that crinkling of thin CNT films creates secondary mesoscale features that enhance attachment, growth, and electron transfer.

    View details for DOI 10.1021/nn504898p

    View details for PubMedID 25415858

  • Disassembly and reassembly of polyhydroxyalkanoates: Recycling through abiotic depolymerization and biotic repolymerization BIORESOURCE TECHNOLOGY Myung, J., Strong, N. I., Galega, W. M., Sundstrom, E. R., Flanagan, J. C., Woo, S., Waymouth, R. M., Criddle, C. S. 2014; 170: 167-174
  • Recovery of freshwater from wastewater: upgrading process configurations to maximize energy recovery and minimize residuals. Environmental science & technology Scherson, Y. D., Criddle, C. S. 2014; 48 (15): 8420-8432


    Analysis of conventional and novel wastewater treatment configurations reveals large differences in energy consumed or produced and solids generated per cubic meter of domestic wastewater treated. Complete aerobic BOD removal consumes 0.45 kWh and produces 153 g of solids, whereas complete anaerobic treatment produces 0.25 kWh and 80 g of solids. Emerging technologies, that include short-circuit nitrogen removal (SHARON, CANON with Anammox, CANDO) and mainstream anaerobic digestion, can potentially remove both BOD and nitrogen with an energy surplus of 0.17 kWh and production of 95 g of solids. Heat from biogas combustion can completely dry the solids, and these solids can be converted to syngas without imported energy. Syngas combustion can produce ∼0.1 kWh with an inorganic residue of just 10 g. If salt is removed, freshwater can be recovered with net production of electrical energy from methane (0.03-0.13 kWh) and syngas (∼0.1 kWh) and an inorganic residue of ∼0.1-0.3 kg as brine. Current seawater desalination requires 3-4 kWh (thermodynamic limit of 1 kWh) and results in an inorganic residue of ∼35 kg as brine.

    View details for DOI 10.1021/es501701s

    View details for PubMedID 24963949

  • Performance of a mixing entropy battery alternately flushed with wastewater effluent and seawater for recovery of salinity-gradient energy ENERGY & ENVIRONMENTAL SCIENCE Ye, M., Pasta, M., Xie, X., Cui, Y., Criddle, C. S. 2014; 7 (7): 2295-2300

    View details for DOI 10.1039/c4ee01034e

    View details for Web of Science ID 000337977600021

  • Production of Nitrous Oxide From Anaerobic Digester Centrate and Its Use as a Co-oxidant of Biogas to Enhance Energy Recovery ENVIRONMENTAL SCIENCE & TECHNOLOGY Scherson, Y. D., Woo, S., Criddle, C. S. 2014; 48 (10): 5612-5619


    Coupled Aerobic-anoxic Nitrous Decomposition Operation (CANDO) is a new process for wastewater treatment that removes nitrogen from wastewater and recovers energy from the nitrogen in three steps: (1) NH4(+) oxidation to NO2(-); (2) NO2(-) reduction to N2O gas; and (3) N2O conversion to N2 with energy production. In this work, we optimize Steps 1 and 2 for anaerobic digester centrate, and we evaluate Step 3 for a full-scale biogas-fed internal combustion engine. Using a continuous stirred reactor coupled to a bench-scale sequencing batch reactor, we observed sustained partial oxidation of NH4(+) to NO2(-) and sustained (3 months) partial reduction of NO2(-) to N2O (75-80% conversion, mass basis), with >95% nitrogen removal (Step 2). Alternating pulses of acetate and NO2(-) selected for Comamonas (38%), Ciceribacter (16%), and Clostridium (11%). Some species stored polyhydroxybutyrate (PHB) and coupled oxidation of PHB to reduction of NO2(-) to N2O. Some species also stored phosphorus as polyphosphate granules. Injections of N2O into a biogas-fed engine at flow rates simulating a full-scale system increased power output by 5.7-7.3%. The results underscore the need for more detailed assessment of bioreactor community ecology and justify pilot- and full-scale testing.

    View details for DOI 10.1021/es501009j

    View details for Web of Science ID 000336415200032

  • Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Wells, G. F., Wu, C. H., Piceno, Y. M., Eggleston, B., Brodie, E. L., DeSantis, T. Z., Andersen, G. L., Hazen, T. C., Francis, C. A., Criddle, C. S. 2014; 98 (10): 4723-4736


    Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO2 (-) entering the reactor from an upstream trickling filter. Here, to further examine this puzzling association, we profile within-plant microbial biogeography (spatial variation) and test the hypothesis that substantial microbial immigration occurs along a transect (raw influent, trickling filter biofilm, trickling filter effluent, and activated sludge) at the same full-scale wastewater treatment plant. AOB amoA gene abundance increased >30-fold between influent and trickling filter effluent concomitant with NO2 (-) production, indicating unexpected growth and activity of AOB within the trickling filter. Nitrosomonas europaea was the dominant AOB phylotype in trickling filter biofilm and effluent, while a distinct "Nitrosomonas-like" lineage dominated in activated sludge. Prior time series indicated that this "Nitrosomonas-like" lineage was dominant when NO2 (-) levels in the trickling filter effluent (i.e., activated sludge influent) were low, while N. europaea became dominant in the activated sludge when NO2 (-) levels were high. This is consistent with the hypothesis that NO2 (-) production may cooccur with biofilm sloughing, releasing N. europaea from the trickling filter into the activated sludge bioreactor. Phylogenetic microarray (PhyloChip) analyses revealed significant spatial variation in taxonomic diversity, including a large excess of methanogens in the trickling filter relative to activated sludge and attenuation of Enterobacteriaceae across the transect, and demonstrated transport of a highly diverse microbial community via the trickling filter effluent to the activated sludge bioreactor. Our results provide compelling evidence that substantial immigration between coupled process units occurs and may exert significant influence over microbial community dynamics within staged bioreactors.

    View details for DOI 10.1007/s00253-014-5564-3

    View details for Web of Science ID 000335460700039

    View details for PubMedID 24553968

  • Recovery of Freshwater from Wastewater: Upgrading Process Configurations to Maximize Energy Recovery and Minimize Residuals Environmental Science and Technology Yaniv, S. D., Craig, C. S. 2014

    View details for DOI 10.1021/es501701s

  • Surge block method for controlling well clogging and sampling sediment during bioremediation WATER RESEARCH Wu, W., Watson, D. B., Luo, J., Carley, J., Mehlhorn, T., Kitanidis, P. K., Jardine, P. M., Criddle, C. S. 2013; 47 (17): 6566-6573


    A surge block treatment method (i.e. inserting a solid rod plunger with a flat seal that closely fits the casing interior into a well and stocking it up and down) was performed for the rehabilitation of wells clogged with biomass and for the collection of time series sediment samples during in situ bioremediation tests for U(VI) immobilization at a the U.S. Department of Energy site in Oak Ridge, TN. The clogging caused by biomass growth had been controlled by using routine surge block treatment for18 times over a nearly four year test period. The treatment frequency was dependent of the dosage of electron donor injection and microbial community developed in the subsurface. Hydraulic tests showed that the apparent aquifer transmissivity at a clogged well with an inner diameter (ID) of 10.16 cm was increased by 8-13 times after the rehabilitation, indicating the effectiveness of the rehabilitation. Simultaneously with the rehabilitation, the surge block method was successfully used for collecting time series sediment samples composed of fine particles (clay and silt) from wells with ID 1.9-10.16 cm for the analysis of mineralogical and geochemical composition and microbial community during the same period. Our results demonstrated that the surge block method provided a cost-effective approach for both well rehabilitation and frequent solid sampling at the same location.

    View details for DOI 10.1016/j.watres.2013.08.033

    View details for Web of Science ID 000327911700015

    View details for PubMedID 24070865

  • Microbial battery for efficient energy recovery PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Xie, X., Ye, M., Hsu, P., Liu, N., Criddle, C. S., Cui, Y. 2013; 110 (40): 15925-15930


    By harnessing the oxidative power of microorganisms, energy can be recovered from reservoirs of less-concentrated organic matter, such as marine sediment, wastewater, and waste biomass. Left unmanaged, these reservoirs can become eutrophic dead zones and sites of greenhouse gas generation. Here, we introduce a unique means of energy recovery from these reservoirs-a microbial battery (MB) consisting of an anode colonized by microorganisms and a reoxidizable solid-state cathode. The MB has a single-chamber configuration and does not contain ion-exchange membranes. Bench-scale MB prototypes were constructed from commercially available materials using glucose or domestic wastewater as electron donor and silver oxide as a coupled solid-state oxidant electrode. The MB achieved an efficiency of electrical energy conversion of 49% based on the combustion enthalpy of the organic matter consumed or 44% based on the organic matter added. Electrochemical reoxidation of the solid-state electrode decreased net efficiency to about 30%. This net efficiency of energy recovery (unoptimized) is comparable to methane fermentation with combined heat and power.

    View details for DOI 10.1073/pnas.1307327110

    View details for Web of Science ID 000325105500034

  • Assessing the Scale of Resource Recovery for Centralized and Satellite Wastewater Treatment ENVIRONMENTAL SCIENCE & TECHNOLOGY Lee, E. J., Criddle, C. S., Bobel, P., Freyberg, D. L. 2013; 47 (19): 10762-10770


    Wastewater treatment to recover water, energy, and other resources is largely carried out at centralized treatment facilities. An alternative is local treatment at satellite facilities where wastewater is removed from a collection system, resources are recovered locally, and the residuals are returned to the collection system. Satellite systems decrease the pipe and energy required for delivery of treated water and may decrease cost. But decisions regarding the geographic scale of resource recovery require consideration of many criteria. In this study, we rank water and energy recovery options for a simplified test case at three scale configurations: a centralized configuration and two hybrid configurations. We first choose criteria for decision-making. Quantitative performance metrics are defined for each criterion, weighted, and computed for each configuration. We then rank configurations. Rankings depend upon the decision-making strategy. For our test case, though, several strategies yield the same top-ranked configuration: a hybrid where communities close to the centralized facility use centralized resource recovery; communities far from the centralized facility use satellite resource recovery. Our ranking is sensitive to initial investment cost for satellite treatment. The results underscore the importance of cost-effective treatment systems and of an accurate and comprehensive analysis of design components.

    View details for DOI 10.1021/es401011k

    View details for Web of Science ID 000330094900007

  • Use of on-site bioreactors to estimate the biotransformation rate of N-ethyl perfluorooctane sulfonamidoethanol (N-EtFOSE) during activated sludge treatment CHEMOSPHERE Rhoads, K. R., Rostkowski, K. H., Kitanidis, P. K., Criddle, C. S. 2013; 92 (6): 702-707


    Accurate rates are needed for models that predict the fate of xenobiotic chemicals and impact of inhibitors at full-scale wastewater treatment plants. On-site rates for aerobic biotransformation of N-ethyl perfluorooctane sulfonamidoethanol (N-EtFOSE), a fluorinated repellent, were determined by continuously pumping mixed liquor from an aeration basin into two well-mixed acrylic bioreactors (4-L) operated in parallel. Known masses of N-EtFOSE and bromide were continuously added to the reactors. Reactor effluents were then monitored for bromide, N-EtFOSE, and metabolites of N-EtFOSE. Of the six transformation products reported in batch studies, only N-ethyl perfluorooctane sulfonamido acetate (N-EtFOSAA) was detected in the effluents. Bromide addition to the reactors enabled rate estimates despite variations in flow rate. Pseudo-second order rate coefficients for the N-EtFOSE biotransformation to N-EtFOSAA, predicted using a dynamic model of the reactor system, were k=2.0 and 2.4Lg(-1)VSSd(-1) for the two reactors, which are slower than the rates previously obtained using batch reactors. Given the relatively slow rate of N-EtFOSE transformation, its sorption and volatilization may be important in wastewater processes. The methodology used in this study should be suitable for similar on-site rate assessments with other contaminants or inhibitors.

    View details for DOI 10.1016/j.chemosphere.2013.04.059

    View details for Web of Science ID 000320897700011

    View details for PubMedID 23711409

  • In Situ Bioremediation of Uranium with Emulsified Vegetable Oil as the Electron Donor ENVIRONMENTAL SCIENCE & TECHNOLOGY Watson, D. B., Wu, W., Mehlhorn, T., Tang, G., Earles, J., Lowe, K., Gihring, T. M., Zhang, G., Phillips, J., Boyanov, M. I., Spalding, B. P., Schadt, C., Kemner, K. M., Criddle, C. S., Jardine, P. M., Brooks, S. C. 2013; 47 (12): 6440-6448


    A field test with a one-time emulsified vegetable oil (EVO) injection was conducted to assess the capacity of EVO to sustain uranium bioreduction in a high-permeability gravel layer with groundwater concentrations of (mM) U, 0.0055; Ca, 2.98; NO3(-), 0.11; HCO3(-), 5.07; and SO4(2-), 1.23. Comparison of bromide and EVO migration and distribution indicated that a majority of the injected EVO was retained in the subsurface from the injection wells to 50 m downgradient. Nitrate, uranium, and sulfate were sequentially removed from the groundwater within 1-2 weeks, accompanied by an increase in acetate, Mn, Fe, and methane concentrations. Due to the slow release and degradation of EVO with time, reducing conditions were sustained for approximately one year, and daily U discharge to a creek, located approximately 50 m from the injection wells, decreased by 80% within 100 days. Total U discharge was reduced by 50% over the one-year period. Reduction of U(VI) to U(IV) was confirmed by synchrotron analysis of recovered aquifer solids. Oxidants (e.g., dissolved oxygen, nitrate) flowing in from upgradient appeared to reoxidize and remobilize uranium after the EVO was exhausted as evidenced by a transient increase of U concentration above ambient values. Occasional (e.g., annual) EVO injection into a permeable Ca and bicarbonate-containing aquifer can sustain uranium bioreduction/immobilization and decrease U migration/discharge.

    View details for DOI 10.1021/es3033555

    View details for Web of Science ID 000320749000046

  • Stoichiometry and kinetics of the PHB-producing Type II methanotrophs Methylosinus trichosporium OB3b and Methylocystis parvus OBBP BIORESOURCE TECHNOLOGY Rostkowski, K. H., Pfluger, A. R., Criddle, C. S. 2013; 132: 71-77


    In this study, modeling is used to describe how oxygen and nitrogen source affect the stoichiometry and kinetics of growth and PHB production in the Type II methanotrophs Methylosinus trichosporium OB3b and Methylocystis parvus OBBP. Significant differences were observed, with major implications for the use of these species in biotechnology applications. Such analyses can better inform bioreactor design, scale-up models, and life cycle assessments (LCAs).

    View details for DOI 10.1016/j.biortech.2012.12.129

    View details for Web of Science ID 000316707200011

    View details for PubMedID 23395757

  • Nitrogen removal with energy recovery through N2O decomposition ENERGY & ENVIRONMENTAL SCIENCE Scherson, Y. D., Wells, G. F., Woo, S., Lee, J., Park, J., Cantwell, B. J., Criddle, C. S. 2013; 6 (1): 241-248

    View details for DOI 10.1039/c2ee22487a

    View details for Web of Science ID 000312337700029

  • Bioaugmentation with Pseudomonas stutzeri KC for Remediation of Carbon Tetrachloride. Bioaugmentation for Remediation. Criddle, C., S., Dybas, M., J., Tatara, G., M., Warnick, L., B., Vidal-Gavilan, G., Robertson, A., P. edited by Stroo, H., F., Leeson, A., Ward, C., H. Springer Science + Business Media, New York. 2013: 257-285
  • Chemical and biological processes: the need for mixing. Delivery and Mixing in the Subsurface: Process and Design Principles for In Situ Remediation. McCarty, P., L., Criddle, C., S. edited by Kitanidis, P., K., McCarty, P., L., Ward, C., Herb Springer Science + Business Media, New York. 2013: 7-52
  • A microbial battery for efficient energy recovery Proc. National Acad. Science Xie, X., Ye, M., Hsu, P. -., Liu, N., Criddle, C. S., Cui, Y. 2013
  • Magnetically ultraresponsive nanoscavengers for next-generation water purification systems. Nature communications Zhang, M., Xie, X., Tang, M., Criddle, C. S., Cui, Y., Wang, S. X. 2013; 4: 1866-?


