Bulbul Ahmed - Academia.edu (original) (raw)

Papers by Bulbul Ahmed

Vaccine, 2011

The magnitude of animal bite and utilization of rabies vaccine was determined at the Infectious D... more The magnitude of animal bite and utilization of rabies vaccine was determined at the Infectious Disease Hospital, Dhaka, Bangladesh. From January 2004 to December 2008, 150,068 patients with animal bite visited the hospital, 86.2% and 13.8% of them received nerve tissue and tissue culture vaccine (TCV), respectively. Dog bite was most frequent, found in 90.7% cases. In 794 rabies cases only 24.4% had a history of post-exposure vaccination. Only a negligible number of patients received rabies immunoglobulin (RIG). To prevent further human deaths and economic losses intra-dermal TCV regime and equine RIG should be immediately introduced in Bangladesh.

Journal of Applied Aquaculture, 2011

A ten-week feeding trial was carried out to evaluate animal proteins, either alone or in combinat... more A ten-week feeding trial was carried out to evaluate animal proteins, either alone or in combination (1:1:1), on the growth performances and economic benefit of climbing perch, Anabas testudineus. Four iso-proteinous (40%) diets were prepared, using fishmeal, protein concentrate, and meat and bone meal as major protein source in diets 1, 2 and 3, respectively, while diet 4 consisted of an equal proportion (1:1:1) of the above protein sources. Triplicate groups of fish (0.53 ± 0.02 g) were randomly stocked in 12 earthen ponds at a stocking density of 40,000 ha−1. Fish fed diet 4 had significantly (P < 0.05) higher percent weight gain and SGR % per day−1 compared to the fish fed diets 1, 2, or 3. Significantly higher apparent protein efficiency ratio (1.25) and lower apparent feed conversion ratio (2.00) were also observed in fish fed diet 4. Total yield (1,123 kg ha−1) and net profit (Tk. 116,569 ha−1) were also higher in fish fed diet 4. It can be concluded that the combination of fishmeal, protein concentrate, and meat and bone meal is more effective for climbing perch than any of the three protein sources alone.

Traditional image-based approaches for personal identification have almost exclusively employed f... more Traditional image-based approaches for personal identification have almost exclusively employed front views of the individual&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s face. Ear has a more uniform distribution of color, so that almost all information is conserved when converting the original image to gray scales. A face, lip can change its appearance with the expression of the subject but the shape and appearance of an ear

In this paper, a method to recognize human using ear biometrics has been proposed.

Uranium is one of the most common radionuclides in soils, sediments, and groundwater at radionucl... more Uranium is one of the most common radionuclides in soils, sediments, and groundwater at radionuclides-contaminated sites. At these contaminated sites, uranium leaches into the groundwater, which has become a widespread problem at mining and milling sites across North America, South America, and Eastern Europe. The movement of groundwater usually transports soluble uranium contaminants beyond their original boundaries, causing a global problem in aquifers, water supplies, and related ecosystems and posing a serious threat to human health and the natural environment. In order to meet the EPA standards, extensive efforts have been made to assess and remediate uranium-contaminated sites. As a cost-effective technology with minimal disruption to the environment, bioremediation harnessing indigenous microbial processes for cleanup has been utilized for uranium remediation. In the first part of this chapter, various uranium remediation technologies are discussed. Emphasis is placed on the principles and mechanisms of uranium bioremediation and the key factors affecting it. The second part of this chapter focuses on the use of biofilms for uranium immobilization in groundwater from subsurface environments. Most of the literature studies on uranium bioremediation have been conducted with suspended microorganisms or enriched sediments, which were eventually spiked with micro- or nano-particles of other minerals. However, biofilms are the commonly found microbial growth pattern in natural soils and water-sediment interfaces. With heterogeneous and complex biotic, abiotic and redox conditions significantly different from those in bulk conditions, biofilms pose challenges in predicting the mobility of uranium. Although previous studies have improved our understanding of uranium immobilization processes in biofilms, in order to efficiently and sustainably immobilize uranium at contaminated sites using indigenous biofilms, more knowledge is needed on the complex interactions among uranium, biofilms, and various redox-sensitive minerals during in situ uranium bioremediation.

