Nitrate-Reducing Bacteria at the Nitrate and Radionuclide Contaminated Oak Ridge Integrated Field Research Challenge Site: A Review

ABSTRACT Anaeromyxobacter spp. respire soluble hexavalent uranium, U(VI), leading to the formation of insoluble U(IV), and are present at the uranium-contaminated Oak Ridge Integrated Field Research Challenge (IFC) site. Pilot-scale in situ bioreduction of U(VI) has been accomplished in area 3 of the Oak Ridge IFC site following biostimulation, but the susceptibility of the reduced material to oxidants (i.e., oxygen) compromises long-term U immobilization. Following oxygen intrusion, attached Anaeromyxobacter dehalogenans cells increased approximately 5-fold from 2.2 × 107 ± 8.6 × 106 to 1.0 × 108 ± 2.2 × 107 cells per g of sediment collected from well FW101-2. In the same samples, the numbers of cells of Geobacter lovleyi, a population native to area 3 and also capable of U(VI) reduction, decreased or did not change. A. dehalogenans cells captured via groundwater sampling (i.e., not attached to sediment) were present in much lower numbers (<1.3 × 104 ± 1.1 × 104 cells per liter) than sediment-associated cells, suggesting that A. dehalogenans cells occur predominantly in association with soil particles. Laboratory studies confirmed aerobic growth of A. dehalogenans strain 2CP-C at initial oxygen partial pressures (pO2) at and below 0.18 atm. A negative linear correlation [μ = (−0.09 × pO2) + 0.051; R 2 = 0.923] was observed between the instantaneous specific growth rate μ and pO2, indicating that this organism should be classified as a microaerophile. Quantification of cells during aerobic growth revealed that the fraction of electrons released in electron donor oxidation and used for biomass production (fs ) decreased from 0.52 at a pO2 of 0.02 atm to 0.19 at a pO2 of 0.18 atm. Hence, the apparent fraction of electrons utilized for energy generation (i.e., oxygen reduction) (fe ) increased from 0.48 to 0.81 with increasing pO2, suggesting that oxygen is consumed in a nonrespiratory process at a high pO2. The ability to tolerate high oxygen concentrations, perform microaerophilic oxygen respiration, and preferentially associate with soil particles represents an ecophysiology that distinguishes A. dehalogenans from other known U(VI)-reducing bacteria in area 3, and these features may play roles for stabilizing immobilized radionuclides in situ.

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Hydrogeophysical investigations of the former S-3 ponds contaminant plumes, Oak Ridge Integrated Field Research Challenge site, Tennessee

Geophysics ◽

10.1190/geo2012-0177.1 ◽

2013 ◽

Vol 78 (4) ◽

pp. EN29-EN41 ◽

Cited By ~ 20

Author(s):

A. Revil ◽

M. Skold ◽

M. Karaoulis ◽

M. Schmutz ◽

S. S. Hubbard ◽

...

Keyword(s):

Field Research ◽

Clay Content ◽

Surface Conductivity ◽

Dc Resistivity ◽

High Concentration ◽

Resistivity Tomography ◽

Contaminant Plumes ◽

Oak Ridge ◽

Nitrate Concentrations ◽

Research Challenge

At the Oak Ridge Integrated Field Research Challenge site, near Oak Ridge, Tennessee, contaminants from the former S-3 ponds have infiltrated the shallow saprolite for over 60 years. Two- and three-dimensional DC-resistivity tomography is used to characterize the number and location of the main contaminant plumes, which include high concentration of nitrate. These contaminant plumes have typically an electrical resistivity in the range 2–20 ohm-m while the background saprolite resistivity is in the range 60–120 ohm-m, so the difference of resistivity can be easily mapped using DC-resistivity tomography to locate the contaminant pathways. We develop a relationship to derive the in situ nitrate concentrations from the 3D resistivity tomograms accounting for the effect of surface conductivity. The footprint of the contamination upon the resistivity is found to be much stronger than the local variations associated with changes in the porosity and the clay content. With this method, we identified a total of five main plumes (termed CP1 to CP5). Plume CP2 corresponds to the main plume in terms of nitrate concentration (∼50,000 [Formula: see text]). We also used an active time constrained approach to perform time-lapse resistivity tomography over a section crossing the plumes CP1 and CP2. The sequence of tomograms is used to determine the changes in the nitrate concentrations associated with infiltration of fresh (meteoritic) water from a perched aquifer. This study highlights the importance of accounting for surface conductivity when characterizing plume distributions in clay-rich subsurface systems.

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Petrophysical properties of saprolites from the Oak Ridge Integrated Field Research Challenge site, Tennessee

Geophysics ◽

10.1190/geo2012-0176.1 ◽

2013 ◽

Vol 78 (1) ◽

pp. D21-D40 ◽

Cited By ~ 27

Author(s):

André Revil ◽

Magnus Skold ◽

Susan S. Hubbard ◽

Yuxin Wu ◽

David B. Watson ◽

...

