Daniel Noguera - Academia.edu (original) (raw)

Papers by Daniel Noguera

Fluorescence in situ hybridization (FISH) and microarray hybridization are two powerful methods f... more Fluorescence in situ hybridization (FISH) and microarray hybridization are two powerful methods for qualitat ive and quantitative analyses of microbial ecology in environmental samples. In gen eral, both techniques rely on efficient but specific binding of DNA oligonucleoti des (probes) to ribosomal RNA (rRNA) of target organisms. Probe design approache s in the past involved trial and error based experimental

Proceedings of the Water Environment Federation, 2013

Anaerobic digester foaming is a common operational problem in wastewater treatment plants. Severa... more Anaerobic digester foaming is a common operational problem in wastewater treatment plants. Several factors contribute to foaming. This study focused on filamentous organisms and solids retention time (SRT). PAX-18, which has been used in other facilities for foaming control in activated sludge basins, was added into one treatment train at the facility of study. These solids were digested in a bench-scale anaerobic digester with a 15 day SRT and compared to others that were operated with 10, 15, and 25 day SRTs without PAX-18 treatment. It was not possible to determine if PAX-18 had a significant effect on foaming from study results. The 25 day SRT bench-scale digester had less foaming than the ones with 10 and 15 day SRTs. Higher than average extracellular polymeric substance concentrations and lower than average calcium concentrations were associated with foaming events, but this only indicates correlation, not causality.

Journal of environmental management, Jan 2, 2015

Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (... more Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (SAT), which has been considered as a renewable approach in regenerating potable and non-potable water, is welcome in arid and semi-arid regions throughout the world. In this study, the effect of a coal slag additive on the bulk removal of the dissolved organic matter (DOM) in WWTP effluent during SAT operation was explored via the matrix configurations of both coal slag layer and natural soil layer. Azide inhibition and XAD-resins fractionation experiments indicated that the appropriate configuration designing of an upper soil layer (25 cm) and a mixture of soil/coal slag underneath would enhance the removal efficiency of adsorption and anaerobic biodegradation to the same level as that of aerobic biodegradation (31.7% vs 32.2%), while it was only 29.4% compared with the aerobic biodegradation during traditional 50 cm soil column operation. The added coal slag would preferentially adsorb...

Applied and environmental microbiology, 2014

Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their na... more Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for ...

Water science and technology : a journal of the International Association on Water Pollution Research, 2004

A benchmark problem was defined to evaluate the performance of different mathematical biofilm mod... more A benchmark problem was defined to evaluate the performance of different mathematical biofilm models. The biofilm consisted of heterotrophic bacteria degrading organic substrate and oxygen. Mathematical models tested ranged from simple analytical to multidimensional numerical models. For simple and more or less flat biofilms it was shown that analytical biofilm models provide very similar results compared to more complex numerical solutions. When considering a heterogeneous biofilm morphology it was shown that the effect of an increased external mass transfer resistance was much more significant compared to the effect of an increased surface area inside the biofilm.

Applied and environmental microbiology, 1994

The microbial community structure of anaerobic biological reactors was evaluated by using oligonu... more The microbial community structure of anaerobic biological reactors was evaluated by using oligonucleotide probes complementary to conserved tracts of the 16S rRNAs of phylogenetically defined groups of methanogens. Phylogenetically defined groups of methanogens were quantified and visualized, respectively, by hybridization of 32P- and fluorescent-dye-labeled probes to the 16S rRNAs from samples taken from laboratory acetate-fed chemostats, laboratory municipal solid waste digestors, and full-scale sewage sludge digestors. Methanosarcina species, members of the order Methanobacteriales, and Methanosaeta species were the most abundant methanogens present in the chemostats, the solid-waste digestors, and the sewage sludge digestors, respectively.