Campylobacter jejuni, one of the most common causes of human gastroenteritis, is a thermophilic a... more Campylobacter jejuni, one of the most common causes of human gastroenteritis, is a thermophilic and microaerophilic bacterium. These characteristics make it a fastidious organism, which limits its ability to survive outside animal hosts. Nevertheless, C. jejuni can be transmitted to both humans and animals via environmental pathways, especially through contaminated water. Biofilms may play a crucial role in the survival of the bacterium under unfavorable environmental conditions. The goal of this study was to investigate survival strategies of C. jejuni in mono-and mixed-culture biofilms. We grew monoculture biofilms of C. jejuni and mixed-culture biofilms of C. jejuni with Pseudomonas aeruginosa. We found that mono-and mixed-culture biofilms had significantly different structures and activities. Monoculture C. jejuni biofilms did not consume a measurable quantity of oxygen. Using a confocal laser scanning microscope (CLSM), we found that cells from monoculture biofilms were alive according to live/dead staining but that these cells were not culturable. In contrast, in mixed-culture biofilms, C. jejuni remained in a culturable physiological state. Monoculture C. jejuni biofilms could persist under lower flow rates (0.75 ml/min) but were unable to persist at higher flow rates (1 to 2.5 ml/min). In sharp contrast, mixed-culture biofilms were more robust and were unaffected by higher flow rates (2.5 ml/min). Our results indicate that biofilms provide an environmental refuge that is conducive to the survival of C. jejuni.

The contribution of extracellular polymeric substances (EPS), including loosely bound EPS (LB-EPS... more The contribution of extracellular polymeric substances (EPS), including loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS), to the aggregation of both aerobic and anaerobic sludge is explored using the extended DLVO theory. It is observed that the aggregation abilities of both sludge samples decrease with the extraction of LB-EPS and TB-EPS, implying the crucial roles of EPS in sludge aggregation. Furthermore, through analyzing the interaction energy curves of sludge before and after the EPS extraction using the extended DLVO theory, it is found that both LB-EPS and TB-EPS have a substantial contribution to the sludge aggregation. The interaction energy of LB-EPS is always negative, suggesting that the LB-EPS always display a positive effect on the sludge aggregation. On the other hand, the interaction energy of TB-EPS is not always negative, depending on the separation distance between sludge cells. These results imply that the LB-EPS and TB-EPS have different contributions to the sludge aggregation.

Regions within the U.S. Department of Energy Hanford 300 Area (300 A) site experience periodic hy... more Regions within the U.S. Department of Energy Hanford 300 Area (300 A) site experience periodic hydrologic influences from the nearby Columbia River as a result of changing river stage, which causes changes in groundwater elevation, flow direction and water chemistry. An important question is the extent to which the mixing of Columbia River water and groundwater impacts the speciation and mobility of uranium (U). In this study, we designed experiments to mimic interactions among U, oxic groundwater or Columbia River water, and 300 A sediments in the subsurface environment of Hanford 300 A. The goals were to investigate mechanisms of: 1) U immobilization in 300 A sediments under bulk oxic conditions and 2) U remobilization from U-immobilized 300 A sediments exposed to oxic Columbia River water. Initially, 300 A sediments in column reactors were fed with U(VI)-containing oxic 1) synthetic groundwater (SGW), 2) organic-amended SGW (OA-SGW), and 3) de-ionized (DI) water to investigate U immobilization processes. After that, the sediments were exposed to oxic Columbia River water for U remobilization studies. The results reveal that U was immobilized by 300 A sediments predominantly through reduction (80-85%) when the column reactor was fed with oxic OA-SGW. However, U was immobilized by 300 A sediments through adsorption (100%) when the column reactors were fed with oxic SGW or DI water. The reduced U in the 300 A sediments fed with OA-SGW was relatively resistant to remobilization by oxic Columbia River water. Oxic Columbia River water resulted in U remobilization (∼7%) through desorption, and most of the U that remained in the 300 A sediments fed with OA-SGW (∼93%) was in the form of uraninite nanoparticles. These results reveal that: 1) the reductive immobilization of U through OA-SGW stimulation of indigenous 300 A sediment microorganisms may be viable in the relatively oxic Hanford 300 A subsurface environments and 2) with the intrusion of Columbia River water, desorption may be the primary process resulting in U remobilization from OA-SGW-stimulated 300 A sediments at the subsurface of the Hanford 300 A site.

Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It i... more Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface-averaging methods are used, position-dependent measurements of the effective diffusion coefficient are currently: (1) invasive to the biofilm, (2) performed under unnatural conditions, (3) lethal to cells, and/or (4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate results and prohibit further (time-dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: (1) measure the effective diffusion coefficient for water in live biofilms, (2) monitor how the effective diffusion coefficient changes over time under growth conditions, and (3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two-dimensional effective diffusion coefficient maps within Shewanella oneidensis MR-1 biofilms using pulsed-field gradient nuclear magnetic resonance methods, and used them to calculate surface-averaged relative effective diffusion coefficient (Drs) profiles. We found that (1) Drs decreased from the top of the biofilm to the bottom, (2) Drs profiles differed for biofilms of different ages, (3) Drs profiles changed over time and generally decreased with time, (4) all the biofilms showed very similar Drs profiles near the top of the biofilm, and (5) the Drs profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm. Biotechnol. Bioeng. 2010;106: 928–937. © 2010 Wiley Periodicals, Inc.

Biofilms are core to a range of biological processes, including the bioremediation of environment... more Biofilms are core to a range of biological processes, including the bioremediation of environmental contaminants. Within a biofilm population, cells with diverse genotypes and phenotypes coexist, suggesting that distinct metabolic pathways may be expressed based on the local environmental conditions in a biofilm. However, metabolic responses to local environmental conditions in a metabolically active biofilm interacting with environmental contaminants have never been quantitatively elucidated. In this study, we monitored the spatiotemporal metabolic responses of metabolically active Shewanella oneidensis MR-1 biofilms to U(VI) (uranyl, UO 2 2+ ) and Cr(VI) (chromate, CrO4 2-) using non-invasive nuclear magnetic resonance imaging (MRI) and spectroscopy (MRS) approaches to obtain insights into adaptation in biofilms during biofilm-contaminant interactions. While overall biomass distribution was not significantly altered upon exposure to U(VI) or Cr(VI), MRI and spatial mapping of the diffusion revealed localized changes in the water diffusion coefficients in the biofilms, suggesting significant contaminant-induced changes in structural or hydrodynamic properties during bioremediation. Finally, we quantitatively demonstrated that the metabolic responses of biofilms to contaminant exposure are spatially stratified, implying that adaptation in biofilms is custom-developed based on local microenvironments. Received

Biofilms used in bioelectrochemical systems are expected to transfer electrons using electron tra... more Biofilms used in bioelectrochemical systems are expected to transfer electrons using electron transfer mediators. One mediator type, flavins, which includes flavin mononucleotide, riboflavin, and flavin adenine dinucleotide, has been found to be endogenously produced by Shewanella oneidensis MR-1. However, the presence and concentration of flavins inside a S. oneidensis MR-1 biofilm have never been reported. The goal of this study was to develop a flavin microelectrode capable of measuring flavins inside a living biofilm and apply it to a biofilm which produces flavins. Because flavins are electrochemically active molecules, the flavin microelectrode was based on detection via square-wave voltammetry. The microelectrode consisted of a carbon working electrode with a 10-30 μm tip diameter, a built-in platinum counter electrode, and a Ag/ AgCl reference electrode, all enclosed in a glass outer case. The microelectrode was calibrated between 0.1 μM and 10 μM flavins and showed a linear correlation between flavin concentration and peak currents located at −424 mV Ag/AgCl on a square-wave voltammogram. We also developed a model to explain the electrochemical mechanism of flavin detection, and to determine the effective surface area of the microelectrode, the standard reduction potential, and the transfer coefficient. We found that the effective surface area of the microelectrode was close to 100 times the projected surface area. The model predicted a standard reduction potential for RF/RFH2 of −419 mV Ag/AgCl at 20 °C and a transfer coefficient of 0.45. Lastly, we measured flavin concentration inside a S. oneidensis MR-1 biofilm grown on a glass surface using oxygen as the electron acceptor. The flavin concentration reached 0.7 μM, increasing near the bottom of the biofilm, where no oxygen was present. This shows the possibility that flavins are produced in the anaerobic zone to act as intermediate electron acceptors in the deeper parts of the biofilm, where there is no oxygen.

