Microbial communities and geochemistry were analyzed within floodplain alluvia of the San Juan Ri... more Microbial communities and geochemistry were analyzed within floodplain alluvia of the San Juan River, New Mexico, down-gradient of a uranium mill tailings disposal cell. A multi-level sampling device was used to investigate vertical variations in geochemistry and microbial community structure within the uranium contaminant plume within this shallow aquifer. Chemical analyses indicate that the interaction of uncontaminated artesian water and
Ecological community assembly is governed by a combination of (i) selection resulting from among-... more Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.
An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southea... more An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds (J. K. Fredrickson, F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens, Appl. Environ. Microbiol. 57:796-803, 1991) was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1 omega 7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16S rRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequence analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains...
ABSTRACT Microbiological reduction and immobilization of U(VI) and Tc(VII) has been proposed as a... more ABSTRACT Microbiological reduction and immobilization of U(VI) and Tc(VII) has been proposed as a strategy for remediating radionuclide-contaminated environments. Numerous studies focusing on the reduction kinetics and speciation of these metals have been carried out using contaminated sediment samples, microbial consortia, and pure bacterial cultures. While previous work with model organisms has increased the general understanding of radionuclide transformation processes, fundamental questions regarding radionuclide reduction mechanisms by indigenous microorganisms are poorly understood, especially under the commonly encountered scenario where multiple electron acceptors are present. Therefore, the overall goal of the proposed research is to elucidate the molecular mechanisms of radionuclide biotransformation by Anaeromyxobacter dehalogenans, a predominant member of indigenous microorganism commonly found in contaminated subsurface environments, and to assess the effects of relevant environmental factors affecting these transformation reactions.
A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land ... more A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores, Growth was observed over the temperature range 20-50 degreesC (optimum 40 degreesC; 45 min doubling time)
A ~1:1 mixture of ferrihydrite and nanocrystalline akaganeite (-FeOOH; 10-15 nm) was incubated wi... more A ~1:1 mixture of ferrihydrite and nanocrystalline akaganeite (-FeOOH; 10-15 nm) was incubated with Shewanella putrefaciens (strain CN32) under anoxic conditions with lactate as an electron donor and anthraquinone-2,6-disulfonate (AQDS) as an electron shuttle. The incubation was carried out in a 1,4-piperazinediethanesulfonic acid (PIPES)-buffered medium, without PO³ at circumneutral pH. Iron reduction was measured as a function of time (as
To gain insight into the complex structure of the energy-generating networks in the dissimilatory... more To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing
Mechanisms by which dissimilatory iron-reducing bacteria utilize iron and manganese oxide mineral... more Mechanisms by which dissimilatory iron-reducing bacteria utilize iron and manganese oxide minerals as terminal electron acceptors for respiration are poorly understood. In the absence of exogenous electron shuttle compounds, extracellular electron transfer is generally thought to occur through the interfacial contact area between mineral surfaces and attached cells. Possible alternative reduction pathways have been proposed based on the discovery of
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.
Diversity begets higher-order properties such as functional stability and robustness in microbial... more Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this 'system' that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.The ISME Journal advance online publication, 19 December 2014; doi:10.1038/ismej.2014.251.
... Biogeochemical U(VI) Reduction Scott C. Brooks*1, Wenming Dong1, Sue Carroll1, James K. Fredr... more ... Biogeochemical U(VI) Reduction Scott C. Brooks*1, Wenming Dong1, Sue Carroll1, James K. Fredrickson2, Kenneth M. Kemner3, Shelly Kelly3 Collaborators: Kent Orlandini3, John Zachara2 1 Oak Ridge National Laboratory 2 Pacific Northwest National Laboratory ...
Thermus strain SA-01, previously isolated from a deep (3.2Â km) South African gold mine, is closel... more Thermus strain SA-01, previously isolated from a deep (3.2Â km) South African gold mine, is closely related to Thermus strains NMX2 A.1 and VI-7 (previously isolated from thermal springs in New Mexico, USA, and Portugal, respectively). Thermus strains SA-01 and NMX2 A.1 have also been shown previously to grow using nitrate, Fe(III), Mn(IV) or S O as terminal electron acceptors and
The geochemical, isotopic and microbial attributes of over 100 water and gas samples taken from S... more The geochemical, isotopic and microbial attributes of over 100 water and gas samples taken from South African deep mines in at 0.8 to 3.3 km depth, temperatures up to 60oC and over 40,000 km2 area have been analyzed. Noble gas isotopic estimates of the subsurface residence times for some of the deepest, most saline water samples from the 2.7 Ga
SUMMARY: An extensive proteome analysis will help understand how D. radiodurans survives under ex... more SUMMARY: An extensive proteome analysis will help understand how D. radiodurans survives under extreme conditions
Abstract The Integrated Field-Scale Subsurface Research Challenge (IFC) at the Hanford Site 300 A... more Abstract The Integrated Field-Scale Subsurface Research Challenge (IFC) at the Hanford Site 300 Area uranium (U) plume addresses multi-scale mass transfer processes in a complex hydrogeologic setting. A series of forefront science questions on mass transfer ...
The Energy Citations Database (ECD) provides access to historical and current research (1948 to t... more The Energy Citations Database (ECD) provides access to historical and current research (1948 to the present) from the Department of Energy (DOE) and predecessor agencies.