Water Science and Technology, 1998

ABSTRACT

Journal of Bacteriology, 2015

Understanding the mechanisms of lipid accumulation in microorganisms is important for several rea... more Understanding the mechanisms of lipid accumulation in microorganisms is important for several reasons. In addition to providing insight into assembly of biological membranes, lipid accumulation has important applications in the production of renewable fuels and chemicals. The photosynthetic bacterium Rhodobacter sphaeroides is an attractive organism to study lipid accumulation, as it has the ability to increase membrane production at low O 2 tensions. Under these conditions, R. sphaeroides develops invaginations of the cytoplasmic membrane to increase its membrane surface area for housing of the membrane-bound components of its photosynthetic apparatus. Here we use fatty acid levels as a reporter of membrane lipid content. We show that, under low-O 2 and anaerobic conditions, the total fatty acid content per cell increases 3-fold. We also find that the increases in the amount of fatty acid and photosynthetic pigment per cell are correlated as O 2 tensions or light intensity are changed. To ask if lipid and pigment accumulation were genetically separable, we analyzed strains with mutations in known photosynthetic regulatory pathways. While a strain lacking AppA failed to induce photosynthetic pigment-protein complex accumulation, it increased fatty acid content under low-O 2 conditions. We also found that an intact PrrBA pathway is required for low-O 2 -induced fatty acid accumulation. Our findings suggest a previously unknown role of R. sphaeroides transcriptional regulators in increasing fatty acid and phospholipid accumulation in response to decreased O 2 tension.

PLOS Computational Biology, 2015

Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene expressi... more Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. In this study, we develop a novel workflow for generating large-scale TRN models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (TFs). An assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium Escherichia coli showed that it outperforms expression-based inference approaches, having a significantly larger area under the precision-recall curve. Further analysis indicated that this integrated workflow captures different aspects of the E. coli TRN than expression-based approaches, potentially making them highly complementary. We leveraged this new workflow and observations to build a large-scale TRN model for the α-Proteobacterium Rhodobacter sphaeroides that comprises 120 gene clusters, 1211 genes (including 93 TFs), 1858 predicted protein-DNA interactions and 76 DNA binding motifs. We found that~67% of the predicted gene clusters in this TRN are enriched for functions ranging from photosynthesis or central carbon metabolism to environmental stress responses. We also found that members of many of the predicted gene clusters were consistent with prior knowledge in R. sphaeroides and/or other bacteria. Experimental validation of predictions from this R. sphaeroides TRN model showed that high precision and recall was also obtained for TFs involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341). In addition, this integrative approach enabled generation of TRNs with increased information content relative to R. sphaeroides TRN models built via other approaches. We also show how this approach can be used to simultaneously produce TRN models for each related organism used in the comparative genomics analysis. Our results highlight the advantages of integrating comparative genomics of closely related organisms with gene expression data to assemble large-scale TRN models with high-quality predictions.

Biofouling, 2008

The increasing needs for environmental friendly antifouling coatings have led to investigation of... more The increasing needs for environmental friendly antifouling coatings have led to investigation of new alternatives for replacing copper and TBT-based paints. In this study, results are presented from larval settlement assays of the barnacle Amphibalanus (¼ Balanus) amphitrite on planar, interdigitated electrodes (IDE), having 8 or 25 mm of inter-electrode spacing, upon the application of pulsed electric fields (PEF). Using pulses of 100 ms in duration, 200 Hz in frequency and 10 V in pulse amplitude, barnacle settlement below 5% was observed, while similar IDE surfaces without pulse application had an average of 40% settlement. The spacing between the electrodes did not affect cyprid settlement. Assays with lower PEF amplitudes did not show significant settlement inhibition. On the basis of the settlement assays, the calculated minimum energy requirement to inhibit barnacle settlement is 2.8 W h m 72 .