    The development of sustainable, robust and energy efficient water purification technology is still challenging. Although use of nanoparticles is promising, methods are needed for their efficient recovery post treatment. Here we address this issue by fabrication of magnetically ultraresponsive 'nanoscavengers', nanoparticles containing synthetic antiferromagnetic core layers and functional capping layers. When dispersed in water, the nanoscavengers efficiently interact with contaminants to remove them from the water. They are then quickly collected (<5?min) with a permanent magnet, owing to their magnetically ultraresponsive core layers. Specifically, we demonstrate fabrication and deployment of Ag-capped nanoscavengers for disinfection followed by application of an external magnetic field for separation. We also develop and validate a collision-based model for pathogen inactivation, and propose a cyclical water purification scheme in which nanoscavengers are recovered and recycled for contaminant removal.

    View details for DOI 10.1038/ncomms2892

    View details for PubMedID 23673651

  • Adaptation of nitrifying microbial biomass to nickel in batch incubations APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Yeung, C., Francis, C. A., Criddle, C. S. 2013; 97 (2): 847-857


    Nitrification-microbial oxidation of ammonia to nitrate-is sensitive to an array of inhibitors. Currently, little is known regarding the ecological processes that enable adaptation to inhibitors and recovery of nitrification. This study evaluated inhibition and recovery of nitrification in batch cultures of activated sludge incubated with different levels of nickel (Ni), a model inhibitor. Incubation with 1 mg/L of added Ni did not adversely affect nitrification, and little inhibition occurred at 5 and 10 mg/L Ni. Incubation with 50 mg/L Ni resulted in significant inhibition, decreased amoA transcript abundance, and delayed recovery of nitrification until amoA transcript abundance rebounded after 24 h. For this dosage, recovery of nitrification occurred without a significant change in ammonia-oxidizing bacteria (AOB) community structure. By contrast, incubation with 150 mg/L of added Ni strongly inhibited nitrification and delayed recovery until a shift in AOB community structure occurred after ∼6 weeks of incubation. The results indicate that inhibitor-resistant nitrifying cultures can be obtained from long-term batch incubations of decaying activated sludge incubated with high levels of added inhibitor.

    View details for DOI 10.1007/s00253-012-3947-x

    View details for Web of Science ID 000313651700035

    View details for PubMedID 22374414

  • Cradle-to-Gate Life Cycle Assessment for a Cradle-to-Cradle Cycle: Biogas-to-Bioplastic (and Back) ENVIRONMENTAL SCIENCE & TECHNOLOGY Rostkowski, K. H., Criddle, C. S., Lepech, M. D. 2012; 46 (18): 9822-9829


    At present, most synthetic organic materials are produced from fossil carbon feedstock that is regenerated over time scales of millions of years. Biobased alternatives can be rapidly renewed in cradle-to-cradle cycles (1-10 years). Such materials extend landfill life and decrease undesirable impacts due to material persistence. This work develops a LCA for synthesis of polyhydroxybutyrate (PHB) from methane with subsequent biodegradation of PHB back to biogas (40-70% methane, 30-60% carbon dioxide). The parameters for this cradle-to-cradle cycle for PHB production are developed and used as the basis for a cradle-to-gate LCA. PHB production from biogas methane is shown to be preferable to its production from cultivated feedstock due to the energy and land required for the feedstock cultivation and fermentation. For the PHB-methane cycle, the major challenges are PHB recovery and demands for energy. Some or all of the energy requirements can be satisfied using renewable energy, such as a portion of the collected biogas methane. Oxidation of 18-26% of the methane in a biogas stream can meet the energy demands for aeration and agitation, and recovery of PHB synthesized from the remaining 74-82%. Effective coupling of waste-to-energy technologies could thus conceivably enable PHB production without imported carbon and energy.

    View details for DOI 10.1021/es204541w

    View details for Web of Science ID 000308787800002

    View details for PubMedID 22775327

  • Graphene-sponges as high-performance low-cost anodes for microbial fuel cells ENERGY & ENVIRONMENTAL SCIENCE Xie, X., Yu, G., Liu, N., Bao, Z., Criddle, C. S., Cui, Y. 2012; 5 (5): 6862-6866

    View details for DOI 10.1039/c2ee03583a

    View details for Web of Science ID 000303251500019

  • Cyclic, alternating methane and nitrogen limitation increases PHB production in a methanotrophic community BIORESOURCE TECHNOLOGY Pieja, A. J., Sundstrom, E. R., Criddle, C. S. 2012; 107: 385-392


    To identify feast-famine strategies that favor PHB accumulation in Type II methanotrophic proteobacteria, three sequencing batch reactors seeded with a defined inoculum of Type II methanotrophs were subjected to 24-h cycles consisting of (1) repeated nitrogen limitation, (2) repeated nitrogen and oxygen limitation, and (3) repeated nitrogen and methane limitation. PHB levels within each reactor and capacity to produce PHB in offline batch incubations were monitored over 11 cycles. PHB content increased only in the reactor limited by both nitrogen and methane. This reactor became dominated by Methylocystis parvus OBBP with no detectable minority populations. It was concluded that repeated nitrogen and methane limitations favored PHB accumulation in strain OBBP and provided it with a competitive advantage under the conditions imposed.

    View details for DOI 10.1016/j.biortech.2011.12.044

    View details for Web of Science ID 000301620600054

    View details for PubMedID 22244897

  • Carbon nanotube-coated macroporous sponge for microbial fuel cell electrodes ENERGY & ENVIRONMENTAL SCIENCE Xie, X., Ye, M., Hu, L., Liu, N., McDonough, J. R., Chen, W., Alshareef, H. N., Criddle, C. S., Cui, Y. 2012; 5 (1): 5265-5270

    View details for DOI 10.1039/c1ee02122b

    View details for Web of Science ID 000299046100016

  • Carbon nanotube-coated sponge electrodes for microbial fuel cell applications. Energy and Environment Xing, X., Ye, M., Hu, L., McDonough, J., R., Criddle, C., S., Cui. 2012; 5: 5265-5270
  • Carbon graphene-sponges as high-performance low-cost anodes for microbial fuel cells. Energy and Environment Xing, X., Yu, G., Liu, N., Bao, Z., Criddle, C., S., Cui, Y. 2012; 5: 6862-6866
  • Selection of Type I and Type II methanotrophic proteobacteria in a fluidized bed reactor under non-sterile conditions BIORESOURCE TECHNOLOGY Pfluger, A. R., Wu, W., Pieja, A. J., Wan, J., Rostkowski, K. H., Criddle, C. S. 2011; 102 (21): 9919-9926


    Type II methanotrophs produce polyhydroxybutyrate (PHB), while Type I methanotrophs do not. A laboratory-scale fluidized bed reactor was initially inoculated with a Type II Methylocystis-like dominated culture. At elevated levels of dissolved oxygen (DO, 9 mg/L), pH of 6.2-6.5 with nitrate as the N-source, a Methylobacter-like Type I methanotroph became dominant within the biofilms which did not produce PHB. A shift to biofilms capable of PHB production was achieved by re-inoculating with Type II Methylosinus culture, providing dissolved N(2) as the N-source, and maintaining a low influent DO (2.0mg/L). The resulting biofilms contained both Types I and II methanotrophs. Batch tests indicated that biofilm samples grown with N(2) became dominated by Type II methanotrophs and produced PHB. Enrichments with nitrate or ammonium were dominated by Type I methanotrophs without PHB production capability. The key selection factors favoring Type II were N(2) as N-source and low DO.

    View details for DOI 10.1016/j.biortech.2011.08.054

    View details for Web of Science ID 000296124200014

    View details for PubMedID 21906939

  • Fine-scale bacterial community dynamics and the taxa-time relationship within a full-scale activated sludge bioreactor WATER RESEARCH Wells, G. F., Park, H., Eggleston, B., Francis, C. A., Criddle, C. S. 2011; 45 (17): 5476-5488


    In activated sludge bioreactors, aerobic heterotrophic communities efficiently remove organics, nutrients, toxic substances, and pathogens from wastewater, but the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community shifts is the taxa-time relationship, a temporal analog of the species-area curve. To determine whether this metric can be applied to full-scale bioreactors, activated sludge samples were collected weekly over a one-year period at a local municipal wastewater treatment plant. Bacterial community dynamics were evaluated by monitoring 16S rRNA genes using Terminal Restriction Fragment Length Polymorphism (T-RFLP), corroborated by clone libraries. Observed taxa richness increased with time according to a power law model, as predicted by macroecological theory, with a power law exponent of w = 0.209. The results reveal strong long-term temporal dynamics during a period of stable performance (BOD removal and nitrification). Community dynamics followed a gradual succession away from initial conditions rather than periodicity around a mean "equilibrium", with greater within-month then among-month community similarities. Changes in community structure were significantly associated via multivariate statistical analyses with dissolved oxygen, temperature, influent silver, biomass (MLSS), flow rate, and influent nitrite, cadmium and chromium concentrations. Overall, our results suggest patterns of bacterial community dynamics likely regulated in part by operational parameters and provide evidence that the taxa-time relationship may be a fundamental ecological pattern in macro- and microbial systems.

    View details for DOI 10.1016/j.watres.2011.08.006

    View details for Web of Science ID 000295894600013

    View details for PubMedID 21875739

  • Distribution and Selection of Poly-3-Hydroxybutyrate Production Capacity in Methanotrophic Proteobacteria MICROBIAL ECOLOGY Pieja, A. J., Rostkowski, K. H., Criddle, C. S. 2011; 62 (3): 564-573


    Methanotrophs are known to produce poly-3-hydroxybutyrate (PHB), but there is conflicting evidence in the literature as to which genera produce the polymer. We screened type I and II proteobacterial methanotrophs that use the ribulose monophosphate and serine pathways for carbon assimilation, respectively, for both phaC, which encodes for PHB synthase, and the ability to produce PHB under nitrogen-limited conditions. Twelve strains from six different genera were evaluated. All type I strains tested negative for phaC and PHB production; all Type II strains tested positive for phaC and PHB production. In order to identify conditions that favor PHB production, we also evaluated a range of selection conditions using a diverse activated sludge inoculum. Use of medium typically recommended for methanotroph enrichment led to enrichments dominated by type I methanotrophs. Conditions that were selected for enrichments dominated by PHB-producing Type II methanotrophs were: (1) use of nitrogen gas as the sole nitrogen source in the absence of copper, (2) use of a dilute mineral salts media in the absence of copper, and (3) use of media prepared at pH values of 4-5.

    View details for DOI 10.1007/s00248-011-9873-0

    View details for Web of Science ID 000294963300007

    View details for PubMedID 21594594

  • A Limited Microbial Consortium Is Responsible for Extended Bioreduction of Uranium in a Contaminated Aquifer APPLIED AND ENVIRONMENTAL MICROBIOLOGY Gihring, T. M., Zhang, G., Brandt, C. C., Brooks, S. C., Campbell, J. H., Carroll, S., Criddle, C. S., Green, S. J., Jardine, P., Kostka, J. E., Lowe, K., Mehlhorn, T. L., Overholt, W., Watson, D. B., Yang, Z., Wu, W., Schadt, C. W. 2011; 77 (17): 5955-5965


    Subsurface amendments of slow-release substrates (e.g., emulsified vegetable oil [EVO]) are thought to be a pragmatic alternative to using short-lived, labile substrates for sustained uranium bioimmobilization within contaminated groundwater systems. Spatial and temporal dynamics of subsurface microbial communities during EVO amendment are unknown and likely differ significantly from those of populations stimulated by soluble substrates, such as ethanol and acetate. In this study, a one-time EVO injection resulted in decreased groundwater U concentrations that remained below initial levels for approximately 4 months. Pyrosequencing and quantitative PCR of 16S rRNA from monitoring well samples revealed a rapid decline in groundwater bacterial community richness and diversity after EVO injection, concurrent with increased 16S rRNA copy levels, indicating the selection of a narrow group of taxa rather than a broad community stimulation. Members of the Firmicutes family Veillonellaceae dominated after injection and most likely catalyzed the initial oil decomposition. Sulfate-reducing bacteria from the genus Desulforegula, known for long-chain fatty acid oxidation to acetate, also dominated after EVO amendment. Acetate and H(2) production during EVO degradation appeared to stimulate NO(3)(-), Fe(III), U(VI), and SO(4)(2-) reduction by members of the Comamonadaceae, Geobacteriaceae, and Desulfobacterales. Methanogenic archaea flourished late to comprise over 25% of the total microbial community. Bacterial diversity rebounded after 9 months, although community compositions remained distinct from the preamendment conditions. These results demonstrated that a one-time EVO amendment served as an effective electron donor source for in situ U(VI) bioreduction and that subsurface EVO degradation and metal reduction were likely mediated by successive identifiable guilds of organisms.

    View details for DOI 10.1128/AEM.00220-11

    View details for Web of Science ID 000294205700014

    View details for PubMedID 21764967

  • Poly-3-Hydroxybutyrate Metabolism in the Type II Methanotroph Methylocystis parvus OBBP APPLIED AND ENVIRONMENTAL MICROBIOLOGY Pieja, A. J., Sundstrom, E. R., Criddle, C. S. 2011; 77 (17): 6012-6019


    Differences in carbon assimilation pathways and reducing power requirements among organisms are likely to affect the role of the storage polymer poly-3-hydroxybutyrate (PHB). Previous researchers have demonstrated that PHB functions as a sole growth substrate in aerobic cultures enriched on acetate during periods of carbon deficiency, but it is uncertain how C(1) metabolism affects the role of PHB. In the present study, the type II methanotroph Methylocystis parvus OBBP did not replicate using stored PHB in the absence of methane, even when all other nutrients were provided in excess. When PHB-rich cultures of M. parvus OBBP were deprived of carbon and nitrogen for 48 h, they did not utilize significant amounts of stored PHB, and neither cell concentrations nor concentrations of total suspended solids changed significantly. When methane and nitrogen both were present, PHB and methane were consumed simultaneously. Cells with PHB had significantly higher specific growth rates than cells lacking PHB. The addition of formate (a source of reducing power) to PHB-rich cells delayed PHB consumption, but the addition of glyoxylate (a source of C(2) units) did not. This and results from other researchers suggest that methanotrophic PHB metabolism is linked to the supply of reducing power as opposed to the supply of C(2) units for synthesis.

    View details for DOI 10.1128/AEM.00509-11

    View details for Web of Science ID 000294205700021

    View details for PubMedID 21724874

  • Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer (vol 77, pg 3860, 2011) APPLIED AND ENVIRONMENTAL MICROBIOLOGY Van Nostrand, J. D., Wu, L., Wu, W., Huang, Z., Gentry, T. J., Deng, Y., Carley, J., Carroll, S., He, Z., Gu, B., Luo, J., Criddle, C. S., Watson, D. B., Jardine, P. M., Marsh, T. L., Tiedje, J. M., Hazen, T. C., Zhou, J. 2011; 77 (14): 5063-5063
  • Reduction of Uranium(VI) by Soluble Iron(II) Conforms with Thermodynamic Predictions ENVIRONMENTAL SCIENCE & TECHNOLOGY Du, X., Boonchayaanant, B., Wu, W., Fendorf, S., Bargar, J., Criddle, C. S. 2011; 45 (11): 4718-4725


    Soluble Fe(II) can reduce soluble U(VI) at rapid rates and in accordance with thermodynamic predictions. This was established by initially creating acidic aqueous solutions in which the sole oxidants were soluble U(VI) species and the sole reductants were soluble Fe(II) species. The pH of the solution was then increased by stepwise addition of OH(-), thereby increasing the potential for electron transfer from Fe(II) to U(VI). For each new pH value resulting from addition of base, values of ?G for the Fe(II)-mediated reduction of U(VI) were calculated using the computed distribution of U and Fe species and possible half reaction combinations. For initial conditions of pH 2.4 and a molar ratio of Fe(II) to U(VI) of 5:1 (1 mM Fe(II) and 0.2 mM U(VI)), ?G for U(VI) reduction was greater than zero, and U(VI) reduction was not observed. When sufficient OH(-) was added to exceed the computed equilibrium pH of 5.4, ?G for U(VI) reduction was negative and soluble Fe(II) species reacted with U(VI) in a molar ratio of ?2:1. X-ray absorption near-edge structure (XANES) spectroscopy confirmed production of U(IV). A decrease in pH confirmed production of acidity as the reaction advanced. As solution pH decreased to the equilibrium value, the rate of reaction declined, stopping completely at the predicted equilibrium pH. Initiation of the reaction at a higher pH resulted in a higher final ratio of U(IV) to U(VI) at equilibrium.