A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford... more A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable of reducing soluble Fe(III) complexes [Fe(III)-nitrilotriacetic acid and Fe(III)-citrate] but unable to reduce poorly crystalline ferrihydrite (Fh). However, Paenibacillus sp. 300A was capable of reducing Fh in the presence of low concentrations (2 M) of either of the electron transfer mediators (ETMs) flavin mononucleotide (FMN) or anthraquinone-2,6disulfonate (AQDS). Maximum initial Fh reduction rates were observed at catalytic concentrations (<10 M) of either FMN or AQDS. Higher FMN concentrations inhibited Fh reduction, while increased AQDS concentrations did not. We also found that Paenibacillus sp. 300A could reduce Fh in the presence of natural ETMs from Hanford 300A subsurface sediments. In the absence of ETMs, Paenibacillus sp. 300A was capable of immobilizing U(VI) through both reduction and adsorption. The relative contributions of adsorption and microbial reduction to U(VI) removal from the aqueous phase were ϳ7:3 in PIPES [piperazine-N,N=-bis(2-ethanesulfonic acid)] and ϳ1:4 in bicarbonate buffer. Our study demonstrated that Paenibacillus sp. 300A catalyzes Fe(III) reduction and U(VI) immobilization and that these reactions benefit from externally added or naturally existing ETMs in 300A subsurface sediments.

Vaccine, 2011

The magnitude of animal bite and utilization of rabies vaccine was determined at the Infectious D... more The magnitude of animal bite and utilization of rabies vaccine was determined at the Infectious Disease Hospital, Dhaka, Bangladesh. From January 2004 to December 2008, 150,068 patients with animal bite visited the hospital, 86.2% and 13.8% of them received nerve tissue and tissue culture vaccine (TCV), respectively. Dog bite was most frequent, found in 90.7% cases. In 794 rabies cases only 24.4% had a history of post-exposure vaccination. Only a negligible number of patients received rabies immunoglobulin (RIG). To prevent further human deaths and economic losses intra-dermal TCV regime and equine RIG should be immediately introduced in Bangladesh.

Journal of Applied Aquaculture, 2011

A ten-week feeding trial was carried out to evaluate animal proteins, either alone or in combinat... more A ten-week feeding trial was carried out to evaluate animal proteins, either alone or in combination (1:1:1), on the growth performances and economic benefit of climbing perch, Anabas testudineus. Four iso-proteinous (40%) diets were prepared, using fishmeal, protein concentrate, and meat and bone meal as major protein source in diets 1, 2 and 3, respectively, while diet 4 consisted of an equal proportion (1:1:1) of the above protein sources. Triplicate groups of fish (0.53 ± 0.02 g) were randomly stocked in 12 earthen ponds at a stocking density of 40,000 ha−1. Fish fed diet 4 had significantly (P < 0.05) higher percent weight gain and SGR % per day−1 compared to the fish fed diets 1, 2, or 3. Significantly higher apparent protein efficiency ratio (1.25) and lower apparent feed conversion ratio (2.00) were also observed in fish fed diet 4. Total yield (1,123 kg ha−1) and net profit (Tk. 116,569 ha−1) were also higher in fish fed diet 4. It can be concluded that the combination of fishmeal, protein concentrate, and meat and bone meal is more effective for climbing perch than any of the three protein sources alone.