The partitioning of reducing power into different electron-accepting pathways was evaluated durin... more The partitioning of reducing power into different electron-accepting pathways was evaluated during growth and stationary phases of H 2 -producing Rhodobacter sphaeroides cultures. For this, an electron balance method was developed using the chemical oxygen demand concept to quantitatively analyze the partitioning of nutrient electrons into H 2 , cell biomass, polyhydroxybutyrate (PHB), and soluble microbial products (SMP). Overall, these four electron sinks were accounted for greater than 85% of the electrons provided by the nutrients. Glucose, lactate, succinate, fumarate, and pyruvate were individually provided as the main carbon source, and in all cases, glutamate was provided as a nitrogen source in order to enhance H 2 production. About 25-35% of the electrons ended up in H 2 during growth, while up to 60% of the electrons partitioned into H 2 in some stationary phase cultures. The other two major electron sinks in the growth phase were cell mass and PHB, while in stationary phase, SMP were accounted for >30% of the substrate electrons utilized. In general, the largest portion of SMP comprised low-molecular weight (<3 kDa) compounds mostly produced during stationary phase, although larger-size molecules were also detected in both phases. Overall, the fractions of electrons that partitioned into H 2 (0.21 to 0.35) and PHB (0.06 to 0.21) were highly correlated with the standard free energy change of the substrate oxidation half-reaction equation, normalized per electron equivalent. In a PHB(−) mutant, electron redistribution increased H 2 production, the extent of which depended on the carbon source provided.

Proceedings of the Water Environment Federation, 2007

To simulate a Cannibal-EBPR system, a sequencing batch reactor (SBR) operated with anaerobic and ... more To simulate a Cannibal-EBPR system, a sequencing batch reactor (SBR) operated with anaerobic and aerobic cycles was coupled with an anaerobic sidestream bioreactor, which received mixed liquor from the SBR and returned same amount of treated sludge back to the SBR. A mathematical model of the system was used to evaluate the biomass decay coefficient, b, for a control SBR without the sidestream bioreactor and the decay coefficients for the Cannibal-EBPR system. A 40% reduction in the decay coefficient was observed between the control SBR and the Cannibal system. The Cannibal system tripled the sludge inventory in the process increasing the overall rate of biomass decay. The observed biomass yield in the Cannibal-EBPR system was estimated to be 0.17 mg VSS/mg COD removed, which represented a 56% reduction in yield compared to a Control-EBPR system operated with a 10-day solids retention time. The implication of these observations for modeling and evaluation of these types of systems are discussed..

PLoS Genetics, 2014

Photosynthesis is a crucial biological process that depends on the interplay of many components. ... more Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

Water Research, 2004

The effect of dissolved oxygen (DO) on the communities of ammonia-oxidizing bacteria (AOB) in act... more The effect of dissolved oxygen (DO) on the communities of ammonia-oxidizing bacteria (AOB) in activated sludge was evaluated in lab-scale and full-scale reactors using the amoA gene as the basis for phylogenetic comparisons. Under controlled laboratory conditions, two chemostats seeded with activated sludge from the same source were operated with high-DO (8.5 mg/L) and low-DO (0.24 and 0.12 mg/L) concentrations for a period of 300 days. At the end of the operation period, the chemostats had enriched AOB communities that belonged to the Nitrosomonas europaea lineage, but were differentiable based on phylogenetic and kinetic analyses. The low-DO chemostat harbored the growth of two different groups within this lineage, differentiable by the amoA sequence comparison and by terminal fragment signatures. The difference in oxygen affinity between high-DO and low-DO enrichments was demonstrated by evaluating the growth kinetics as a function of oxygen concentration. The low-DO enrichment had a higher growth rate at DO concentrations below 4.7 mg/L, but the growth rate significantly decreased at higher DO concentrations, for which the high-DO enrichment experienced higher growth rates. In addition, the dynamic changes in AOB populations in two parallel trains within one full-scale treatment plant were evaluated in response to a significant reduction of DO in one of the treatment trains. Only the train operated with DO concentrations below 1 mg/L favored the establishment of a population of AOB related to the N. europaea lineage.