    View details for DOI 10.1021/es2006012

    View details for Web of Science ID 000291128700011

    View details for PubMedID 21553877

  • Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer APPLIED AND ENVIRONMENTAL MICROBIOLOGY Van Nostrand, J. D., Wu, L., Wu, W., Huang, Z., Gentry, T. J., Deng, Y., Carley, J., Carroll, S., He, Z., Gu, B., Luo, J., Criddle, C. S., Watson, D. B., Jardine, P. M., Marsh, T. L., Tiedje, J. M., Hazen, T. C., Zhou, J. 2011; 77 (11): 3860-3869


    A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter(-1)). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process.

    View details for DOI 10.1128/AEM.01981-10

    View details for Web of Science ID 000290847800038

    View details for PubMedID 21498771

  • Nano-structured textiles as high-performance aqueous cathodes for microbial fuel cells ENERGY & ENVIRONMENTAL SCIENCE Xie, X., Pasta, M., Hu, L., Yang, Y., McDonough, J., Cha, J., Criddle, C. S., Cui, Y. 2011; 4 (4): 1293-1297

    View details for DOI 10.1039/c0ee00793e

    View details for Web of Science ID 000289001400020

  • Anaerobic biodegradation of the microbial copolymer poly(3-hydroxybutyrate-co-3-hydroxyhexanoate): Effects of comonomer content, processing history, and semi-crystalline morphology POLYMER Morse, M., Liao, Q., Criddle, C. S., Frank, C. W. 2011; 52 (2): 547-556
  • Three-Dimensional Carbon Nanotube-Textile Anode for High-Performance Microbial Fuel Cells NANO LETTERS Xie, X., Hu, L., Pasta, M., Wells, G. F., Kong, D., Criddle, C. S., Cui, Y. 2011; 11 (1): 291-296


    Microbial fuel cells (MFCs) harness the metabolism of microorganisms, converting chemical energy into electrical energy. Anode performance is an important factor limiting the power density of MFCs for practical application. Improving the anode design is thus important for enhancing the MFC performance, but only a little development has been reported. Here, we describe a biocompatible, highly conductive, two-scale porous anode fabricated from a carbon nanotube-textile (CNT-textile) composite for high-performance MFCs. The macroscale porous structure of the intertwined CNT-textile fibers creates an open 3D space for efficient substrate transport and internal colonization by a diverse microflora, resulting in a 10-fold-larger anolyte-biofilm-anode interfacial area than the projective surface area of the CNT-textile. The conformally coated microscale porous CNT layer displays strong interaction with the microbial biofilm, facilitating electron transfer from exoelectrogens to the CNT-textile anode. An MFC equipped with a CNT-textile anode has a 10-fold-lower charge-transfer resistance and achieves considerably better performance than one equipped with a traditional carbon cloth anode: the maximum current density is 157% higher, the maximum power density is 68% higher, and the energy recovery is 141% greater.

    View details for DOI 10.1021/nl103905t

    View details for Web of Science ID 000286029400050

    View details for PubMedID 21158405

  • Taxa-time in a full-scale activated sludge bioreactor. Water Research Wells, G., F., Park, H. -D., Eggleston, B., Francis, C., A. 2011; 45: 5476-5488
  • Engineered biomaterials for construction: A cradle-to-cradle design methodology for green material development. The International J. of Environmental, Cultural, Economic and Social Sustainability Srubar III, W., V., Michel, A., T., Criddle, C., S., Frank, C., W., Billington, S., L. 2011; 5 (7): 157-166
  • Bioreduction and immobilization of uranium in situ: a case study at a USA Department of Energy radioactive waste site, Oak Ridge, Tennessee. Acta Scientiae Circumstaniae Wu, W., M., Carley, J., Watson, D., Gu, B., Brooks, S., Kelly, S., D., Criddle, C. 2011; 1 (31): 449-459
  • Membrane fouling in an anaerobic membrane bioreactor: Differences in relative abundance of bacterial species in the membrane foulant layer and in suspension JOURNAL OF MEMBRANE SCIENCE Gao, D., Zhang, T., Tang, C. Y., Wu, W., Wong, C., Lee, Y. H., Yeh, D. H., Criddle, C. S. 2010; 364 (1-2): 331-338
  • Kinetic analysis and modeling of oleate and ethanol stimulated uranium (VI) bio-reduction in contaminated sediments under sulfate reduction conditions JOURNAL OF HAZARDOUS MATERIALS Zhang, F., Wu, W., Parker, J. C., Mehlhorn, T., Kelly, S. D., Kemner, K. M., Zhang, G., Schadt, C., Brooks, S. C., Criddle, C. S., Watson, D. B., Jardine, P. M. 2010; 183 (1-3): 482-489


    Microcosm tests with uranium contaminated sediments were performed to explore the feasibility of using oleate as a slow-release electron donor for U(VI) reduction in comparison to ethanol. Oleate degradation proceeded more slowly than ethanol with acetate produced as an intermediate for both electron donors under a range of initial sulfate concentrations. A kinetic microbial reduction model was developed and implemented to describe and compare the reduction of sulfate and U(VI) with oleate or ethanol. The reaction path model considers detailed oleate/ethanol degradation and the production and consumption of intermediates, acetate and hydrogen. Although significant assumptions are made, the model tracked the major trend of sulfate and U(VI) reduction and describes the successive production and consumption of acetate, concurrent with microbial reduction of aqueous sulfate and U(VI) species. The model results imply that the overall rate of U(VI) bioreduction is influenced by both the degradation rate of organic substrates and consumption rate of intermediate products.

    View details for DOI 10.1016/j.jhazmat.2010.07.049

    View details for Web of Science ID 000282607600061

    View details for PubMedID 20702039

  • Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach APPLIED AND ENVIRONMENTAL MICROBIOLOGY Cardenas, E., Wu, W., Leigh, M. B., Carley, J., Carroll, S., Gentry, T., Luo, J., Watson, D., Gu, B., Ginder-Vogel, M., Kitanidis, P. K., Jardine, P. M., Zhou, J., Criddle, C. S., Marsh, T. L., Tiedje, J. M. 2010; 76 (20): 6778-6786


    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 ?M and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

    View details for DOI 10.1128/AEM.01097-10

    View details for Web of Science ID 000282595100009

    View details for PubMedID 20729318

  • Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation ISME JOURNAL Xu, M., Wu, W., Wu, L., He, Z., Van Nostrand, J. D., Deng, Y., Luo, J., Carley, J., Ginder-Vogel, M., Gentry, T. J., Gu, B., Watson, D., Jardine, P. M., Marsh, T. L., Tiedje, J. M., Hazen, T., Criddle, C. S., Zhou, J. 2010; 4 (8): 1060-1070


    A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 microg l(-1)) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

    View details for DOI 10.1038/ismej.2010.31

    View details for Web of Science ID 000280592600010

    View details for PubMedID 20237512

  • Effects of Nitrate on the Stability of Uranium in a Bioreduced Region of the Subsurface ENVIRONMENTAL SCIENCE & TECHNOLOGY Wu, W., Carley, J., Green, S. J., Luo, J., Kelly, S. D., Van Nostrand, J., Lowe, K., Mehlhorn, T., Carroll, S., Boonchayanant, B., Loefller, F. E., Watson, D., Kemner, K. M., Zhou, J., Kitanidis, P. K., Kostka, J. E., Jardine, P. M., Criddle, C. S. 2010; 44 (13): 5104-5111


    The effects of nitrate on the stability of reduced, immobilized uranium were evaluated in field experiments at a U.S. Department of Energy site in Oak Ridge, TN. Nitrate (2.0 mM) was injected into a reduced region of the subsurface containing high levels of previously immobilized U(IV). The nitrate was reduced to nitrite, ammonium, and nitrogen gas; sulfide levels decreased; and Fe(II) levels increased then deceased. Uranium remobilization occurred concomitant with nitrite formation, suggesting nitrate-dependent, iron-accelerated oxidation of U(IV). Bromide tracer results indicated changes in subsurface flowpaths likely due to gas formation and/or precipitate. Desorption-adsorption of uranium by the iron-rich sediment impacted uranium mobilization and sequestration. After rereduction of the subsurface through ethanol additions, background groundwater containing high levels of nitrate was allowed to enter the reduced test zone. Aqueous uranium concentrations increased then decreased. Clone library analyses of sediment samples revealed the presence of denitrifying bacteria that can oxidize elemental sulfur, H(2)S, Fe(II), and U(IV) (e.g., Thiobacillus spp.), and a decrease in relative abundance of bacteria that can reduce Fe(III) and sulfate. XANES analyses of sediment samples confirmed changes in uranium oxidation state. Addition of ethanol restored reduced conditions and triggered a short-term increase in Fe(II) and aqueous uranium, likely due to reductive dissolution of Fe(III) oxides and release of sorbed U(VI). After two months of intermittent ethanol addition, sulfide levels increased, and aqueous uranium concentrations gradually decreased to <0.1 microM.

    View details for DOI 10.1021/es1000837

    View details for Web of Science ID 000279304700047

    View details for PubMedID 20527772

  • Effect of solution chemistry on the adsorption of perfluorooctane sulfonate onto mineral surfaces. Water research Tang, C. Y., Shiang Fu, Q., Gao, D., Criddle, C. S., Leckie, J. O. 2010; 44 (8): 2654-2662


    Perfluorooctane sulfonate (PFOS) is an emergent contaminant of substantial environmental concerns, yet very limited information has been available on PFOS adsorption onto mineral surfaces. PFOS adsorption onto goethite and silica was investigated by batch adsorption experiments under various solution compositions. Adsorption onto silica was only marginally affected by pH, ionic strength, and calcium concentration, likely due to the dominance of non-electrostatic interactions. In contrast, PFOS uptake by goethite increased significantly at high [H+] and [Ca2+], which was likely due to enhanced electrostatic attraction between the negatively charged PFOS molecules and positively charged goethite surface. The effect of pH was less significant at high ionic strength, likely due to electrical double layer compression. PFOS uptake was reduced at higher ionic strength for a strongly positively charged goethite surface (pH 3), while it increased for a weakly charged surface (pH 7 and 9), which could be attributed to the competition between PFOS-surface electrostatic attraction and PFOS-PFOS electrostatic repulsion. A conceptual model that captures PFOS-surface and PFOS-PFOS electrostatic interactions as well as non-electrostatic interaction was also formulated to understand the effect of solution chemistry on PFOS adsorption onto goethite and silica surfaces.

    View details for DOI 10.1016/j.watres.2010.01.038

    View details for PubMedID 20172580

  • Can microbially-generated hydrogen sulfide account for the rates of U(VI) reduction by a sulfate-reducing bacterium? BIODEGRADATION Boonchayaanant, B., Gu, B., Wang, W., Ortiz, M. E., Criddle, C. S. 2010; 21 (1): 81-95


    In situ remediation of uranium contaminated soil and groundwater is attractive because a diverse range of microbial and abiotic processes reduce soluble and mobile U(VI) to sparingly soluble and immobile U(IV). Often these processes are linked. Sulfate-reducing bacteria (SRB), for example, enzymatically reduce U(VI) to U(IV), but they also produce hydrogen sulfide that can itself reduce U(VI). This study evaluated the relative importance of these processes for Desulfovibrio aerotolerans, a SRB isolated from a U(VI)-contaminated site. For the conditions evaluated, the observed rate of SRB-mediated U(VI) reduction can be explained by the abiotic reaction of U(VI) with the microbially-generated H(2)S. The presence of trace ferrous iron appeared to enhance the extent of hydrogen sulfide-mediated U(VI) reduction at 5 mM bicarbonate, but had no clear effect at 15 mM. During the hydrogen sulfide-mediated reduction of U(VI), a floc formed containing uranium and sulfur. U(VI) sequestered in the floc was not available for further reduction.

    View details for DOI 10.1007/s10532-009-9283-x

    View details for Web of Science ID 000273082700008

    View details for PubMedID 19597947

  • Uranium Transformations in Static Microcosms ENVIRONMENTAL SCIENCE & TECHNOLOGY Kelly, S. D., Wu, W., Yang, F., Criddle, C. S., Marsh, T. L., O'Loughlin, E. J., Ravel, B., Watson, D., Jardine, P. M., Kemner, K. M. 2010; 44 (1): 236-242


    Elucidation of complex biogeochemical processes and their effects on speciation of U in the subsurface is critical for developing remediation strategies with an understanding of stability. We have developed static microcosms that are similar to bioreduction process studies in situ under laminar flow conditions or in sediment pores. Uranium L(3)-edge X-ray absorption near-edge spectroscopy analysis with depth in the microcosms indicated that transformation of U(VI) to U(IV) occurred by at least two distinct processes. Extended X-ray absorption fine structure (EXAFS) analysis indicated that initial U(VI) species associated with C- and P-containing ligands were transformed to U(IV) in the form of uraninite and U associated with Fe-bound ligands. Microbial community analysis identified putative Fe(III) and sulfate reducers at two different depths in the microcosms. The slow reduction of U(VI) to U(IV) may contribute the stability of U(IV) within microcosms at 11 months after a decrease in bioreducing conditions due to limited electron donors.

    View details for DOI 10.1021/es902191s

    View details for Web of Science ID 000273267000041

    View details for PubMedID 19958005

  • Impact of nitrate on the stability of uranium within a bioreduced region of the subsurface. Environ. Sci. Technol. Wu, W., M., Carley, J., Green, S., Luo, J., Zhang, G., Kelly, S., D., Criddle, C. 2010; 13 (44): 5104–5111
  • A combined massively parallel sequencing – indicator species approach revealed significant association between sulfate-reducing bacteria and uranium-reducing microbial communities. Applied Environ. Microbio. Cardenas, E., Wu, W., M., Leigh, M., B., Carley, J., Carroll, S., Gentry, T., Criddle, C. 2010; 20 (76): 6778-6786
  • GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer ENVIRONMENTAL MICROBIOLOGY Van Nostrand, J. D., Wu, W., Wu, L., Deng, Y., Carley, J., Carroll, S., He, Z., Gu, B., Luo, J., Criddle, C. S., Watson, D. B., Jardine, P. M., Marsh, T. L., Tiedje, J. M., Hazen, T. C., Zhou, J. 2009; 11 (10): 2611-2626


    A pilot-scale system was established for in situ biostimulation of U(VI) reduction by ethanol addition at the US Department of Energy's (DOE's) Field Research Center (Oak Ridge, TN). After achieving U(VI) reduction, stability of the bioreduced U(IV) was evaluated under conditions of (i) resting (no ethanol injection), (ii) reoxidation by introducing dissolved oxygen (DO), and (iii) reinjection of ethanol. GeoChip, a functional gene array with probes for N, S and C cycling, metal resistance and contaminant degradation genes, was used for monitoring groundwater microbial communities. High diversity of all major functional groups was observed during all experimental phases. The microbial community was extremely responsive to ethanol, showing a substantial change in community structure with increased gene number and diversity after ethanol injections resumed. While gene numbers showed considerable variations, the relative abundance (i.e. percentage of each gene category) of most gene groups changed little. During the reoxidation period, U(VI) increased, suggesting reoxidation of reduced U(IV). However, when introduction of DO was stopped, U(VI) reduction resumed and returned to pre-reoxidation levels. These findings suggest that the community in this system can be stimulated and that the ability to reduce U(VI) can be maintained by the addition of electron donors. This biostimulation approach may potentially offer an effective means for the bioremediation of U(VI)-contaminated sites.