Traditional image-based approaches for personal identification have almost exclusively employed f... more Traditional image-based approaches for personal identification have almost exclusively employed front views of the individual&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s face. Ear has a more uniform distribution of color, so that almost all information is conserved when converting the original image to gray scales. A face, lip can change its appearance with the expression of the subject but the shape and appearance of an ear

In this paper, a method to recognize human using ear biometrics has been proposed.

Uranium is one of the most common radionuclides in soils, sediments, and groundwater at radionucl... more Uranium is one of the most common radionuclides in soils, sediments, and groundwater at radionuclides-contaminated sites. At these contaminated sites, uranium leaches into the groundwater, which has become a widespread problem at mining and milling sites across North America, South America, and Eastern Europe. The movement of groundwater usually transports soluble uranium contaminants beyond their original boundaries, causing a global problem in aquifers, water supplies, and related ecosystems and posing a serious threat to human health and the natural environment. In order to meet the EPA standards, extensive efforts have been made to assess and remediate uranium-contaminated sites. As a cost-effective technology with minimal disruption to the environment, bioremediation harnessing indigenous microbial processes for cleanup has been utilized for uranium remediation. In the first part of this chapter, various uranium remediation technologies are discussed. Emphasis is placed on the principles and mechanisms of uranium bioremediation and the key factors affecting it. The second part of this chapter focuses on the use of biofilms for uranium immobilization in groundwater from subsurface environments. Most of the literature studies on uranium bioremediation have been conducted with suspended microorganisms or enriched sediments, which were eventually spiked with micro- or nano-particles of other minerals. However, biofilms are the commonly found microbial growth pattern in natural soils and water-sediment interfaces. With heterogeneous and complex biotic, abiotic and redox conditions significantly different from those in bulk conditions, biofilms pose challenges in predicting the mobility of uranium. Although previous studies have improved our understanding of uranium immobilization processes in biofilms, in order to efficiently and sustainably immobilize uranium at contaminated sites using indigenous biofilms, more knowledge is needed on the complex interactions among uranium, biofilms, and various redox-sensitive minerals during in situ uranium bioremediation.

Campylobacter jejuni, one of the most common causes of human gastroenteritis, is a thermophilic a... more Campylobacter jejuni, one of the most common causes of human gastroenteritis, is a thermophilic and microaerophilic bacterium. These characteristics make it a fastidious organism, which limits its ability to survive outside animal hosts. Nevertheless, C. jejuni can be transmitted to both humans and animals via environmental pathways, especially through contaminated water. Biofilms may play a crucial role in the survival of the bacterium under unfavorable environmental conditions. The goal of this study was to investigate survival strategies of C. jejuni in mono-and mixed-culture biofilms. We grew monoculture biofilms of C. jejuni and mixed-culture biofilms of C. jejuni with Pseudomonas aeruginosa. We found that mono-and mixed-culture biofilms had significantly different structures and activities. Monoculture C. jejuni biofilms did not consume a measurable quantity of oxygen. Using a confocal laser scanning microscope (CLSM), we found that cells from monoculture biofilms were alive according to live/dead staining but that these cells were not culturable. In contrast, in mixed-culture biofilms, C. jejuni remained in a culturable physiological state. Monoculture C. jejuni biofilms could persist under lower flow rates (0.75 ml/min) but were unable to persist at higher flow rates (1 to 2.5 ml/min). In sharp contrast, mixed-culture biofilms were more robust and were unaffected by higher flow rates (2.5 ml/min). Our results indicate that biofilms provide an environmental refuge that is conducive to the survival of C. jejuni.