Journal of Environmental Engineering, 2006

The potential for simultaneous sludge minimization and enhanced biological phosphorus removal ͑EB... more The potential for simultaneous sludge minimization and enhanced biological phosphorus removal ͑EBPR͒ in Cannibal solids reduction processes was investigated. To simulate a Cannibal-EBPR system, a sequencing batch reactor ͑SBR͒ operated with anaerobic and aerobic cycles was coupled with an anaerobic sidestream bioreactor, which received mixed liquor from the SBR and returned the same amount of treated sludge back to the SBR. The biomass yield in the Cannibal-EBPR system was estimated to be 0.16 mg volatile suspended solids ͑VSS͒/mg chemical oxygen demand, which represented a 16-33% reduction in solids production compared to a Control-EBPR system operated with a 10-day solids retention time, for which conventional digestion of excess sludge was assumed. Regarding EBPR, greater than 98% phosphorus removal was sustainable in the Cannibal-EBPR system, but a mass balance on total phosphorus could not be closed, with nearly 33% of the phosphorus unaccounted. The fate of the missing phosphorus could not be resolved.

Environmental Microbiology Reports, 2009

Environmental Microbiology, 2006

Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natu... more Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natural habitats, and play a key role in nitrogen elimination during biological wastewater treatment. Phylogenetic analyses of cloned 16S rRNA genes and fluorescence in situ hybridization with newly developed rRNA-targeted oligonucleotide probes revealed coexistence of uncultured members of sublineages I and II of the genus Nitrospira in biofilm and activated sludge samples taken from nitrifying wastewater treatment plants. Quantitative microscopic analyses of their spatial arrangement relative to ammonia oxidizers in the biofilm and activated sludge flocs showed that members of the Nitrospira sublineage I occurred significantly more often in immediate vicinity to ammonia oxidizers than would be expected from random community assembly while such a relationship was not observed for Nitrospira sublineage II. This spatial distribution suggested a niche differentiation of these coexisting Nitrospira populations with respect to their preferred concentrations of nitrite. This hypothesis was tested by mathematical modelling of nitrite consumption and resulting nitrite gradients in nitrifying biofilms and by quantifying the abundance of sublineage I and II Nitrospira in activated sludge during incubations with nitrite in different concentrations. Consistent with the observed localization patterns, a higher nitrite concentration selected for sublineage I but suppressed sublineage II Nitrospira .

Fluorescence in situ hybridization (FISH) and microarray hybridization are two powerful methods f... more Fluorescence in situ hybridization (FISH) and microarray hybridization are two powerful methods for qualitat ive and quantitative analyses of microbial ecology in environmental samples. In gen eral, both techniques rely on efficient but specific binding of DNA oligonucleoti des (probes) to ribosomal RNA (rRNA) of target organisms. Probe design approache s in the past involved trial and error based experimental

Proceedings of the Water Environment Federation, 2013

Anaerobic digester foaming is a common operational problem in wastewater treatment plants. Severa... more Anaerobic digester foaming is a common operational problem in wastewater treatment plants. Several factors contribute to foaming. This study focused on filamentous organisms and solids retention time (SRT). PAX-18, which has been used in other facilities for foaming control in activated sludge basins, was added into one treatment train at the facility of study. These solids were digested in a bench-scale anaerobic digester with a 15 day SRT and compared to others that were operated with 10, 15, and 25 day SRTs without PAX-18 treatment. It was not possible to determine if PAX-18 had a significant effect on foaming from study results. The 25 day SRT bench-scale digester had less foaming than the ones with 10 and 15 day SRTs. Higher than average extracellular polymeric substance concentrations and lower than average calcium concentrations were associated with foaming events, but this only indicates correlation, not causality.

Journal of environmental management, Jan 2, 2015

Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (... more Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (SAT), which has been considered as a renewable approach in regenerating potable and non-potable water, is welcome in arid and semi-arid regions throughout the world. In this study, the effect of a coal slag additive on the bulk removal of the dissolved organic matter (DOM) in WWTP effluent during SAT operation was explored via the matrix configurations of both coal slag layer and natural soil layer. Azide inhibition and XAD-resins fractionation experiments indicated that the appropriate configuration designing of an upper soil layer (25 cm) and a mixture of soil/coal slag underneath would enhance the removal efficiency of adsorption and anaerobic biodegradation to the same level as that of aerobic biodegradation (31.7% vs 32.2%), while it was only 29.4% compared with the aerobic biodegradation during traditional 50 cm soil column operation. The added coal slag would preferentially adsorb...

Applied and environmental microbiology, 2014

Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their na... more Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for ...