    View details for DOI 10.1111/j.1462-2920.2009.01986.x

    View details for Web of Science ID 000270433700012

    View details for PubMedID 19624708

  • Uranium reduction and resistance to reoxidation under iron-reducing and sulfate-reducing conditions WATER RESEARCH Boonchayaanant, B., Nayak, D., Du, X., Criddle, C. S. 2009; 43 (18): 4652-4664


    Oxidation and mobilization of microbially-generated U(IV) is of great concern for in situ uranium bioremediation. This study investigated the reoxidation of uranium by oxygen and nitrate in a sulfate-reducing enrichment and an iron-reducing enrichment derived from sediment and groundwater from the Field Research Center in Oak Ridge, Tennessee. Both enrichments were capable of reducing U(VI) rapidly. 16S rRNA gene clone libraries of the two enrichments revealed that Desulfovibrio spp. are dominant in the sulfate-reducing enrichment, and Clostridium spp. are dominant in the iron-reducing enrichment. In both the sulfate-reducing enrichment and the iron-reducing enrichment, oxygen reoxidized the previously reduced uranium but to a lesser extent in the iron-reducing enrichment. Moreover, in the iron-reducing enrichment, the reoxidized U(VI) was eventually re-reduced to its previous level. In both, the sulfate-reducing enrichment and the iron-reducing enrichment, uranium reoxidation did not occur in the presence of nitrate. The results indicate that the Clostridium-dominated iron-reducing communities created conditions that were more favorable for uranium stability with respect to reoxidation despite the fact that fewer electron equivalents were added to these systems. The likely reason is that more of the added electrons are present in a form that can reduce oxygen to water and U(VI) back to U(IV).

    View details for DOI 10.1016/j.watres.2009.07.013

    View details for Web of Science ID 000271439600022

    View details for PubMedID 19651424

  • Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea ENVIRONMENTAL MICROBIOLOGY Wells, G. F., Park, H., Yeung, C., Eggleston, B., Francis, C. A., Criddle, C. S. 2009; 11 (9): 2310-2328


    Ammonia-oxidizing bacteria (AOB) have long been considered key to the removal of nitrogen in activated sludge bioreactors. Culture-independent molecular analyses have established that AOB lineages in bioreactors are dynamic, but the underlying operational or environmental factors are unclear. Furthermore, the contribution of ammonia-oxidizing archaea (AOA) to nitrogen removal in bioreactors has not been studied. To this end, we investigated the abundance of AOA and AOB as well as correlations between dynamics in AOB lineages and operational parameters at a municipal wastewater treatment plant sampled weekly over a 1 year period. Quantitative PCR measurements of bacterial and archaeal ammonia monooxygenase subunit A (amoA) genes revealed that the bacterial homologue predominated by at least three orders of magnitude in all samples. Archaeal amoA was only detectable in approximately 15% of these samples. Using terminal restriction fragment length polymorphism analysis, we monitored AOB lineages based on amoA genes. The Nitrosomonas europaea lineage and a novel Nitrosomonas-like cluster were the dominant AOB signatures, with a Nitrosospira lineage present at lower relative abundance. These lineages exhibited strong temporal oscillations, with one becoming sequentially dominant over the other. Using non-metric multidimensional scaling and redundancy analyses, we tested correlations between terminal restriction fragment length polymorphism profiles and 20 operational and environmental parameters. The redundancy analyses indicated that the dynamics of AOB lineages correlated most strongly with temperature, dissolved oxygen and influent nitrite and chromium. The Nitrosospira lineage signal had a strong negative correlation to dissolved oxygen and temperature, while the Nitrosomonas-like (negative correlations) and N. europaea lineages (positive correlations) were inversely linked (relative to one another) to influent nitrite and chromium. Overall, this study suggests that AOA may be minor contributors to ammonia oxidation in highly aerated activated sludge, and provides insight into parameters controlling the diversity and dominance of AOB lineages within bioreactors during periods of stable nitrification.

    View details for DOI 10.1111/j.1462-2920.2009.01958.x

    View details for Web of Science ID 000269539700013

    View details for PubMedID 19515200

  • Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants JOURNAL OF APPLIED MICROBIOLOGY Zhang, T., Jin, T., Yan, Q., Shao, M., Wells, G., Criddle, C., Fang, H. H. 2009; 107 (3): 970-977


    Characterization of the ammonia-oxidizing archaea (AOA) community in activated sludge from a nitrogen removal bioreactor and wastewater treatment plants (WWTPs).Three primer sets specific for ammonia mono-oxygenase alpha-subunit (amoA) were used to construct clone libraries for activated sludge sample from a nitrogen removal bioreactor. One primer set resulted in strong nonspecific PCR products. The other two clone libraries retrieved both shared and unique AOA amoA sequences. One primer set was chosen to study the AOA communities of activated sludge samples from Shatin and Stanley WWTPs. In total, 18 AOA amoA sequences were recovered and compared to the previous reported sequences. A phylogenetic analysis indicated that sequences found in this study fell into three clusters.Different primers resulted in varied AOA communities from the same sample. The AOA found from Hong Kong WWTPs were closely similar to those from sediment and soil, but distinct from those from activated sludge in other places. A comparison of clone libraries between Shatin WWTP and bioreactor indicated the AOA community significantly shifted only after 30-day enrichment.This study confirmed the occurrence of AOA in a laboratory scale nitrogen removal bioreactor and Hong Kong WWTPs treating saline or freshwater wastewater. AOA communities found in this study were significantly different from those found in other places. To retrieve diverse AOA communities from environmental samples, a combination of different primers for the amoA gene is needed.

    View details for DOI 10.1111/j.1365-2672.2009.04283.x

    View details for Web of Science ID 000268854000028

    View details for PubMedID 19486399

  • Simple menaquinones reduce carbon tetrachloride and iron (III) BIODEGRADATION Fu, Q. S., Boonchayaanant, B., Tang, W., Trost, B. M., Criddle, C. S. 2009; 20 (1): 109-116


    Cell-free supernatant from Shewanella oneidensis MR-1 reduced carbon tetrachloride to chloroform, a suspension of Fe(III) and solid Fe(III) to iron (II). The putative reducing agent was tentatively identified as menaquinone-1 (MQ-1)-a water-soluble menaquinone with a single isoprenoid residue in the side chain. Synthetic MQ-1 reduced carbon tetrachloride to chloroform and amorphous iron (III) hydroxide to iron (II). To test the generality of this result among menaquinones, the reductive activities of vitamin K(2) (MQ-7)-a lipid-associated menaquinone with 7 or 8 isoprenoid residues-was evaluated. This molecule also reduced carbon tetrachloride to chloroform and iron (III) to iron (II). The results indicate that molecules within the menaquinone family may contribute to both the extracellular and cell-associated reduction of carbon tetrachloride and iron (III).

    View details for DOI 10.1007/s10532-008-9204-4

    View details for Web of Science ID 000262085700011

    View details for PubMedID 18594993

  • Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths ISME JOURNAL Hwang, C., Wu, W., Gentry, T. J., Carley, J., Corbin, G. A., Carroll, S. L., Watson, D. B., Jardine, P. M., Zhou, J., Criddle, C. S., Fields, M. W. 2009; 3 (1): 47-64


    Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5-year period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate and ethanol were strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate reducers and metal reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared with the population variation through canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bioreduction; however, the two biostimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.

    View details for DOI 10.1038/ismej.2008.77

    View details for Web of Science ID 000262297400005

    View details for PubMedID 18769457

  • GeoChip-based analysis of functional microbial communities in a bioreduced uranium-contaminated aquifer during reoxidation by oxygen. Environmental Microbiology Van Nostrand, J., D., Wu, W, M., Wu, L., Deng, Y., Carley, J., Carroll, S., Criddle, C. 2009; 10 (11): 2611-2626
  • Reassessing authorship of the Book of Mormon using delta and nearest shrunken centroid classification LITERARY AND LINGUISTIC COMPUTING Jockers, M. L., Witten, D. M., Criddle, C. S. 2008; 23 (4): 465-491

    View details for DOI 10.1093/llc/fqn040

    View details for Web of Science ID 000207735600005

  • Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels APPLIED AND ENVIRONMENTAL MICROBIOLOGY Cardenas, E., Wu, W., Leigh, M. B., Carley, J., Carroll, S., Gentry, T., Luo, J., Watson, D., Gu, B., Ginder-Vogel, M., Kitanidis, P. K., Jardine, P. M., Zhou, J., Criddle, C. S., Marsh, T. L., Tiedje, J. A. 2008; 74 (12): 3718-3729


    Microbial enumeration, 16S rRNA gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(VI) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the U.S. Department of Energy in Oak Ridge, TN. Bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria in situ through weekly injection of ethanol into the subsurface. After nearly 2 years of intermittent injection of ethanol, aqueous U levels fell below the U.S. Environmental Protection Agency maximum contaminant level for drinking water and groundwater (<30 microg/liter or 0.126 microM). Sediment microbial communities from the treatment zone were compared with those from a control well without biostimulation. Most-probable-number estimations indicated that microorganisms implicated in bioremediation accumulated in the sediments of the treatment zone but were either absent or in very low numbers in an untreated control area. Organisms belonging to genera known to include U(VI) reducers were detected, including Desulfovibrio, Geobacter, Anaeromyxobacter, Desulfosporosinus, and Acidovorax spp. The predominant sulfate-reducing bacterial species were Desulfovibrio spp., while the iron reducers were represented by Ferribacterium spp. and Geothrix spp. Diversity-based clustering revealed differences between treated and untreated zones and also within samples of the treated area. Spatial differences in community structure within the treatment zone were likely related to the hydraulic pathway and to electron donor metabolism during biostimulation.

    View details for DOI 10.1128/AEM.02308-07

    View details for Web of Science ID 000256899700013

    View details for PubMedID 18456853

  • Aerobic biotransformation and fate of N-ethyl perfluorooctane sulfonamidoethanol (N-EtFOSE) in activated sludge ENVIRONMENTAL SCIENCE & TECHNOLOGY Rhoads, K. R., Janssen, E. M., Luthy, R. G., Criddle, C. S. 2008; 42 (8): 2873-2878


    Processes affecting the fate of perfluorinated organics are of increasing concern due to the global dispersal, persistence, and bioaccumulation of these contaminants. The volatile compound N-ethyl perfluorooctane sulfonamidoethanol (N-EtFOSE) and its phosphate esters have been used in protective surface coatings. In this report, we describe the fate of N-EtFOSE in aerobic batch assays. These assays were performed using undiluted activated sludge in serum bottles that were sealed to prevent the escape of N-EtFOSE and volatile transformation products. Separate assays were performed with N-EtFOSE and reported transformation products. N-EtFOSE degraded to N-ethyl perfluorooctane sulfonamido acetic acid (N-EtFOSAA) with an observed first-order rate of 0.99 +/- 0.08 day(-1) and a pseudosecond order rate of 0.26 +/- 0.02 L/mg VSS day(-1). N-EtFOSAA underwent further transformation at a slower rate (0.093 +/- 0.012 day(-1)) to N-ethylperfluorooctane sulfonamide (N-EtFOSA). N-EtFOSA then transformed to perfluorooctane sulfonamide (FOSA). FOSA transformed to perfluorooctane sulfinate (PFOSI), and PFOSI transformed to perfluorooctane sulfonate (PFOS). Perfluorooctanoic acid (PFOA) was not detected as a transformation product of any compound. Using the measured rate of N-EtFOSE biotransformation and literature values for phase partitioning and mass transfer in aeration basins, we modeled the fate of N-EtFOSE in a typical activated sludge aeration basin open to the atmosphere. The model predicts that 76% of the N-EtFOSE is stripped into the atmosphere, 5% sorbs to waste solids, 13% undergoes transformation to N-EtFOSAA, and 6% is discharged in the wastewater effluent.

    View details for DOI 10.1021/es702866c

    View details for Web of Science ID 000254890400033

    View details for PubMedID 18497137

  • Growth and cometabolic reduction kinetics of a uranium- and sulfate-reducing Desulfovibrio Clostridia mixed culture: Temperature effects BIOTECHNOLOGY AND BIOENGINEERING Boonchayaanant, B., Kitanidis, P. K., Criddle, C. S. 2008; 99 (5): 1107-1119


    Bioremediation of contaminated soils and aquifers is subject to spatial and temporal temperature changes that can alter the kinetics of key microbial processes. This study quantifies temperature effects on the kinetics of an ethanol-fed sulfate-reducing mixed culture derived from a uranium-contaminated aquifer subject to seasonal temperature fluctuations. The mixed culture contains Desulfovibrio sp. and a Clostridia-like organism. Rates of growth, ethanol utilization, decay, and uranium reduction decreased with decreasing temperature. No significant uranium reduction was observed at 10 degrees C. While both Monod saturation kinetics and pseudo second-order kinetics adequately described the rates of growth and utilization of electron donor (ethanol), model parameters for the pseudo second-order expression had smaller uncertainties. Uranium reduction kinetics were best described by pseudo second-order kinetics modified to include a term for inactivation/death of cells.

    View details for DOI 10.1002/bit.21670

    View details for Web of Science ID 000253925800007

    View details for PubMedID 17929318

  • Speciation of uranium in sediments before and after in situ biostimulation ENVIRONMENTAL SCIENCE & TECHNOLOGY Kelly, S. D., Kemner, K. M., Carley, J., Criddle, C., Jardine, P. M., Marsh, T. L., Phillips, D., Watson, D., Wu, W. 2008; 42 (5): 1558-1564


    The success of sequestration-based remediation strategies will depend on detailed information, including the predominant U species present as sources before biostimulation and the products produced during and after in situ biostimulation. We used X-ray absorption spectroscopy to determine the valence state and chemical speciation of U in sediment samples collected at a variety of depths through the contaminant plume at the Field Research Center at Oak Ridge, TN, before and after approximately 400 days of in situ biostimulation, as well as in duplicate bioreduced sediments after 363 days of resting conditions. The results indicate that U(VI) in subsurface sediments was partially reduced to 10-40% U(IV) during biostimulation. After biostimulation, U was no longer bound to carbon ligands and was adsorbed to Fe/Mn minerals. Reduction of U(VI) to U(IV) continued in sediment samples stored under anaerobic condition at < 4 degrees C for 12 months, with the fraction of U(IV) in sediments more than doubling and U concentrations in the aqueous phase decreasing from 0.5-0.74 to < 0.1 microM. A shift of uranyl species from uranyl bound to phosphorus ligands to uranyl bound to carbon ligands and the formation of nanoparticulate uraninite occurred in the sediment samples during storage.

    View details for DOI 10.1021/es071764i

    View details for Web of Science ID 000253521300032

    View details for PubMedID 18441803

  • Bacterial community succession during in-situ bioremediation of U(VI): spatial similarities along controlled flow paths. The ISME Journal Hwang, C., Wu, W., M., Gentry, T., J., Carley, J., Carroll, S., L., Watson, D., Criddle, C. 2008; 3: 47-64
  • Aerobic biotransformation and fate of ethyl perfluorooctane sulfonamide ethanol (N-EtFOSE) in activated sludge. Environ. Sci. Technol. Rhoads, K., R., Janssen, E., M.-L., Luthy, R., Criddle, C., S. 2008; 8 (42): 2873-2878
  • Correlation of patterns of denitrification instability in replicated bioreactor communities with shifts in the relative abundance and the denitrification patterns of specific populations ISME JOURNAL Gentile, M. E., Nyman, J. L., Criddle, C. S. 2007; 1 (8): 714-728


    To assess the effects of community structure on the stability of denitrification, six chemostat cultures derived from the same denitrifying community were subjected to step increases in feed nitrate concentration and monitored for evidence that denitrification was either not occurring (indicated by the presence of nitrate) or was incomplete (indicated by the presence of nitrite or nitrous oxide). Functional stability was defined and quantified from the pattern of effluent concentration trends of nitrate and denitrification intermediates. Microbial community structure and dynamics were analyzed by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. Functional stability varied: one chemostat community lost the ability to reduce all of the influent nitrate; others continued to reduce all of the influent nitrate, but accumulated varying amounts of nitrous oxide. The microbial community structure in two of the chemostats diverged from the others, and variation of functional response among chemostats corresponded with the divergence of community structure. The Acidovorax-like terminal restriction fragment (T-RF) dominated the chemostat that accumulated nitrate, and an Acidovorax-like isolate reduced nitrate directly to dinitrogen gas in batch nitrate reduction assays. In the nitrous oxide-accumulating chemostats, the relative abundance of the Pseudomonas-like T-RF was strongly and significantly correlated with the magnitude of nitrous oxide accumulation, and a Pseudomonas-like isolate accumulated nitrous oxide in batch assays.