The contribution of extracellular polymeric substances (EPS), including loosely bound EPS (LB-EPS... more The contribution of extracellular polymeric substances (EPS), including loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS), to the aggregation of both aerobic and anaerobic sludge is explored using the extended DLVO theory. It is observed that the aggregation abilities of both sludge samples decrease with the extraction of LB-EPS and TB-EPS, implying the crucial roles of EPS in sludge aggregation. Furthermore, through analyzing the interaction energy curves of sludge before and after the EPS extraction using the extended DLVO theory, it is found that both LB-EPS and TB-EPS have a substantial contribution to the sludge aggregation. The interaction energy of LB-EPS is always negative, suggesting that the LB-EPS always display a positive effect on the sludge aggregation. On the other hand, the interaction energy of TB-EPS is not always negative, depending on the separation distance between sludge cells. These results imply that the LB-EPS and TB-EPS have different contributions to the sludge aggregation.

Regions within the U.S. Department of Energy Hanford 300 Area (300 A) site experience periodic hy... more Regions within the U.S. Department of Energy Hanford 300 Area (300 A) site experience periodic hydrologic influences from the nearby Columbia River as a result of changing river stage, which causes changes in groundwater elevation, flow direction and water chemistry. An important question is the extent to which the mixing of Columbia River water and groundwater impacts the speciation and mobility of uranium (U). In this study, we designed experiments to mimic interactions among U, oxic groundwater or Columbia River water, and 300 A sediments in the subsurface environment of Hanford 300 A. The goals were to investigate mechanisms of: 1) U immobilization in 300 A sediments under bulk oxic conditions and 2) U remobilization from U-immobilized 300 A sediments exposed to oxic Columbia River water. Initially, 300 A sediments in column reactors were fed with U(VI)-containing oxic 1) synthetic groundwater (SGW), 2) organic-amended SGW (OA-SGW), and 3) de-ionized (DI) water to investigate U immobilization processes. After that, the sediments were exposed to oxic Columbia River water for U remobilization studies. The results reveal that U was immobilized by 300 A sediments predominantly through reduction (80-85%) when the column reactor was fed with oxic OA-SGW. However, U was immobilized by 300 A sediments through adsorption (100%) when the column reactors were fed with oxic SGW or DI water. The reduced U in the 300 A sediments fed with OA-SGW was relatively resistant to remobilization by oxic Columbia River water. Oxic Columbia River water resulted in U remobilization (∼7%) through desorption, and most of the U that remained in the 300 A sediments fed with OA-SGW (∼93%) was in the form of uraninite nanoparticles. These results reveal that: 1) the reductive immobilization of U through OA-SGW stimulation of indigenous 300 A sediment microorganisms may be viable in the relatively oxic Hanford 300 A subsurface environments and 2) with the intrusion of Columbia River water, desorption may be the primary process resulting in U remobilization from OA-SGW-stimulated 300 A sediments at the subsurface of the Hanford 300 A site.

Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It i... more Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface-averaging methods are used, position-dependent measurements of the effective diffusion coefficient are currently: (1) invasive to the biofilm, (2) performed under unnatural conditions, (3) lethal to cells, and/or (4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate results and prohibit further (time-dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: (1) measure the effective diffusion coefficient for water in live biofilms, (2) monitor how the effective diffusion coefficient changes over time under growth conditions, and (3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two-dimensional effective diffusion coefficient maps within Shewanella oneidensis MR-1 biofilms using pulsed-field gradient nuclear magnetic resonance methods, and used them to calculate surface-averaged relative effective diffusion coefficient (Drs) profiles. We found that (1) Drs decreased from the top of the biofilm to the bottom, (2) Drs profiles differed for biofilms of different ages, (3) Drs profiles changed over time and generally decreased with time, (4) all the biofilms showed very similar Drs profiles near the top of the biofilm, and (5) the Drs profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm. Biotechnol. Bioeng. 2010;106: 928–937. © 2010 Wiley Periodicals, Inc.