Water science and technology : a journal of the International Association on Water Pollution Research, 2004

A benchmark problem was defined to evaluate the performance of different mathematical biofilm mod... more A benchmark problem was defined to evaluate the performance of different mathematical biofilm models. The biofilm consisted of heterotrophic bacteria degrading organic substrate and oxygen. Mathematical models tested ranged from simple analytical to multidimensional numerical models. For simple and more or less flat biofilms it was shown that analytical biofilm models provide very similar results compared to more complex numerical solutions. When considering a heterogeneous biofilm morphology it was shown that the effect of an increased external mass transfer resistance was much more significant compared to the effect of an increased surface area inside the biofilm.

Applied and environmental microbiology, 1994

The microbial community structure of anaerobic biological reactors was evaluated by using oligonu... more The microbial community structure of anaerobic biological reactors was evaluated by using oligonucleotide probes complementary to conserved tracts of the 16S rRNAs of phylogenetically defined groups of methanogens. Phylogenetically defined groups of methanogens were quantified and visualized, respectively, by hybridization of 32P- and fluorescent-dye-labeled probes to the 16S rRNAs from samples taken from laboratory acetate-fed chemostats, laboratory municipal solid waste digestors, and full-scale sewage sludge digestors. Methanosarcina species, members of the order Methanobacteriales, and Methanosaeta species were the most abundant methanogens present in the chemostats, the solid-waste digestors, and the sewage sludge digestors, respectively.

Water Science and Technology, 1998

ABSTRACT

Journal of Bacteriology, 2015

Understanding the mechanisms of lipid accumulation in microorganisms is important for several rea... more Understanding the mechanisms of lipid accumulation in microorganisms is important for several reasons. In addition to providing insight into assembly of biological membranes, lipid accumulation has important applications in the production of renewable fuels and chemicals. The photosynthetic bacterium Rhodobacter sphaeroides is an attractive organism to study lipid accumulation, as it has the ability to increase membrane production at low O 2 tensions. Under these conditions, R. sphaeroides develops invaginations of the cytoplasmic membrane to increase its membrane surface area for housing of the membrane-bound components of its photosynthetic apparatus. Here we use fatty acid levels as a reporter of membrane lipid content. We show that, under low-O 2 and anaerobic conditions, the total fatty acid content per cell increases 3-fold. We also find that the increases in the amount of fatty acid and photosynthetic pigment per cell are correlated as O 2 tensions or light intensity are changed. To ask if lipid and pigment accumulation were genetically separable, we analyzed strains with mutations in known photosynthetic regulatory pathways. While a strain lacking AppA failed to induce photosynthetic pigment-protein complex accumulation, it increased fatty acid content under low-O 2 conditions. We also found that an intact PrrBA pathway is required for low-O 2 -induced fatty acid accumulation. Our findings suggest a previously unknown role of R. sphaeroides transcriptional regulators in increasing fatty acid and phospholipid accumulation in response to decreased O 2 tension.

PLOS Computational Biology, 2015

Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene expressi... more Transcriptional regulatory networks (TRNs) program cells to dynamically alter their gene expression in response to changing internal or environmental conditions. In this study, we develop a novel workflow for generating large-scale TRN models that integrates comparative genomics data, global gene expression analyses, and intrinsic properties of transcription factors (TFs). An assessment of this workflow using benchmark datasets for the well-studied γ-proteobacterium Escherichia coli showed that it outperforms expression-based inference approaches, having a significantly larger area under the precision-recall curve. Further analysis indicated that this integrated workflow captures different aspects of the E. coli TRN than expression-based approaches, potentially making them highly complementary. We leveraged this new workflow and observations to build a large-scale TRN model for the α-Proteobacterium Rhodobacter sphaeroides that comprises 120 gene clusters, 1211 genes (including 93 TFs), 1858 predicted protein-DNA interactions and 76 DNA binding motifs. We found that~67% of the predicted gene clusters in this TRN are enriched for functions ranging from photosynthesis or central carbon metabolism to environmental stress responses. We also found that members of many of the predicted gene clusters were consistent with prior knowledge in R. sphaeroides and/or other bacteria. Experimental validation of predictions from this R. sphaeroides TRN model showed that high precision and recall was also obtained for TFs involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341). In addition, this integrative approach enabled generation of TRNs with increased information content relative to R. sphaeroides TRN models built via other approaches. We also show how this approach can be used to simultaneously produce TRN models for each related organism used in the comparative genomics analysis. Our results highlight the advantages of integrating comparative genomics of closely related organisms with gene expression data to assemble large-scale TRN models with high-quality predictions.