    View details for DOI 10.1038/ismej.2007.87

    View details for Web of Science ID 000251946500005

    View details for PubMedID 18059495

  • Inhibition of a U(VI)- and sulfate-reducing consortia by U(VI) ENVIRONMENTAL SCIENCE & TECHNOLOGY Nyman, J. L., Wu, H., Gentile, M. E., Kitanidis, P. K., Criddle, C. S. 2007; 41 (18): 6528-6533


    The stimulation of microbial U(VI) reduction is currently being investigated as a means to reduce uranium's mobility in groundwater, but little is known about the concentration at which U(VI) might inhibit microbial activity, or the effect of U(VI) on bacterial community structure. We investigated these questions with an ethanol-fed U(VI)- and sulfate-reducing enrichment developed from sediment from the site of an ongoing field biostimulation experiment at Area 3 of the Oak Ridge Field Research Center (FRC). Sets of triplicate enrichments were spiked with increasing concentrations of U(VI) (from 49 microm to 9.2 mM). As the U(VI) concentration increased to 224 microM, the culture's production of acetate from ethanol slowed, and at or above 1.6 mM U(VI) little acetate was produced over the time frame of the experiment. An uncoupling inhibition model was applied to the data, and the inhibition coefficient for U(VI), Ku, was found to be approximately 100 microM U(VI), or 24 mg/L, indicating the inhibitory effect is relevant at highly contaminated sites. Microbial community structure at the conclusion of the experiment was analyzed with terminal restriction fragment length polymorphism (T-RFLP) analysis. T-RFs associated with Desulfovibrio-like organisms decreased in relative abundance with increasing U(VI) concentration, whereas Clostridia-like T-RFs increased.

    View details for DOI 10.1021/es062985b

    View details for Web of Science ID 000249500700039

    View details for PubMedID 17948804

  • In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen ENVIRONMENTAL SCIENCE & TECHNOLOGY Wu, W., Carley, J., Luo, J., Ginder-Vogel, M. A., Cardenas, E., Leigh, M. B., Hwang, C., Kelly, S. D., Ruan, C., Wu, L., Van Nostrand, J., Gentry, T., Lowe, K., Mehlhorn, T., Carroll, S., Luo, W., Fields, M. W., Gu, B., Watson, D., Kemner, K. M., Marsh, T., Tiedje, J., Zhou, J., Fendorf, S., Kitanidis, P. K., Jardine, P. M., Criddle, C. S. 2007; 41 (16): 5716-5723


    Groundwater within Area 3 of the U.S. Department of Energy (DOE) Environmental Remediation Sciences Program (ERSP) Field Research Center at Oak Ridge, TN (ORFRC) contains up to 135 microM uranium as U(VI). Through a series of experiments at a pilot scale test facility, we explored the lower limits of groundwater U(VI) that can be achieved by in-situ biostimulation and the effects of dissolved oxygen on immobilized uranium. Weekly 2 day additions of ethanol over a 2-year period stimulated growth of denitrifying, Fe(III)-reducing, and sulfate-reducing bacteria, and immobilization of uranium as U(IV), with dissolved uranium concentrations decreasing to low levels. Following sulfite addition to remove dissolved oxygen, aqueous U(VI) concentrations fell below the U.S. Environmental Protection Agengy maximum contaminant limit (MCL) for drinking water (< 30/microg L(-1) or 0.126 microM). Under anaerobic conditions, these low concentrations were stable, even in the absence of added ethanol. However, when sulfite additions stopped, and dissolved oxygen (4.0-5.5 mg L(-1)) entered the injection well, spatially variable changes in aqueous U(VI) occurred over a 60 day period, with concentrations increasing rapidly from < 0.13 to 2.0 microM at a multilevel sampling (MLS) well located close to the injection well, but changing little at an MLS well located further away. Resumption of ethanol addition restored reduction of Fe(III), sulfate, and U(VI) within 36 h. After 2 years of ethanol addition, X-ray absorption near-edge structure spectroscopy (XANES) analyses indicated that U(IV) comprised 60-80% of the total uranium in sediment samples. Atthe completion of the project (day 1260), U concentrations in MLS wells were less than 0.1 microM. The microbial community at MLS wells with low U(VI) contained bacteria that are known to reduce uranium, including Desulfovibrio spp. and Geobacter spp., in both sediment and groundwater. The dominant Fe(III)-reducing species were Geothrix spp.

    View details for DOI 10.1021/es062657b

    View details for Web of Science ID 000248886000026

    View details for PubMedID 17874778

  • GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes ISME JOURNAL He, Z., Gentry, T. J., Schadt, C. W., Wu, L., Liebich, J., Chong, S. C., Huang, Z., Wu, W., Gu, B., Jardine, P., Criddle, C., Zhou, J. 2007; 1 (1): 67-77


    Owing to their vast diversity and as-yet uncultivated status, detection, characterization and quantification of microorganisms in natural settings are very challenging, and linking microbial diversity to ecosystem processes and functions is even more difficult. Microarray-based genomic technology for detecting functional genes and processes has a great promise of overcoming such obstacles. Here, a novel comprehensive microarray, termed GeoChip, has been developed, containing 24,243 oligonucleotide (50 mer) probes and covering >10,000 genes in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The developed GeoChip was successfully used for tracking the dynamics of metal-reducing bacteria and associated communities for an in situ bioremediation study. This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.

    View details for DOI 10.1038/ismej.2007.2

    View details for Web of Science ID 000249215800010

    View details for PubMedID 18043615

  • Correlation of functional instability and community dynamics in denitrifying dispersed-growth reactors APPLIED AND ENVIRONMENTAL MICROBIOLOGY Gentile, M. E., Jessup, C. M., Nyman, J. L., Criddle, C. S. 2007; 73 (3): 680-690


    Understanding the relationship between microbial community dynamics and functional instability is an important step towards designing reliable biological water treatment systems. In this study, the community dynamics of two dispersed-growth denitrifying reactors were examined during periods of functional stability and instability. In both reactors during the period of functional instability, the effluent chemistry changed over time, with periods of high nitrate concentrations followed by periods of fluctuating nitrite concentrations. Community structure was examined by clone library analysis of the 16S rRNA gene. Community dynamics were investigated with terminal restriction fragment (T-RF) length polymorphism, and the functional diversity represented by T-RFs was assessed through nitrate reduction assays of representative isolates. During the period of functional instability, the community structure changed considerably, and the dynamics correlated significantly with effluent chemistry. The nitrite concentration was significantly correlated with the relative abundances of the nitrate-reducing Delftia- and Achromobacter-like T-RFs. The isolate representing the Acidovorax-like T-RF reduced nitrate directly to nitrogen in batch assays without the accumulation of any intermediates. The Acidovorax-like T-RF relative abundance was significantly negatively correlated with nitrite concentration, indicating that it was associated with good functional performance. The results of this study reveal a clear relationship between community dynamics and functional instability and the importance of diversity among nitrate-reducing populations within a denitrifying community.

    View details for DOI 10.1128/AEM.01519-06

    View details for Web of Science ID 000244263800003

    View details for PubMedID 17142382

  • Sulfate requirement for growth of U(VI)-reducing organisms in an ethanol-fed enrichment. Bioremediation Journal Nyman, J., Gentile, M., Criddle, C., S. 2007; 1: 21-32
  • In-situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environ. Sci. Technol. Wu, W., Carley, J., Luo, J., Ginder-Vogel, M., A., Cardenas, E., Leigh, M., B., Criddle, C. 2007; 41: 5716-5723
  • Stability in a denitrifying fluidized bed reactor MICROBIAL ECOLOGY Gentile, M., Yan, T., Tiquia, S. M., Fields, M. W., Nyman, J., Zhou, J., Criddle, C. S. 2006; 52 (2): 311-321


    This study evaluates changes in the microbial community structure and function of a pilot-scale denitrifying fluidized bed reactor during periods of constant operating conditions and periods of perturbation. The perturbations consisted of a shutdown period without feed, two disturbances in which biofilms were mechanically sheared from carrier particles, and a twofold step increase in feed nitrate concentration. In the absence of perturbations, nitrate removal was stable and consistently greater than 99%. The structure and dynamics of the microbial community were studied using cloning and sequencing techniques and terminal restriction fragment length polymorphism (T-RFLP) of the SSU rRNA gene. Under unperturbed operating conditions, stable function was accompanied by high constancy and low variability of community structure with the majority of terminal restriction fragments (T-RFs) appearing throughout operation at consistent relative abundances. Several of the consistently present T-RFs correlated with clone sequences closely related to Acidovorax (98% similarity), Dechloromonas (99% similarity), and Zoogloea (98% similarity), genera recently identified by molecular analyses of similar systems. Significant changes in community structure and function were not observed after the shutdown period. In contrast, following the increase in loading rate and the mechanical disturbances, new T-RFs appeared. After both mechanical disturbances, function and community structure recovered. However, function was much more resilient than community structure. The similarity of response to the mechanical disturbances despite differences in community structure and operating conditions suggests that flexible community structure and potentially the activity of minor members under nonperturbation conditions promotes system recovery.

    View details for DOI 10.1007/s00248-006-9024-1

    View details for Web of Science ID 000240481000015

    View details for PubMedID 16874554

  • Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors APPLIED AND ENVIRONMENTAL MICROBIOLOGY Park, H., Wells, G. F., Bae, H., Criddle, C. S., Francis, C. A. 2006; 72 (8): 5643-5647


    We report molecular evidence that ammonia-oxidizing archaea (AOA) occur in activated sludge bioreactors used to remove ammonia from wastewater. Using PCR primers targeting archaeal ammonia monooxygenase subunit A (amoA) genes, we retrieved and compared 75 sequences from five wastewater treatment plants operating with low dissolved oxygen levels and long retention times. All of these sequences showed similarity to sequences previously found in soil and sediments, and they were distributed primarily in four major phylogenetic clusters. One of these clusters contained virtually identical amoA sequences obtained from all five activated sludge samples (from Oregon, Wisconsin, Pennsylvania, and New Jersey) and accounted for 67% of all the sequences, suggesting that this AOA phylotype may be widespread in nitrifying bioreactors.

    View details for DOI 10.1128/AEM.00402-06

    View details for Web of Science ID 000239780400065

    View details for PubMedID 16885322

  • Heterogeneous response to biostimulation for U(VI) reduction in replicated sediment microcosms BIODEGRADATION Nyman, J. L., Marsh, T. L., Ginder-Vogel, M. A., Gentile, M., Fendorf, S., Criddle, C. 2006; 17 (4): 303-316


    A field-scale experiment to assess biostimulation of uranium reduction is underway at the Natural and Accelerated Bioremediation Research Field Research Center (FRC) in Oak Ridge, Tennessee. To simulate the field experiment, we established replicate batch microcosms containing well-mixed contaminated sediment from a well within the FRC treatment zone, and we added an inoculum from a pilot-scale fluidized bed reactor representing the inoculum in the field experiment. After reduction of nitrate, both sulfate and soluble U(VI) concentration decreased. X-ray absorption near edge structure (XANES) spectroscopy confirmed formation of U(IV) in sediment from biostimulated microcosms, but did not detect reduction of solid-phase Fe(III). Two to three fragments dominated terminal restriction fragment length polymorphism (T-RFLP) profiles of the 16S rDNA gene. Comparison to a clone library indicated these fragments represented denitrifying organisms related to Acidovorax, and Acidovorax isolates from the inoculum were subsequently shown to reduce U(VI). Investigation using the T-RFLP Analysis Program (TAP T-RFLP) and chemical analyses detected the presence and activity of fermenting and sulfate-reducing bacteria after 2 weeks. These organisms likely contributed to uranium reduction. In some microcosms, soluble U(VI) concentration leveled off or rebounded, indicating microbial and/or mineralogical heterogeneity among samples. Sulfate, acetate, and ethanol were depleted only in those microcosms exhibiting a rebound in soluble U(VI). This suggests that rates of U(VI) desorption can exceed rates of U(VI) reduction when sulfate-reducing bacteria become substrate-limited. These observations underscore the importance of effective chemical delivery and the role of serial and parallel processes in uranium reduction.

    View details for DOI 10.1007/s10532-005-9000-3

    View details for Web of Science ID 000238773600002

    View details for PubMedID 16491308

  • Changes in bacterial community structure correlate with initial operating conditions of a field-scale denitrifying fluidized bed reactor APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Hwang, C., Wu, W., Gentry, T. J., Carley, J., Carroll, S. L., Schadt, C., Watson, D., Jardine, P. M., Zhou, J., Hickey, R. F., Criddle, C. S., Fields, M. W. 2006; 71 (5): 748-760


    High levels of nitrate are present in groundwater migrating from the former waste disposal ponds at the Y-12 National Security Complex in Oak Ridge, TN. A field-scale denitrifying fluidized bed reactor (FBR) was designed, constructed, and operated with ethanol as an electron donor for the removal of nitrate. After inoculation, biofilms developed on the granular activated carbon particles. Changes in the bacterial community of the FBR were evaluated with clone libraries (n = 500 partial sequences) of the small-subunit rRNA gene for samples taken over a 4-month start-up period. Early phases of start-up operation were characterized by a period of selection, followed by low diversity and predominance by Azoarcus-like sequences. Possible explanations were high pH and nutrient limitations. After amelioration of these conditions, diversification increased rapidly, with the appearance of Dechloromonas, Pseudomonas, and Hydrogenophaga sequences. Changes in NO3, SO4, and pH also likely contributed to shifts in community composition. The detection of sulfate-reducing-bacteria-like sequences closely related to Desulfovibrio and Desulfuromonas in the FBR have important implications for downstream applications at the field site.

    View details for DOI 10.1007/s00253-005-0189-1

    View details for Web of Science ID 000239171400019

    View details for PubMedID 16292532

  • Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability ENVIRONMENTAL SCIENCE & TECHNOLOGY Wu, W., Carley, J., Gentry, T., Ginder-Vogel, M. A., Fienen, M., Mehlhorn, T., Yan, H., Caroll, S., Pace, M. N., Nyman, J., Luo, J., Gentile, M. E., Fields, M. W., Hickey, R. F., Gu, B., Watson, D., Cirpka, O. A., Zhou, J., Fendorf, S., Kitanidis, P. K., Jardine, P. M., Criddle, C. S. 2006; 40 (12): 3986-3995


    In situ microbial reduction of soluble U(VI) to sparingly soluble U(IV) was evaluated at the site of the former S-3 Ponds in Area 3 of the U.S. Department of Energy Natural and Accelerated Bioremediation Research Field Research Center, Oak Ridge, TN. After establishing conditions favorable for bioremediation (Wu, et al. Environ. Sci. Technol. 2006, 40, 3988-3995), intermittent additions of ethanol were initiated within the conditioned inner loop of a nested well recirculation system. These additions initially stimulated denitrification of matrix-entrapped nitrate, but after 2 months, aqueous U levels fell from 5 to approximately 1 microM and sulfate reduction ensued. Continued additions sustained U(VI) reduction over 13 months. X-ray near-edge absorption spectroscopy (XANES) confirmed U(VI) reduction to U(IV) within the inner loop wells, with up to 51%, 35%, and 28% solid-phase U(IV) in sediment samples from the injection well, a monitoring well, and the extraction well, respectively. Microbial analyses confirmed the presence of denitrifying, sulfate-reducing, and iron-reducing bacteria in groundwater and sediments. System pH was generally maintained at less than 6.2 with low bicarbonate level (0.75-1.5 mM) and residual sulfate to suppress methanogenesis and minimize uranium mobilization. The bioavailability of sorbed U(VI) was manipulated by addition of low-level carbonate (< 5 mM) followed by ethanol (1-1.5 mM). Addition of low levels of carbonate increased the concentration of aqueous U, indicating an increased rate of U desorption due to formation of uranyl carbonate complexes. Upon ethanol addition, aqueous U(VI) levels fell, indicating that the rate of microbial reduction exceeded the rate of desorption. Sulfate levels simultaneously decreased, with a corresponding increase in sulfide. When ethanol addition ended but carbonate addition continued, soluble U levels increased, indicating faster desorption than reduction. When bicarbonate addition stopped, aqueous U levels decreased, indicating adsorption to sediments. Changes in the sequence of carbonate and ethanol addition confirmed that carbonate-controlled desorption increased bioavailability of U(VI) for reduction.