Biofilms are core to a range of biological processes, including the bioremediation of environment... more Biofilms are core to a range of biological processes, including the bioremediation of environmental contaminants. Within a biofilm population, cells with diverse genotypes and phenotypes coexist, suggesting that distinct metabolic pathways may be expressed based on the local environmental conditions in a biofilm. However, metabolic responses to local environmental conditions in a metabolically active biofilm interacting with environmental contaminants have never been quantitatively elucidated. In this study, we monitored the spatiotemporal metabolic responses of metabolically active Shewanella oneidensis MR-1 biofilms to U(VI) (uranyl, UO 2 2+ ) and Cr(VI) (chromate, CrO4 2-) using non-invasive nuclear magnetic resonance imaging (MRI) and spectroscopy (MRS) approaches to obtain insights into adaptation in biofilms during biofilm-contaminant interactions. While overall biomass distribution was not significantly altered upon exposure to U(VI) or Cr(VI), MRI and spatial mapping of the diffusion revealed localized changes in the water diffusion coefficients in the biofilms, suggesting significant contaminant-induced changes in structural or hydrodynamic properties during bioremediation. Finally, we quantitatively demonstrated that the metabolic responses of biofilms to contaminant exposure are spatially stratified, implying that adaptation in biofilms is custom-developed based on local microenvironments. Received

Biofilms used in bioelectrochemical systems are expected to transfer electrons using electron tra... more Biofilms used in bioelectrochemical systems are expected to transfer electrons using electron transfer mediators. One mediator type, flavins, which includes flavin mononucleotide, riboflavin, and flavin adenine dinucleotide, has been found to be endogenously produced by Shewanella oneidensis MR-1. However, the presence and concentration of flavins inside a S. oneidensis MR-1 biofilm have never been reported. The goal of this study was to develop a flavin microelectrode capable of measuring flavins inside a living biofilm and apply it to a biofilm which produces flavins. Because flavins are electrochemically active molecules, the flavin microelectrode was based on detection via square-wave voltammetry. The microelectrode consisted of a carbon working electrode with a 10-30 μm tip diameter, a built-in platinum counter electrode, and a Ag/ AgCl reference electrode, all enclosed in a glass outer case. The microelectrode was calibrated between 0.1 μM and 10 μM flavins and showed a linear correlation between flavin concentration and peak currents located at −424 mV Ag/AgCl on a square-wave voltammogram. We also developed a model to explain the electrochemical mechanism of flavin detection, and to determine the effective surface area of the microelectrode, the standard reduction potential, and the transfer coefficient. We found that the effective surface area of the microelectrode was close to 100 times the projected surface area. The model predicted a standard reduction potential for RF/RFH2 of −419 mV Ag/AgCl at 20 °C and a transfer coefficient of 0.45. Lastly, we measured flavin concentration inside a S. oneidensis MR-1 biofilm grown on a glass surface using oxygen as the electron acceptor. The flavin concentration reached 0.7 μM, increasing near the bottom of the biofilm, where no oxygen was present. This shows the possibility that flavins are produced in the anaerobic zone to act as intermediate electron acceptors in the deeper parts of the biofilm, where there is no oxygen.

A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford... more A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable of reducing soluble Fe(III) complexes [Fe(III)-nitrilotriacetic acid and Fe(III)-citrate] but unable to reduce poorly crystalline ferrihydrite (Fh). However, Paenibacillus sp. 300A was capable of reducing Fh in the presence of low concentrations (2 M) of either of the electron transfer mediators (ETMs) flavin mononucleotide (FMN) or anthraquinone-2,6disulfonate (AQDS). Maximum initial Fh reduction rates were observed at catalytic concentrations (<10 M) of either FMN or AQDS. Higher FMN concentrations inhibited Fh reduction, while increased AQDS concentrations did not. We also found that Paenibacillus sp. 300A could reduce Fh in the presence of natural ETMs from Hanford 300A subsurface sediments. In the absence of ETMs, Paenibacillus sp. 300A was capable of immobilizing U(VI) through both reduction and adsorption. The relative contributions of adsorption and microbial reduction to U(VI) removal from the aqueous phase were ϳ7:3 in PIPES [piperazine-N,N=-bis(2-ethanesulfonic acid)] and ϳ1:4 in bicarbonate buffer. Our study demonstrated that Paenibacillus sp. 300A catalyzes Fe(III) reduction and U(VI) immobilization and that these reactions benefit from externally added or naturally existing ETMs in 300A subsurface sediments.