Biofouling, 2008

The increasing needs for environmental friendly antifouling coatings have led to investigation of... more The increasing needs for environmental friendly antifouling coatings have led to investigation of new alternatives for replacing copper and TBT-based paints. In this study, results are presented from larval settlement assays of the barnacle Amphibalanus (¼ Balanus) amphitrite on planar, interdigitated electrodes (IDE), having 8 or 25 mm of inter-electrode spacing, upon the application of pulsed electric fields (PEF). Using pulses of 100 ms in duration, 200 Hz in frequency and 10 V in pulse amplitude, barnacle settlement below 5% was observed, while similar IDE surfaces without pulse application had an average of 40% settlement. The spacing between the electrodes did not affect cyprid settlement. Assays with lower PEF amplitudes did not show significant settlement inhibition. On the basis of the settlement assays, the calculated minimum energy requirement to inhibit barnacle settlement is 2.8 W h m 72 .

The partitioning of reducing power into different electron-accepting pathways was evaluated durin... more The partitioning of reducing power into different electron-accepting pathways was evaluated during growth and stationary phases of H 2 -producing Rhodobacter sphaeroides cultures. For this, an electron balance method was developed using the chemical oxygen demand concept to quantitatively analyze the partitioning of nutrient electrons into H 2 , cell biomass, polyhydroxybutyrate (PHB), and soluble microbial products (SMP). Overall, these four electron sinks were accounted for greater than 85% of the electrons provided by the nutrients. Glucose, lactate, succinate, fumarate, and pyruvate were individually provided as the main carbon source, and in all cases, glutamate was provided as a nitrogen source in order to enhance H 2 production. About 25-35% of the electrons ended up in H 2 during growth, while up to 60% of the electrons partitioned into H 2 in some stationary phase cultures. The other two major electron sinks in the growth phase were cell mass and PHB, while in stationary phase, SMP were accounted for >30% of the substrate electrons utilized. In general, the largest portion of SMP comprised low-molecular weight (<3 kDa) compounds mostly produced during stationary phase, although larger-size molecules were also detected in both phases. Overall, the fractions of electrons that partitioned into H 2 (0.21 to 0.35) and PHB (0.06 to 0.21) were highly correlated with the standard free energy change of the substrate oxidation half-reaction equation, normalized per electron equivalent. In a PHB(−) mutant, electron redistribution increased H 2 production, the extent of which depended on the carbon source provided.

Proceedings of the Water Environment Federation, 2007

To simulate a Cannibal-EBPR system, a sequencing batch reactor (SBR) operated with anaerobic and ... more To simulate a Cannibal-EBPR system, a sequencing batch reactor (SBR) operated with anaerobic and aerobic cycles was coupled with an anaerobic sidestream bioreactor, which received mixed liquor from the SBR and returned same amount of treated sludge back to the SBR. A mathematical model of the system was used to evaluate the biomass decay coefficient, b, for a control SBR without the sidestream bioreactor and the decay coefficients for the Cannibal-EBPR system. A 40% reduction in the decay coefficient was observed between the control SBR and the Cannibal system. The Cannibal system tripled the sludge inventory in the process increasing the overall rate of biomass decay. The observed biomass yield in the Cannibal-EBPR system was estimated to be 0.17 mg VSS/mg COD removed, which represented a 56% reduction in yield compared to a Control-EBPR system operated with a 10-day solids retention time. The implication of these observations for modeling and evaluation of these types of systems are discussed..