    View details for DOI 10.1021/es051960u

    View details for Web of Science ID 000238217200052

    View details for PubMedID 16830572

  • Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 1. Conditioning of a treatment zone ENVIRONMENTAL SCIENCE & TECHNOLOGY Wu, W., Carley, J., Fienen, M., Mehlhorn, T., Lowe, K., Nyman, J., Luo, J., Gentile, M. E., Rajan, R., Wagner, D., Hickey, R. F., Gu, B., Watson, D., Cirpka, O. A., Kitanidis, P. K., Jardine, P. M., Criddle, C. S. 2006; 40 (12): 3978-3985


    To evaluate the potential for in situ bioremediation of U(VI) to sparingly soluble U(IV), we constructed a pilot test facility at Area 3 of the U.S. Department of Energy Natural and Accelerated Bioremediation Research (NABIR) Field Research Center (FRC) in Oak Ridge, TN. The facility is adjacent to the former S-3 Ponds which received trillions of liters of acidic plating wastes. High levels of uranium are present, with up to 800 mg kg(-1) in the soil and 84-210 microM in the groundwater. Ambient groundwater has a highly buffered pH of approximately 3.4 and high levels of aluminum (12-13 mM), calcium (22-25 mM), and nitrate (80-160 mM). Adjusting the pH of groundwater to approximately 5 within the aquifer would deposit extensive aluminum hydroxide precipitate. Calcium is present in the groundwater at levels that inhibit U(VI) reduction, but its removal by injection of a high pH solution would generate clogging precipitate. Nitrate also inhibits U(VI) reduction and is present at such high concentrations that its removal by in situ denitrification would generate large amounts of N2 gas and biomass. To establish and maintain hydraulic control, we installed a four well recirculation system parallel to geologic strike, with an inner loop nested within an outer loop. For monitoring, we drilled three boreholes perpendicular to strike across the inner loop and installed multilevel sampling tubes within them. A tracer pulse with clean water established travel times and connectivity between wells and enabled the assessment of contaminant release from the soil matrix. Subsequently, a highly conductive region of the subsurface was prepared for biostimulation by removing clogging agents and inhibitors and increasing pH. For 2 months, groundwater was pumped from the hydraulically conductive zone; treated to remove aluminum, calcium, and nitrate, and supplemented with tap water; adjusted to pH 4.3-4.5; then returned to the hydraulically conductive zone. This protocol removed most of the aqueous aluminum and calcium. The pH of the injected treated water was then increased to 6.0-6.3. With additional flushing, the pH of the extracted water gradually increased to 5.5-6.0, and nitrate concentrations fell to 0.5-1.0 mM. These conditions were judged suitable for biostimulation. In a companion paper (Wu et al., Environ. Sci. Technol. 2006, 40, 3978-3987), we describe the effects of ethanol addition on in situ denitrification and U(VI) reduction and immobilization.

    View details for DOI 10.1021/es051954y

    View details for Web of Science ID 000238217200051

    View details for PubMedID 16830571

  • Thermodynamic constraints on the oxidation of biogenic UO2 by Fe(III) (hydr) oxides ENVIRONMENTAL SCIENCE & TECHNOLOGY Ginder-Vogel, M., Criddle, C. S., Fendorf, S. 2006; 40 (11): 3544-3550


    Uranium mobility in the environment is partially controlled by its oxidation state, where it exists as either U(VI) or U(IV). In aerobic environments, uranium is generally found in the hexavalent form, is quite soluble, and readily forms complexes with carbonate and calcium. Under anaerobic conditions, common metal respiring bacteria can reduce soluble U(VI) species to sparingly soluble UO2 (uraninite); stimulation of these bacteria, in fact, is being explored as an in situ uranium remediation technique. However, the stability of biologically precipitated uraninite within soils and sediments is not well characterized. Here we demonstrate that uraninite oxidation by Fe(III) (hydr)oxides is thermodynamically favorable under limited geochemical conditions. Our analysis reveals that goethite and hematite have a limited capacity to oxidize UO2(biogenic) while ferrihydrite can lead to UO2(biogenic) oxidation. The extent of UO2(biogenic) oxidation by ferrihydrite increases with increasing bicarbonate and calcium concentration, but decreases with elevated Fe(II)(aq) and U(VI)(aq) concentrations. Thus, our results demonstrate that the oxidation of UO2(biogenic) by Fe(III) (hydr)oxides may transpire under mildly reducing conditions when ferrihydrite is present.

    View details for DOI 10.1021/es052305p

    View details for Web of Science ID 000237921200023

    View details for PubMedID 16786692

  • Changes in microbial community structure correlate with stressed operating conditions during start-up of a field-scale denitrifying fluidized bed reactor. Applied Microbiology and Biotechnology Hwang, C., Wu, W., M., Gentry, T., Carley, J., Carroll, S., L., Schadt, C., Criddle, C. 2006; 71: 748-760
  • Mass-transfer limitations for nitrate removal in a uranium-contaminated aquifer ENVIRONMENTAL SCIENCE & TECHNOLOGY Luo, J., Cirpka, O. A., Wu, W. M., Fienen, M. N., Jardine, P. M., Mehlhorn, T. L., Watson, D. B., Criddle, C. S., Kitanidis, P. K. 2005; 39 (21): 8453-8459


    A field test on in situ subsurface bioremediation of uranium(VI) is underway at the Y-12 National Security Complex in the Oak Ridge Reservation, Oak Ridge, TN. Nitrate has a high concentration at the site, which prevents U(VI) reduction, and thus must be removed. An acidic-flush strategy for nitrate removal was proposed to create a treatment zone with low levels of accessible nitrate. The subsurface at the site contains highly interconnected fractures surrounded by matrix blocks of low permeability and high porosity and is therefore subject to preferential flow and matrix diffusion. To identify the heterogeneous mass transfer properties, we performed a novel forced-gradient tracer test, which involved the addition of bromide, the displacement of nitrate, and the rebound of nitrate after completion of pumping. The simplest conceptualization consistent with the data is that the pore-space consists of a single mobile domain, as well as a fast and a slowly reacting immobile domain. The slowly reacting immobile domain (shale matrix) constitutes over 80% of the pore volume and acts as a long-term reservoir of nitrate. According to simulations, the nitrate stored in the slowly interacting immobile domain in the fast flow layer, at depths of about 12.2-13.7 m, will be reduced by an order of magnitude over a period of about a year. By contrast, the mobile domain rapidly responds to flushing, and a low average nitrate concentration can be maintained if the nitrate is removed as soon as it enters the mobile domain. A field-scale experiment in which the aquifer was flushed with acidic solution confirmed our understanding of the system. For the ongoing experiments on microbial U(VI) reduction, nitrate concentrations must be low in the mobile domain to ensure U(VI) reducing conditions. We therefore conclude that the nitrate leaching out of the immobile pore space must continuously be removed by in situ denitrification to maintain favorable conditions.

    View details for DOI 10.1021/es050195g

    View details for Web of Science ID 000233078000054

    View details for PubMedID 16294887

  • Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction APPLIED AND ENVIRONMENTAL MICROBIOLOGY Bencheikh-Latmani, R., Williams, S. M., Haucke, L., Criddle, C. S., Wu, L. Y., Zhou, J. Z., Tebo, B. M. 2005; 71 (11): 7453-7460


    Whole-genome DNA microarrays were used to examine the gene expression profile of Shewanella oneidensis MR-1 during U(VI) and Cr(VI) reduction. The same control, cells pregrown with nitrate and incubated with no electron acceptor, was used for the two time points considered and for both metals. U(VI)-reducing conditions resulted in the upregulation (> or = 3-fold) of 121 genes, while 83 genes were upregulated under Cr(VI)-reducing conditions. A large fraction of the genes upregulated [34% for U(VI) and 29% for Cr(VI)] encode hypothetical proteins of unknown function. Genes encoding proteins known to reduce alternative electron acceptors [fumarate, dimethyl sulfoxide, Mn(IV), or soluble Fe(III)] were upregulated under both U(VI)- and Cr(VI)-reducing conditions. The involvement of these upregulated genes in the reduction of U(VI) and Cr(VI) was tested using mutants lacking one or several of the gene products. Mutant testing confirmed the involvement of several genes in the reduction of both metals: mtrA, mtrB, mtrC, and menC, all of which are involved in Fe(III) citrate reduction by MR-1. Genes encoding efflux pumps were upregulated under Cr(VI)- but not under U(VI)-reducing conditions. Genes encoding proteins associated with general (e.g., groL and dnaJ) and membrane (e.g., pspBC) stress were also upregulated, particularly under U(VI)-reducing conditions, pointing to membrane damage by the solid-phase reduced U(IV) and Cr(III) and/or the direct effect of the oxidized forms of the metals. This study sheds light on the multifaceted response of MR-1 to U(VI) and Cr(VI) under anaerobic conditions and suggests that the same electron transport pathway can be used for more than one electron acceptor.

    View details for DOI 10.1128/AEM.71.11.7453-7460.2005

    View details for Web of Science ID 000233225000118

    View details for PubMedID 16269787

  • Bioreduction of uranium in a contaminated soil column ENVIRONMENTAL SCIENCE & TECHNOLOGY Gu, B. H., Wu, W. M., Ginder-Vogel, M. A., Yan, H., Fields, M. W., Zhou, J., Fendorf, S., Criddle, C. S., Jardine, P. M. 2005; 39 (13): 4841-4847


    The bioreduction of soluble uranium [U(VI)] to sparingly soluble U(IV) species is an attractive remedial technology for contaminated soil and groundwater due to the potential for immobilizing uranium and impeding its migration in subsurface environments. This manuscript describes a column study designed to simulate a three-step strategy proposed for the remediation of a heavily contaminated site at the U.S. Department of Energy's NABIR Field Research Center in Oak Ridge, TN. The soil is contaminated with high concentrations of uranium, aluminum, and nitrate and has a low, highly buffered pH (approximately 3.5). Steps proposed for remediation are (i) flushing to remove nitrate and aluminum, (ii) neutralization to establish pH conditions favorable for biostimulation, and (iii) biostimulation for U(VI) reduction. We simulated this sequence using a packed soil column containing undisturbed aggregates of U(VI)-contaminated saprolite that was flushed with an acidified salt solution (pH 4.0), neutralized with bicarbonate (60 mM), and then biostimulated by adding ethanol. The column was operated anaerobically in a closed-loop recirculation setup. However, during the initial month of biostimulation, ethanol was not utilized, and U(VI) was not reduced. A bacterial culture enriched from the site groundwaterwas subsequently added, and the consumption of ethanol coupled with sulfate reduction immediately ensued. The aqueous concentration of U(VI) initially increased, evidently because of the biological production of carbonate, a ligand known to solubilize uranyl. After approximately 50 days, aqueous U(VI) concentrations rapidly decreased from approximately 17 to <1 mg/L. At the conclusion of the experiment,the presence of reduced solid phase U(IV) was confirmed using X-ray absorption near edge structure spectroscopy. The results indicate that bioreduction to immobilize uranium is potentially feasible at this site; however, the stability of the reduced U(IV) and its potential reoxidation will require further investigation, as do the effects of groundwater chemistry and competitive microbial processes, such as methanogenesis.

    View details for Web of Science ID 000230245500032

    View details for PubMedID 16053082

  • Quantitative determination of perfluorochemicals in sediments and domestic sludge ENVIRONMENTAL SCIENCE & TECHNOLOGY Higgins, C. P., Field, J. A., Criddle, C. S., Luthy, R. G. 2005; 39 (11): 3946-3956


    Perfluorochemicals (PFCs) are the subject of increasingly intense environmental research. Despite their detection both in biota and in aqueous systems, little attention has been paid to the possible presence of this class of compounds in solid environmental matrixes. The limited available data indicate that some PFCs such as perfluorooctane sulfonate (PFOS) may strongly sorb to solids, and sewage sludge is widely suspected as a major sink of PFCs entering municipal waste streams. A quantitative analytical method was developed that consists of liquid solvent extraction of the analytes from sediments and sludge, cleanup via solid-phase extraction, and injection of the extracts with internal standards into a high-performance liquid chromatography (HPLC) system coupled to a tandem mass spectrometer (LC/MS/MS). The limits of detections of the method were analyte and matrix dependent, but ranged from 0.7 to 2.2 ng/g and 0.041 to 0.246 ng/g (dry weight) for sludge and sediment, respectively. A demonstration of the method was performed by conducting a limited survey of domestic sludge and sediments. The concentration of PFCs in domestic sludge ranged from 5 to 152 ng/g for total perfluorocarboxylates and 55 to 3370 ng/g for total perfluoroalkyl sulfonyl-based chemicals. Data from a survey of San Francisco Bay Area sediments suggest widespread occurrence of PFCs in sediments at the low ng/g to sub-ng/g level. Furthermore, substances that may be transformed to PFOS, such as 2-(N-ethylperfluorooctanesulfonamido) acetic acid (N-EtFOSAA) and 2-(N-methylperfluorooctanesulfonamido) acetic acid (N-MeFOSAA), are present in both sediments and sludge at levels often exceeding PFOS.

    View details for DOI 10.1021/es048245p

    View details for Web of Science ID 000229662200019

    View details for PubMedID 15984769

  • Reduction of uranium(VI) by denitrifying biomass. Bioremediation Journal  Wu, W., Gu, B., Fields, M., W., Gentile, M., Ku, Y, K., Yan, H., Criddle, C. 2005; 1 (9): 1-13
  • Perfluorochemicals in sediments and domestic sludge. Environ. Science and Technology Higgins, C., P., Fields, J., A., Criddle, C., S., Luthy., R., G. 2005; 39: 3946-56
  • Assessing the potential for biological Cr(VI) reduction in an aquifer contaminated with mixed wastes. Cr(VI) Handbook. M., J., Williams, M., S., Dybas, C. CRC Press. 2005
  • Correspondence between community structure and function during succession in phenol- and phenol-plus-trichloroethene-fed sequencing batch reactors APPLIED AND ENVIRONMENTAL MICROBIOLOGY Ayala-del-Rio, H. L., Callister, S. J., Criddle, C. S., Tiedje, J. M. 2004; 70 (8): 4950-4960


    The effects of more than 2 years of trichloroethene (TCE) application on community succession and function were studied in two aerobic sequencing batch reactors. One reactor was fed phenol, and the second reactor was fed both phenol and TCE in sequence twice per day. After initiation of TCE loading in the second reactor, the TCE transformation rates initially decreased, but they stabilized with an average second-order rate coefficient of 0.044 liter mg(-1) day(-1) for 2 years. In contrast, the phenol-fed reactor showed higher and unstable TCE transformation rates, with an average rate coefficient of 0.093 liter mg(-1) day(-1). Community analysis by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes showed that the phenol-plus-TCE-fed reactor had marked changes in community structure during the first 100 days and remained relatively stable afterwards, corresponding to the period of stable function. In contrast, the community structure of the phenol-fed reactor changed periodically, and the changes coincided with the periodicity observed in the TCE transformation rates. Correspondence analysis of each reactor community showed that different community structures corresponded with function (TCE degradation rate). Furthermore, the phenol hydroxylase genotypes, as determined by restriction fragment length polymorphism analysis, corresponded to community structure patterns identified by T-RFLP analysis and to periods when the TCE transformation rates were high. Long-term TCE stress appeared to select for a different and stable community structure, with lower but stable TCE degradation rates. In contrast, the community under no stress exhibited a dynamic structure and dynamic function.

    View details for DOI 10.1128/AEM.70.8.4950-4960.2004

    View details for Web of Science ID 000223290100069

    View details for PubMedID 15294835

  • A derivative of the menaquinone precursor 1,4-dihydroxy-2-naphthoate is involved in the reductive transformation of carbon tetrachloride by aerobically grown Shewanella oneidensis MR-1 APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Ward, M. J., Fu, Q. S., Rhoads, K. R., Yeung, C. H., Spormann, A. M., Criddle, C. S. 2004; 63 (5): 571-577


    Transformation of carbon tetrachloride (CT) by Shewanella oneidensis MR-1 has been proposed to involve the anaerobic respiratory-chain component menaquinone. To investigate this hypothesis a series of menaquinone mutants were constructed. The menF mutant is blocked at the start of the menaquinone biosynthetic pathway. The menB, menA and menG mutants are all blocked towards the end of the pathway, being unable to produce 1,4-dihydroxy-2-naphthoic acid (DHNA), demethyl-menaquinone and menaquinone, respectively. Aerobically grown mutants unable to produce the menaquinone precursor DHNA (menF and menB mutants) showed a distinctly different CT transformation profile than mutants able to produce DHNA but unable to produce menaquinone (menA and menG mutants). While DHNA did not reduce CT in an abiotic assay, the addition of DHNA to the menF and menB mutants restored normal CT transformation activity. We conclude that a derivative of DHNA, that is distinct from menaquinone, is involved in the reduction of CT by aerobically grown S. oneidensis MR-1. When cells were grown anaerobically with trimethylamine-N-oxide as the terminal electron acceptor, all the menaquinone mutants showed wild-type levels of CT reduction. We conclude that S. oneidensis MR-1 produces two different factors capable of dehalogenating CT. The factor produced under anaerobic growth conditions is not a product of the menaquinone biosynthetic pathway.