Microbial communities and geochemistry were analyzed within floodplain alluvia of the San Juan Ri... more Microbial communities and geochemistry were analyzed within floodplain alluvia of the San Juan River, New Mexico, down-gradient of a uranium mill tailings disposal cell. A multi-level sampling device was used to investigate vertical variations in geochemistry and microbial community structure within the uranium contaminant plume within this shallow aquifer. Chemical analyses indicate that the interaction of uncontaminated artesian water and
Ecological community assembly is governed by a combination of (i) selection resulting from among-... more Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.
An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southea... more An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds (J. K. Fredrickson, F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens, Appl. Environ. Microbiol. 57:796-803, 1991) was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1 omega 7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16S rRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequence analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains...
ABSTRACT Microbiological reduction and immobilization of U(VI) and Tc(VII) has been proposed as a... more ABSTRACT Microbiological reduction and immobilization of U(VI) and Tc(VII) has been proposed as a strategy for remediating radionuclide-contaminated environments. Numerous studies focusing on the reduction kinetics and speciation of these metals have been carried out using contaminated sediment samples, microbial consortia, and pure bacterial cultures. While previous work with model organisms has increased the general understanding of radionuclide transformation processes, fundamental questions regarding radionuclide reduction mechanisms by indigenous microorganisms are poorly understood, especially under the commonly encountered scenario where multiple electron acceptors are present. Therefore, the overall goal of the proposed research is to elucidate the molecular mechanisms of radionuclide biotransformation by Anaeromyxobacter dehalogenans, a predominant member of indigenous microorganism commonly found in contaminated subsurface environments, and to assess the effects of relevant environmental factors affecting these transformation reactions.
A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land ... more A novel extreme alkaliphile was isolated from a mine water containment dam at 3.2 km bellow land surface in an ultra-deep gold mine near Carletonville, South Africa. The cells of this bacterium were straight to slightly curved rods, motile by flagella and formed endospores, Growth was observed over the temperature range 20-50 degreesC (optimum 40 degreesC; 45 min doubling time)
A ~1:1 mixture of ferrihydrite and nanocrystalline akaganeite (-FeOOH; 10-15 nm) was incubated wi... more A ~1:1 mixture of ferrihydrite and nanocrystalline akaganeite (-FeOOH; 10-15 nm) was incubated with Shewanella putrefaciens (strain CN32) under anoxic conditions with lactate as an electron donor and anthraquinone-2,6-disulfonate (AQDS) as an electron shuttle. The incubation was carried out in a 1,4-piperazinediethanesulfonic acid (PIPES)-buffered medium, without PO³ at circumneutral pH. Iron reduction was measured as a function of time (as
To gain insight into the complex structure of the energy-generating networks in the dissimilatory... more To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing
Mechanisms by which dissimilatory iron-reducing bacteria utilize iron and manganese oxide mineral... more Mechanisms by which dissimilatory iron-reducing bacteria utilize iron and manganese oxide minerals as terminal electron acceptors for respiration are poorly understood. In the absence of exogenous electron shuttle compounds, extracellular electron transfer is generally thought to occur through the interfacial contact area between mineral surfaces and attached cells. Possible alternative reduction pathways have been proposed based on the discovery of
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.
Diversity begets higher-order properties such as functional stability and robustness in microbial... more Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this 'system' that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.The ISME Journal advance online publication, 19 December 2014; doi:10.1038/ismej.2014.251.
... Biogeochemical U(VI) Reduction Scott C. Brooks*1, Wenming Dong1, Sue Carroll1, James K. Fredr... more ... Biogeochemical U(VI) Reduction Scott C. Brooks*1, Wenming Dong1, Sue Carroll1, James K. Fredrickson2, Kenneth M. Kemner3, Shelly Kelly3 Collaborators: Kent Orlandini3, John Zachara2 1 Oak Ridge National Laboratory 2 Pacific Northwest National Laboratory ...
Thermus strain SA-01, previously isolated from a deep (3.2Â km) South African gold mine, is closel... more Thermus strain SA-01, previously isolated from a deep (3.2Â km) South African gold mine, is closely related to Thermus strains NMX2 A.1 and VI-7 (previously isolated from thermal springs in New Mexico, USA, and Portugal, respectively). Thermus strains SA-01 and NMX2 A.1 have also been shown previously to grow using nitrate, Fe(III), Mn(IV) or S O as terminal electron acceptors and
The geochemical, isotopic and microbial attributes of over 100 water and gas samples taken from S... more The geochemical, isotopic and microbial attributes of over 100 water and gas samples taken from South African deep mines in at 0.8 to 3.3 km depth, temperatures up to 60oC and over 40,000 km2 area have been analyzed. Noble gas isotopic estimates of the subsurface residence times for some of the deepest, most saline water samples from the 2.7 Ga
SUMMARY: An extensive proteome analysis will help understand how D. radiodurans survives under ex... more SUMMARY: An extensive proteome analysis will help understand how D. radiodurans survives under extreme conditions
Abstract The Integrated Field-Scale Subsurface Research Challenge (IFC) at the Hanford Site 300 A... more Abstract The Integrated Field-Scale Subsurface Research Challenge (IFC) at the Hanford Site 300 Area uranium (U) plume addresses multi-scale mass transfer processes in a complex hydrogeologic setting. A series of forefront science questions on mass transfer ...
The Energy Citations Database (ECD) provides access to historical and current research (1948 to t... more The Energy Citations Database (ECD) provides access to historical and current research (1948 to the present) from the Department of Energy (DOE) and predecessor agencies.
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Papers by Jim Fredrickson