PLoS Genetics, 2014

Photosynthesis is a crucial biological process that depends on the interplay of many components. ... more Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

Water Research, 2004

The effect of dissolved oxygen (DO) on the communities of ammonia-oxidizing bacteria (AOB) in act... more The effect of dissolved oxygen (DO) on the communities of ammonia-oxidizing bacteria (AOB) in activated sludge was evaluated in lab-scale and full-scale reactors using the amoA gene as the basis for phylogenetic comparisons. Under controlled laboratory conditions, two chemostats seeded with activated sludge from the same source were operated with high-DO (8.5 mg/L) and low-DO (0.24 and 0.12 mg/L) concentrations for a period of 300 days. At the end of the operation period, the chemostats had enriched AOB communities that belonged to the Nitrosomonas europaea lineage, but were differentiable based on phylogenetic and kinetic analyses. The low-DO chemostat harbored the growth of two different groups within this lineage, differentiable by the amoA sequence comparison and by terminal fragment signatures. The difference in oxygen affinity between high-DO and low-DO enrichments was demonstrated by evaluating the growth kinetics as a function of oxygen concentration. The low-DO enrichment had a higher growth rate at DO concentrations below 4.7 mg/L, but the growth rate significantly decreased at higher DO concentrations, for which the high-DO enrichment experienced higher growth rates. In addition, the dynamic changes in AOB populations in two parallel trains within one full-scale treatment plant were evaluated in response to a significant reduction of DO in one of the treatment trains. Only the train operated with DO concentrations below 1 mg/L favored the establishment of a population of AOB related to the N. europaea lineage.

Journal of Environmental Engineering, 2006

The potential for simultaneous sludge minimization and enhanced biological phosphorus removal ͑EB... more The potential for simultaneous sludge minimization and enhanced biological phosphorus removal ͑EBPR͒ in Cannibal solids reduction processes was investigated. To simulate a Cannibal-EBPR system, a sequencing batch reactor ͑SBR͒ operated with anaerobic and aerobic cycles was coupled with an anaerobic sidestream bioreactor, which received mixed liquor from the SBR and returned the same amount of treated sludge back to the SBR. The biomass yield in the Cannibal-EBPR system was estimated to be 0.16 mg volatile suspended solids ͑VSS͒/mg chemical oxygen demand, which represented a 16-33% reduction in solids production compared to a Control-EBPR system operated with a 10-day solids retention time, for which conventional digestion of excess sludge was assumed. Regarding EBPR, greater than 98% phosphorus removal was sustainable in the Cannibal-EBPR system, but a mass balance on total phosphorus could not be closed, with nearly 33% of the phosphorus unaccounted. The fate of the missing phosphorus could not be resolved.

Environmental Microbiology Reports, 2009

Environmental Microbiology, 2006

Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natu... more Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natural habitats, and play a key role in nitrogen elimination during biological wastewater treatment. Phylogenetic analyses of cloned 16S rRNA genes and fluorescence in situ hybridization with newly developed rRNA-targeted oligonucleotide probes revealed coexistence of uncultured members of sublineages I and II of the genus Nitrospira in biofilm and activated sludge samples taken from nitrifying wastewater treatment plants. Quantitative microscopic analyses of their spatial arrangement relative to ammonia oxidizers in the biofilm and activated sludge flocs showed that members of the Nitrospira sublineage I occurred significantly more often in immediate vicinity to ammonia oxidizers than would be expected from random community assembly while such a relationship was not observed for Nitrospira sublineage II. This spatial distribution suggested a niche differentiation of these coexisting Nitrospira populations with respect to their preferred concentrations of nitrite. This hypothesis was tested by mathematical modelling of nitrite consumption and resulting nitrite gradients in nitrifying biofilms and by quantifying the abundance of sublineage I and II Nitrospira in activated sludge during incubations with nitrite in different concentrations. Consistent with the observed localization patterns, a higher nitrite concentration selected for sublineage I but suppressed sublineage II Nitrospira .

Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bond... more Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzy-matic breakdown of aromatic oligomers linked via-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site ser-ine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because-aryl ether bonds account for 50 –70% of all interunit linkages in lignin, understanding the mechanism of enzymatic-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.