    View details for DOI 10.1007/s00253-003-1407-3

    View details for Web of Science ID 000188456900013

    View details for PubMedID 12908086

  • Cometabolism of Cr(VI) by Shewanella oneidensis MR-1 produces cell-associated reduced chromium and inhibits growth BIOTECHNOLOGY AND BIOENGINEERING Middleton, S. S., Bencheikh-Latmani, R., Mackey, M. R., Ellisman, M. H., Tebo, B. M., Criddle, C. S. 2003; 83 (6): 627-637


    Microbial reduction is a promising strategy for chromium remediation, but the effects of competing electron acceptors are still poorly understood. We investigated chromate (Cr(VI)) reduction in batch cultures of Shewanella oneidensis MR-1 under aerobic and denitrifying conditions and in the absence of an additional electron acceptor. Growth and Cr(VI) removal patterns suggested a cometabolic reduction; in the absence of nitrate or oxygen, MR-1 reduced Cr(VI), but without any increase in viable cell counts and rates gradually decreased when cells were respiked. Only a small fraction (1.6%) of the electrons from lactate were transferred to Cr(VI). The 48-h transformation capacity (Tc) was 0.78 mg (15 micromoles) Cr(VI) reduced. [mg protein](-1) for high levels of Cr(VI) added as a single spike. For low levels of Cr(VI) added sequentially, Tc increased to 3.33 mg (64 micromoles) Cr(VI) reduced. [mg protein](-1), indicating that it is limited by toxicity at higher concentrations. During denitrification and aerobic growth, MR-1 reduced Cr(VI), with much faster rates under denitrifying conditions. Cr(VI) had no effect on nitrate reduction at 6 microM, was strongly inhibitory at 45 microM, and stopped nitrate reduction above 200 microM. Cr(VI) had no effect on aerobic growth at 60 microM, but severely inhibited growth above 150 microM. A factor that likely plays a role in Cr(VI) toxicity is intracellular reduced chromium. Transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) of denitrifying cells exposed to Cr(VI) showed reduced chromium precipitates both extracellularly on the cell surface and, for the first time, as electron-dense round globules inside cells.

    View details for Web of Science ID 000184544500001

    View details for PubMedID 12889027

  • Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity BIOTECHNIQUES Crosby, L. D., Criddle, C. S. 2003; 34 (4): 790-?


    Molecular tools based on rRNA (rrn) genes are valuable techniques for the study of microbial communities. However, the presence of operon copy number heterogeneity represents a source of systematic error in community analysis. To understand the types and magnitude of such bias, four commonly used rrn-based techniques were used to perform an in silico analysis of a hypothetical community comprised organisms from the Comprehensive Microbial Resource database. Community profiles were generated, and diversity indices were calculated for length heterogeneity PCR, automated ribosomal integenic spacer analysis, denaturing gradient gel electrophoresis, and terminal RFLP (using RsaI, MspI, and HhaI). The results demonstrate that all techniques present a quantitative bias toward organisms with higher copy numbers. In addition, techniques may underestimate diversity by grouping similar ribotypes or overestimate diversity by allowing multiple signals for one organism. The results of this study suggest that caution should be used when interpreting rrn-based community analysis techniques.

    View details for Web of Science ID 000182176800016

    View details for PubMedID 12703304

  • Understanding systematic error in microbial community analysis techniques as a result of ribosomal RNA (rrn) operon copy number. BioTechniques Crosby, L., D., Criddle, C., S. 2003; 34: 790-803
  • A derivative of the menaquinone precursor 1,4-dihydroxy-2-naphthoate is involved in the reductive transformation of carbon tetrachloride by Shewanella oneidensis MR-1. Applied Microbiology and Biotechnology. Ward, M., J., Fu, Q., S., Rhoads, K., Yeung, C., H., Spormann, A., M., Criddle, C., S. 2003; 63: 551-577
  • Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation ENVIRONMENTAL SCIENCE & TECHNOLOGY Dybas, M. J., Hyndman, D. W., Heine, R., Tiedje, J., Linning, K., Wiggert, D., Voice, T., Zhao, X., Dybas, L., Criddle, C. S. 2002; 36 (16): 3635-3644


    A full-scale field evaluation of bioaugmentation was conducted in a carbon tetrachloride (CT)- and nitrate-impacted aquifer at Schoolcraft, MI. The added organism was Pseudomonas stutzeri KC (strain KC), a denitrifying bacterium that cometabolically degrades CT without producing chloroform (CF). To introduce and maintain strain KC in the aquifer, a row of closely spaced (1-m) injection/extraction wells were installed normal to the direction of groundwater flow near the leading edge of the CT plume. The resulting system of wells was used to establish and maintain a "biocurtain" for CT degradation through the intermittent addition of base to create favorable pH conditions; inoculation; and weekly addition of acetate (electron donor), alkali, and phosphorus. Although half of the test zone was inoculated twice, the long-term performance of both sections was indistinguishable: both had high CT removal efficiencies (median of 98-99.9%) and similar levels of strain KC colonization (>10(5) strain KC/g). Sustained and efficient (98%) removal of CT has now been observed over 4 yr. Transient low levels of CF (<20 ppb) and H2S (<2 ppm) were observed, but both disappeared when the concentration of acetate in the weekly feed was reduced. Nitrate removal efficiencies ranged from 60% at low acetate concentrations to nearly 100% at high acetate concentrations. We conclude that closely spaced wells and intermittent substrate addition are effective means of delivering organisms and substrates to subsurface environments. At the Schoolcraft site, we achieved uniform removal efficiencies over a significant vertical depth (15 m), despite significant variability in hydraulic conductivity. This was accomplished by pumping 65% (v/v) of the natural gradient flow passing through the biocurtain during a given week in a single 6-h pumping event. Approximately 18,600 m3 of contaminated groundwater was treated during the project.

    View details for Web of Science ID 000177448600025

    View details for PubMedID 12214659

  • Analysis of regulatory elements and genes required for carbon tetrachloride degradation in Pseudomonas stutzeri strain KC JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY Sepulveda-Torres, L. D., Huang, A., Kim, H., Criddle, C. S. 2002; 4 (2): 151-161


    Previously, we described the generation and initial characterization of four Tn5 mutants of Pseudomonas stutzeri strain KC with impaired ability to degrade carbon tetrachloride (Sepúlveda-Torres et al., 1999). In this study, we show cloning and sequencing of an 8.3 kbp region in which all four transposons were located. This fragment encodes eight potential genes and is located in the central part of the 25 kbp fragment recently identified by Lewis et al. (2000) and shown by them to be sufficient to confer carbon tetrachloride transformation capability upon other pseudomonads. The four transposon insertion mutants mapped in ORF's F and I designated by Lewis et al. (2000). This is consistent with the results by Lewis et al. (2000) that orfFis required for carbon tetrachloride degradation. We further established that orfl is required for CCl4 degradation since the three mutants in this ORF were unable to degrade carbon tetrachloride. We present our analysis of the gene and protein sequences from the 8.3 kbp region and propose a tentative model for the role of different genes in the synthesis and activity of pyridine-2,6-bis(thiocarboxylate) (PDTC), the secreted factor responsible for carbon tetrachloride dechlorination. We also found a putative promoter that overlaps with a Fur-box-like sequence in the region upstream of mutated genes. To test this putative promoter region and Fur-box, we generated and ligated DNA fragments containing wild-type and mutant Fur-boxes to a lacZ reporter. The wild-type fragment showed promoter activity that is regulated by the concentration of iron in the medium. Finally, we screened a selection of Pseudomonas strains, including P. putida DSMZ 3601--a strain known to produce PDTC--for the presence of the genes characterized in this study. None of the strains tested positive, suggesting that Pseudomonas stutzeri strain KC may possess a distinct biosynthetic pathway for PDTC production.

    View details for Web of Science ID 000174086900005

    View details for PubMedID 11873910

  • The impact of fermentative organisms on carbon flow in methanogenic systems under constant low-substrate conditions APPLIED MICROBIOLOGY AND BIOTECHNOLOGY Dollhopf, S. L., Hashsham, S. A., Dazzo, F. B., Hickey, R. F., Criddle, C. S., Tiedje, J. M. 2001; 56 (3-4): 531-538


    We compared carbon flow under constant low-substrate conditions (below 20 microM glucose in situ) in laboratory-scale glucose-fed methanogenic bioreactors containing two very different microbial communities that removed chemical oxygen demand at similar rates. One community contained approximately equal proportions of spiral and cocci morphologies, while the other community was dominated by cocci. In the former bioreactor, over 50% of the cloned SSU rRNA genes and the most common SSU rDNA terminal restriction fragment corresponded to Spirochaetaceae-related sequences, while in the latter bioreactor over 50% of the cloned SSU rRNA genes and the most common SSU rDNA terminal restriction fragment corresponded to Streptococcus-related sequences. Carbon flow was assessed by measuring 14C-labeled metabolites derived from a feeding of [U-14C]glucose that did not alter the concentration of glucose in the bioreactors. Acetate and ethanol were detected in the Spirochaetaceae-dominated reactor, whereas acetate and propionate were detected in the Streptococcus-dominated reactor. A spirochete isolated from a Spirochaetaceae-dominated reactor fermented glucose to acetate, ethanol, and small amounts of lactate. Maximum substrate utilization assays carried out on fluid from the same reactor indicated that acetate and ethanol were rapidly utilized by this community. These data indicate that an acetate- and ethanol-based food chain was present in the Spirochaetaceae-dominated bioreactor, while the typical acetate- and propionate-based food chain was prevalent in the Streptococcus-dominated bioreactor.

    View details for Web of Science ID 000170608600038

    View details for PubMedID 11549033

  • Stability, persistence, and resilience in anaerobic reactors: a community unveiled. Advances in Water and Wastewater Treatment Technology. Tiedje, J., Hashsham, S., Dollhopf, S., Dazzo, F., Hickey, R., Criddle, C. edited by Matsuo, H., Takizawa, Satoh., Elsevier, Amsterdam. 2001: 13-20
  • Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose APPLIED AND ENVIRONMENTAL MICROBIOLOGY Fernandez, A. S., Hashsham, S. A., Dollhopf, S. L., Raskin, L., Glagoleva, O., Dazzo, F. B., Hickey, R. F., Criddle, C. S., Tiedje, J. M. 2000; 66 (9): 4058-4067


    Methanogenic bioreactor communities were used as model ecosystems to evaluate the relationship between functional stability and community structure. Replicated methanogenic bioreactor communities with two different community structures were established. The effect of a substrate loading shock on population dynamics in each microbial community was examined by using morphological analysis, small-subunit (SSU) rRNA oligonucleotide probes, amplified ribosomal DNA (rDNA) restriction analysis (ARDRA), and partial sequencing of SSU rDNA clones. One set of replicated communities, designated the high-spirochete (HS) set, was characterized by good replicability, a high proportion of spiral and short thin rod morphotypes, a dominance of spirochete-related SSU rDNA genes, and a high percentage of Methanosarcina-related SSU rRNA. The second set of communities, designated the low-spirochete (LS) set, was characterized by incomplete replicability, higher morphotype diversity dominated by cocci, a predominance of Streptococcus-related and deeply branching Spirochaetales-related SSU rDNA genes, and a high percentage of Methanosaeta-related SSU rRNA. In the HS communities, glucose perturbation caused a dramatic shift in the relative abundance of fermentative bacteria, with temporary displacement of spirochete-related ribotypes by Eubacterium-related ribotypes, followed by a return to the preperturbation community structure. The LS communities were less perturbed, with Streptococcus-related organisms remaining prevalent after the glucose shock, although changes in the relative abundance of minor members were detected by morphotype analysis. A companion paper demonstrates that the more stable LS communities were less functionally stable than the HS communities (S. A. Hashsham, A. S. Fernandez, S. L. Dollhopf, F. B. Dazzo, R. F. Hickey, J. M. Tiedje, and C. S. Criddle, Appl. Environ. Microbiol. 66:4050-4057, 2000).

    View details for Web of Science ID 000089109200057

    View details for PubMedID 10966429

  • Parallel processing of substrate correlates with greater functional stability in methanogenic bioreactor communities perturbed by glucose APPLIED AND ENVIRONMENTAL MICROBIOLOGY Hashsham, S. A., Fernandez, A. S., Dollhopf, S. L., Dazzo, F. B., Hickey, R. F., Tiedje, J. M., Criddle, C. S. 2000; 66 (9): 4050-4057


    Parallel processing is more stable than serial processing in many areas that employ interconnected activities. This hypothesis was tested for microbial community function using two quadruplicate sets of methanogenic communities, each set having substantially different populations. The two communities were maintained at a mean cell residence time of 16 days and a mean glucose loading rate of 0.34 g/liter-day in variable-volume reactors. To test stability to perturbation, they were subjected to an instantaneous glucose pulse that resulted in a 6.8-g/liter reactor concentration. The pattern of accumulated products in response to the perturbation was analyzed for various measures of functional stability, including resistance, resilience, and reactivity for each product. A new stability parameter, "moment of amplification envelope," was used to compare the soluble compound stability. These parameters indicated that the communities with predominantly parallel substrate processing were functionally more stable in response to the perturbation than the communities with predominantly serial substrate processing. The data also indicated that there was good replication of function under perturbed conditions; the degrees of replication were 0.79 and 0.83 for the two test communities.

    View details for Web of Science ID 000089109200056

    View details for PubMedID 10966428

  • Hydraulic characterization and design of a full-scale biocurtain GROUND WATER Hyndman, D. W., Dybas, M. J., Forney, L., Heine, R., Mayotte, T., Phanikumar, M. S., Tatara, G., Tiedje, J., Voice, T., Wallace, R., Wiggert, D., Zhao, X., Criddle, C. S. 2000; 38 (3): 462-474
  • Use of bioaugmentation for continuous removal of carbon tetrachloride in model aquifer columns ENVIRONMENTAL ENGINEERING SCIENCE Witt, M. E., Dybas, M. J., Wiggert, D. C., Criddle, C. S. 1999; 16 (6): 475-485
  • Motility-enhanced bioremediation of carbon tetrachloride-contaminated aquifer sediments ENVIRONMENTAL SCIENCE & TECHNOLOGY Witt, M. E., Dybas, M. J., Worden, R. M., Criddle, C. S. 1999; 33 (17): 2958-2964
  • How stable is stable? Function versus community composition APPLIED AND ENVIRONMENTAL MICROBIOLOGY Fernandez, A., Huang, S. Y., Seston, S., Xing, J., Hickey, R., Criddle, C., Tiedje, J. 1999; 65 (8): 3697-3704


    The microbial community dynamics of a functionally stable, well-mixed, methanogenic reactor fed with glucose were analyzed over a 605-day period. The reactor maintained constant pH and chemical oxygen demand removal during this period. Thirty-six rrn clones from each of seven sampling events were analyzed by amplified ribosomal DNA restriction analysis (ARDRA) for the Bacteria and Archaea domains and by sequence analysis of dominant members of the community. Operational taxonomic units (OTUs), distinguished as unique ARDRA patterns, showed reproducible distribution for three sample replicates. The highest diversity was observed in the Bacteria domain. The 16S ribosomal DNA Bacteria clone library contained 75 OTUs, with the dominant OTU accounting for 13% of the total clones, but just 21 Archaea OTUs were found, and the most prominent OTU represented 50% of the clones from the respective library. Succession in methanogenic populations was observed, and two periods were distinguished: in the first, Methanobacterium formicicum was dominant, and in the second, Methanosarcina mazei and a Methanobacterium bryantii-related organism were dominant. Higher variability in Bacteria populations was detected, and the temporal OTU distribution suggested a chaotic pattern. Although dominant OTUs were constantly replaced from one sampling point to the next, phylogenetic analysis indicated that inferred physiologic changes in the community were not as dramatic as were genetic changes. Seven of eight dominant OTUs during the first period clustered with the spirochete group, although a cyclic pattern of substitution occurred among members within this order. A more flexible community structure characterized the second period, since a sequential replacement of a Eubacterium-related organism by an unrelated deep-branched organism and finally by a Propionibacterium-like species was observed. Metabolic differences among the dominant fermenters detected suggest that changes in carbon and electron flow occurred during the stable performance and indicate that an extremely dynamic community can maintain a stable ecosystem function.

    View details for Web of Science ID 000081865000064

    View details for PubMedID 10427068

  • Generation and initial characterization of Pseudomonas stutzeri KC mutants with impaired ability to degrade carbon tetrachloride ARCHIVES OF MICROBIOLOGY Sepulveda-Torres, L. D., Rajendran, N., Dybas, M. J., Criddle, C. S. 1999; 171 (6): 424-429


    Under iron-limiting conditions, Pseudomonas stutzeri KC secretes a small but as yet unidentified factor that transforms carbon tetrachloride (CT) to CO2 and nonvolatile products when activated by reduction at cell membranes. Pseudomonas fluorescens and other cell types activate the factor. Triparental mating was used to generate kanamycin-resistant lux::Tn5 recombinants of strain KC. Recombinants were streaked onto the surface of agar medium plugs in microtiter plates and were then screened for carbon tetrachloride degradation by exposing the plates to gaseous 14C-carbon tetrachloride. CT+ recombinants generated nonvolatile 14C-labeled products, but four CT- recombinants did not generate significant nonvolatile 14C-labeled products and had lost the ability to degrade carbon tetrachloride. When colonies of P. fluorescens were grown next to colonies of CT+ recombinants and were exposed to gaseous 14C-carbon tetrachloride, 14C-labeled products accumulated around the P. fluorescens colonies, indicating that the factor secreted by CT+ colonies had diffused through the agar and become activated. When P. fluorescens was grown next to CT- colonies, little carbon tetrachloride transformation was observed, indicating a lack of active factor. Expression of lux reporter genes in three of the CT- mutants was regulated by added iron and was induced under the same iron-limiting conditions that induce carbon tetrachloride transformation in the wild-type.

    View details for Web of Science ID 000080691400008

    View details for PubMedID 10369898

  • Pilot-scale evaluation of bioaugmentation for in-situ remediation of a carbon tetrachloride contaminated aquifer ENVIRONMENTAL SCIENCE & TECHNOLOGY Dybas, M. J., Barcelona, M., Bezborodnikov, S., Davies, S., Forney, L., Heuer, H., Kawka, O., Mayotte, T., Sepulveda-Torres, L., Smalla, K., Sneathen, M., Tiedje, J., Voice, T., Wiggert, D. C., Witt, M. E., Criddle, C. S. 1998; 32 (22): 3598-3611
  • Defluorination of organofluorine sulfur compounds by Pseudomonas sp. strain D2 ENVIRONMENTAL SCIENCE & TECHNOLOGY Key, B. D., Howell, R. D., Criddle, C. S. 1998; 32 (15): 2283-2287
  • Ground water remediation/frozen soil reactor gates. In Cold Regions Impact on Civil Works Andersland, O., B., Criddle, C., S., Wallace, R., B., Wiggert, D., C. edited by Newcomb, D., E. 1998
  • Accumulation of metabolic intermediates during shock loads in biological fluidized bed reactors JOURNAL OF ENVIRONMENTAL ENGINEERING-ASCE Zhao, X. D., Doh, K., Criddle, C. S., Voice, T. C. 1997; 123 (12): 1185-1193
  • Effects of a long-term periodic substrate perturbation on an anaerobic community WATER RESEARCH Xing, J., Criddle, C., Hickey, R. 1997; 31 (9): 2195-2204
  • Fluorinated organics in the biosphere ENVIRONMENTAL SCIENCE & TECHNOLOGY Key, B. D., Howell, R. D., Criddle, C. S. 1997; 31 (9): 2445-2454
  • Solid phase biodegradation of carbon tetrachloride by Pseudomonas stutzeri strain KC IN SITU AND ON-SITE BIOREMEDIATION, VOL 3 SepulvedaTorres, L. D., Dybas, M. J., Criddle, C. S. 1997; 4(3): 33-37
  • Defluorination of organofluorine sulfur compounds by Pseudomonas sp. strain D2. Environ. Science and Technol. Key, B., Howell, R., Criddle, C., S. 1997; 32: 2283-2287
  • Fluorinated organics in the biosphere. Environ. Science and Technol. Key, B., Howell, R., Criddle, C., S. 1997; 9 (31): 2445-2454
  • Adaptive shifts in anaerobic community structure in response to long-term periodic substrate perturbations. Microbial Ecology Xing, J., Criddle, C., Hickey, R. 1997; 33: 50-58
  • Experimental evaluation of a model for cometabolism: prediction of simultaneous degradation of trichloroethylene and methane by a methanotrophic mixed culture. Biotechnology and Bioengineering Chang, W., K., Criddle, C., S. 1997; 5 (56): 492-501
  • Effects of long-term substrate perturbation on an anaerobic community. Water Research Xing, J., Criddle, C., Hickey, R. 1997; 9 (31): 2195-2204
  • Long-term adaptive shifts in anaerobic community structure in response to a sustained cyclic substrate perturbation MICROBIAL ECOLOGY Xing, J., Criddle, C., Hickey, R. 1997; 33 (1): 50-58
  • Bioaugmentation and numerical simulation of carbon tetrachloride transformation in groundwater IN SITU AND ON-SITE BIOREMEDIATION, VOL 4 Witt, M. E., Wiggert, D. C., Dybas, M. J., Kelly, K. C., Criddle, C. S. 1997; 4(4): 575-580
  • Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene APPLIED AND ENVIRONMENTAL MICROBIOLOGY Shih, C. C., Davey, M. E., Zhou, J. Z., Tiedje, J. M., Criddle, C. S. 1996; 62 (8): 2953-2960


    Cometabolism of trichloroethylene (TCE) by phenol-fed enrichments was evaluated in four reactors with distinct phenol feeding patterns. The reactors were inoculated from the same source, operated at the same average dilution rate, and received the same mass of phenol over time. Only the timing of phenol addition differed. Reactor C received phenol continuously; reactor SC5 received phenol semicontinuously--alternating between 5 h of feed and 3 h without feed; reactor SC2 alternated between 2 h of feed and 6 h without feed; and reactor P received a single pulse every 24 h. The structure of the enrichments and their capacity for TCE transformation were analyzed. In long-term operation, reactors C and SC5 were dominated by fungi, had higher levels of predators, were more susceptible to biomass fluctuations, and exhibited reduced capacity for TCE transformation. Reactors P and SC2 were characterized by lower levels of fungi, higher bacterial biomass, higher concentrations of TCE-degrading organisms, and higher rates of TCE transformation. After 200 days of operation, rates of TCE transformation increased 10-fold in reactor P, resulting in TCE transformation rates that were 20 to 100 times higher than the rates of the other reactor communities. The cause of this shift is unknown. Isolates capable of the highest rates of TCE transformation were obtained from reactor P. We conclude that cometabolic activity depends upon microbial community structure and that the community structure can be manipulated by altering the growth substrate feeding pattern.

    View details for Web of Science ID A1996UZ99600043

    View details for PubMedID 16535382

  • Bench-scale evaluation of bioaugmentation to remediate carbon tetrachloride-contaminated aquifer materials GROUND WATER Mayotte, T. J., Dybas, M. J., Criddle, C. S. 1996; 34 (2): 358-367


    Liquid film and diffusional resistances of brewery granules during acetate, propionate, and ethanol utilization were investigated. Substrate utilization rate increased with decreased granule size. Effectiveness factors for acetate, propionate, and ethanol were calculated by comparing the maximum rates of substrate utilization of whole granules (1.8 to 3.0 mm) and fine flocs (20 to 75 mum) derived by disrupting whole granules. For acetate, propionate, and ethanol, maximum specific substrate utilization rates (k(m') g/g VS . d) for the flocs, were 5.11, 6.25, and 5.49, respectively, and half-velocity coefficients (K(g') mM) were 0.45, 0.40, and 3.37, respectively. Calculated effectiveness factors were 0.32, 0.41, and 0.75 for acetate, propionate, and ethanol, respectively. The effect of temperature on substrate utilization was examined at 26 degrees C, 31 degrees C, and 37 degrees C using acetate as sole carbon source. Utilization rates increased with temperature. Flocs were most sensitive to temperature, and whole granules were least affected. The behavior of flocs was well described by the Van't Hoff-Arrhenius equation. Effectiveness factors for acetate utilization by the granules were 0.36, 0.35, and 0.32 at 26 degrees C, 31 degrees C, and 37 degrees C, respectively, indicating little effect of temperature. Based on these results, we conclude that both liquid film and diffusional resistances influenced the rate of substrate utilization in a UASB reactor with granular sludge. Temperature effects were much less important than diffusional limitations within the granules. (c) 1995 John Wiley & Sons, Inc.

    View details for Web of Science ID A1995QV99400010

    View details for PubMedID 18623339



    Previous research has established that Pseudomonas sp. strain KC rapidly transforms carbon tetrachloride (CT) to carbon dioxide (45 to 55%), a nonvolatile fraction (45 to 55%), and a cell-associated fraction ((equiv)5%) under denitrifying, iron-limited conditions. The present study provides additional characterization of the nonvolatile fraction, demonstrates that electron transfer plays a role in the transformation, and establishes the importance of both extracellular and intracellular factors. Experiments with (sup14)C-labeled CT indicate that more than one nonvolatile product is produced during CT transformation by strain KC. One of these products, accounting for about 20% of the [(sup14)C]CT transformed, was identified as formate on the basis of its elution time from an ion-exchange column, its boiling point, and its conversion to (sup14)CO(inf2) when incubated with formate dehydrogenase. Production of formate requires transfer of two electrons to the CT molecule. The role of electron transfer was also supported by experiments demonstrating that stationary-phase cells that do not transform CT can be stimulated to transform CT when supplemented with acetate (electron donor), nitrate (electron acceptor), or a protonophore (carbonyl cyanide m-chlorophenylhydrazone). The location of transformation activity was also evaluated. By themselves, washed cells did not transform CT to a significant degree. Occasionally, CT transformation was observed by cell-free culture supernatant, but this activity was not reliable. Rapid and reliable CT transformation was only obtained when washed whole cells were reconstituted with culture supernatant, indicating that both extracellular and intracellular factors are normally required for CT transformation. Fractionation of culture supernatant by ultrafiltration established that the extracellular factor or factors are small, with an apparent molecular mass of less than 500 Da. The extracellular factor or factors were stable after lyophilization to powder and were extractable with acetone. Addition of micromolar levels of iron inhibited CT transformation in whole cultures, but the level of iron needed to inhibit CT transformation was over 100-fold higher for washed cells reconstituted with a 10,000-Da supernatant filtrate. Thus, the inhibitory effects of iron are exacerbated by a supernatant factor or factors with a molecular mass greater than 10,000 Da.

    View details for Web of Science ID A1995QF42800053

    View details for PubMedID 16534941

  • Niche adjustment for bioaugmentation with Pseudomonas sp strain KC BIOAUGMENTATION FOR SITE REMEDIATION Dybas, M. J., TATARA, G. M., KNOLL, W. H., Mayotte, T. J., Criddle, C. S. 1995; 3 (3): 77-84
  • Biotransformation of HCFC-22, HCFC-142b, HCFC-123, and HFC-134a by methanotrophic mixed culture MM1. Biodegradation Chang, W., K., Criddle, C., S. 1995: 1-9
  • Biofactor-mediated transformation of carbon tetrachloride by diverse cell types BIOREMEDIATION OF CHLORINATED SOLVENTS TATARA, G. M., Dybas, M. J., Criddle, C. S. 1995; 3 (4): 69-76
  • Bioaugmentation and transformation of carbon tetrachloride in a model aquifer BIOAUGMENTATION FOR SITE REMEDIATION Witt, M. E., Dybas, M. J., Heine, R. L., Nair, S., Criddle, C. S., Wiggert, D. C. 1995; 3 (3): 221-227


    Under denitrifying conditions, Pseudomonas sp. strain KC transforms carbon tetrachloride (CT) to carbon dioxide via a complex but as yet undetermined mechanism. Transformation rates were first order with respect to CT concentration over the CT concentration range examined (0 to 100 micrograms/liter) and proportional to protein concentration, giving pseudo-second-order kinetics overall. Addition of ferric iron (1 to 20 microM) to an actively transforming culture inhibited CT transformation, and the degree of inhibition increased with increasing iron concentration. By removing iron from the trace metals solution or by removing iron-containing precipitate from the growth medium, higher second-order rate coefficients were obtained. Copper also plays a role in CT transformation. Copper was toxic at neutral pH. By adjusting the medium pH to 8.2, soluble iron and copper levels decreased as a precipitate formed, and CT transformation rates increased. However, cultures grown at high pH without any added trace copper (1 microM) exhibited slower growth rates and greatly reduced rates of CT transformation, indicating that copper is required for CT transformation. The use of pH adjustment to decrease iron solubility, to avoid copper toxicity, and to provide a selective advantage for strain KC was evaluated by using soil slurries and groundwater containing high levels of iron. In samples adjusted to pH 8.2 and inoculated with strain KC, CT disappeared rapidly in the absence or presence of acetate or nitrate supplements. CT did not disappear in pH-adjusted controls that were not inoculated with strain KC.

    View details for Web of Science ID A1993LL31000020

    View details for PubMedID 8357248

  • The kinetics of cometabolism. Biotechnology and Bioengineering Criddle, C., S. 1993; 11 (41): 1048-1056


    A denitrifying Pseudomonas sp. (strain KC) capable of transforming carbon tetrachloride (CT) was isolated from groundwater aquifer solids. Major products of the transformation of 14C-labeled CT by Pseudomonas strain KC under denitrification conditions were 14CO2 and an unidentified water-soluble fraction. Little or no chloroform was produced. Addition of dissolved trace metals, notably, ferrous iron and cobalt, to the growth medium appeared to enhance growth of Pseudomonas strain KC while inhibiting transformation of CT. It is hypothesized that transformation of CT by this organism is associated with the mechanism of trace-metal scavenging.

    View details for Web of Science ID A1990EF66300002

    View details for PubMedID 2268146



    The formation of radicals from carbon tetrachloride (CT) is often invoked to explain the product distribution resulting from its transformation. Radicals formed by reduction of CT presumably react with constituents of the surrounding milieu to give the observed product distribution. The patterns of transformation observed in this work were consistent with such a hypothesis. In cultures of Escherichia coli K-12, the pathways and rates of CT transformation were dependent on the electron acceptor condition of the media. Use of oxygen and nitrate as electron acceptors generally prevented CT metabolism. At low oxygen levels (approximately 1%), however, transformation of [14C]CT to 14CO2 and attachment to cell material did occur, in accord with reports of CT fate in mammalian cell cultures. Under fumarate-respiring conditions, [14C]CT was recovered as 14CO2, chloroform, and a nonvolatile fraction. In contrast, fermenting conditions resulted in more chloroform, more cell-bound 14C, and almost no 14CO2. Rates of transformation of CT were faster under fermenting conditions than under fumarate-respiring conditions. Transformation rates also decreased over time, suggesting the gradual exhaustion of transformation activity. This loss was modeled with a simple exponential decay term.

    View details for Web of Science ID A1990EF66300003

    View details for PubMedID 2268147

  • ES Critical Reviews: Transformations of halogenated aliphatic compounds. Environmental science & technology Vogel, T. M., Criddle, C. S., McCarty, P. L. 1987; 21 (8): 722-736

    View details for DOI 10.1021/es00162a001

    View details for PubMedID 19995052

  • Reduction of hexachloroethane to tetrachloroethylene in groundwater. J. Contaminant Hydrology Criddle, C., S., McCarty, P., L., Elliott, C., M., Barker, J., F. 1986; 1: 133-142

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