Keyword(s):

Field Research ◽

Surface Conductivity ◽

Complex Conductivity ◽

Fluid Composition ◽

Excess Charge ◽

Petrophysical Properties ◽

Conductivity Measurements ◽

Oak Ridge ◽

Core Samples ◽

Research Challenge

At the Oak Ridge Integrated Field Research Challenge site, near Oak Ridge, Tennessee, the shallow saprolitic aquifer is contaminated by nitric acid, uranium, and metals originating from the former S3 settling ponds. To interpret low-frequency geophysical methods used to image contaminant plumes, we have characterized the petrophysical properties of three representative saprolite core samples. Their hydraulic conductivity ranges from [Formula: see text] to [Formula: see text] in agreement with field data. Complex conductivity measurements, in the frequency range of 1 mHz to 45 kHz, were performed with NaCl solutions with electrical conductivities in the range [Formula: see text] to [Formula: see text], a range representative of field conditions. The electrical conductivity data were well reproduced with a simple linear conductivity model between the saprolite conductivity and the pore water conductivity. The conductivity plots were used to estimate the formation factor (the cementation exponent was about [Formula: see text]) and the surface conductivity ([Formula: see text]). The magnitude of the surface conductivity depended on the degree of weathering and therefore on the amount of smectite and mixed layer (illite-smectite) clays present in the saprolite. The chargeability of the core samples was in the range of [Formula: see text] and is strongly dependent on the salinity. We also performed streaming potential measurements with the same pore fluid composition as that used for the complex conductivity measurements. We found an excess of movable electrical charges on the order of 100 to [Formula: see text] in agreement with previous investigations connecting the movable excess charge density to permeability. The zeta potential was in the range of [Formula: see text] to [Formula: see text] independent on the salinity. The electrical measurements were consistent with an average cation exchange capacity in the range of 1.4 to [Formula: see text] and a specific surface area on the order of 4000 to about 30,000 [Formula: see text].

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Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

Applied and Environmental Microbiology ◽

10.1128/aem.06435-11 ◽

2011 ◽

Vol 78 (4) ◽

pp. 1039-1047 ◽

Cited By ~ 102

Author(s):

Stefan J. Green ◽

Om Prakash ◽

Puja Jasrotia ◽

Will A. Overholt ◽

Erick Cardenas ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Community Composition ◽

Field Research ◽

Denitrifying Bacteria ◽

Rrna Genes ◽

Content Type ◽

Oak Ridge ◽

Dna And Rna ◽

Research Challenge

ABSTRACTThe effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genusRhodanobacter(classGammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution ofRhodanobacterbacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

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Geochemical and geophysical responses during the infiltration of fresh water into the contaminated saprolite of the Oak Ridge Integrated Field Research Challenge site, Tennessee

Water Resources Research ◽

10.1002/wrcr.20380 ◽

2013 ◽

Vol 49 (8) ◽

pp. 4952-4970 ◽

Cited By ~ 8

Author(s):

A. Revil ◽

Y. Wu ◽

M. Karaoulis ◽

S. S. Hubbard ◽

D. B. Watson ◽

...

Keyword(s):

Fresh Water ◽

Field Research ◽

Oak Ridge ◽

Research Challenge

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Effect of Probiotics and Prebiotics on Oral Health

Dental Journal of Advance Studies ◽

10.1055/s-0040-1722523 ◽

2021 ◽

Author(s):

Goutam Nanavati ◽

T. Prasanth ◽

Manab Kosala ◽

Sujit K. Bhandari ◽

Pamil Banotra

Keyword(s):

Oral Health ◽

Oral Cavity ◽

Periodontal Diseases ◽

Microbial Flora ◽

Gastrointestinal Disorders ◽

Food Ingredients ◽

Multifactorial Diseases ◽

Probiotic Strains ◽

Reducing Bacteria ◽

Nitrate Reducing Bacteria

AbstractProbiotics are the living microorganisms that have been commonly used in the prevention of gastrointestinal disorders. In recent times, probiotic and prebiotics have been used to assess and develop a natural balance of the microbial flora in the respiratory tract and the oral cavity as an adjunct therapy. They are known to augment the existing microbial flora that is beneficial to the host. Prebiotics are nondigestible food ingredients that help in increasing populations of probiotic bacteria. Recent studies have shown that probiotics help in active reduction in gingivitis, dental caries, periodontitis, and halitosis by replacing the harmful oral species, by means of utilizing abundant health-associated oral microbial species. Additionally, the nitrate-reducing bacteria have shown promising effect in improving efficiency of probiotic strains to accentuate oral health benefits. Probiotics along with prebiotics effectively alter the host–microbial interface by achieving homeostasis in multifactorial diseases such as periodontal diseases and oral malodor. The aim of the review is to collate the existing information available on use of probiotics and prebiotics in oral cavity.

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Two Marine Desulfotomaculum spp. of Different Origin are Capable of Utilizing Acetone and Higher Ketones

Current Microbiology ◽

10.1007/s00284-021-02441-9 ◽

2021 ◽

Author(s):

Jasmin Frey ◽

Sophie Kaßner ◽

Bernhard Schink

Keyword(s):

Sulfate Reducing Bacteria ◽

Thiamine Diphosphate ◽

Sulfate Reducers ◽

Sulfate Reducing ◽

Reducing Bacteria ◽

Nitrate Reducing Bacteria ◽

Different Origin

AbstractDegradation of acetone and higher ketones has been described in detail for aerobic and nitrate-reducing bacteria. Among sulfate-reducing bacteria, degradation of acetone and other ketones is still an uncommon ability and has not been understood completely yet. In the present work, we show that Desulfotomaculum arcticum and Desulfotomaculum geothermicum are able to degrade acetone and butanone. Total proteomics of cell-free extracts of both organisms indicated an involvement of a thiamine diphosphate-dependent enzyme, a B12-dependent mutase, and a specific dehydrogenase during acetone degradation. Similar enzymes were recently described to be involved in acetone degradation by Desulfococcus biacutus. As there are so far only two described sulfate reducers able to degrade acetone, D. arcticum and D. geothermicum represent two further species with this capacity. All these bacteria appear to degrade acetone via the same set of enzymes and therefore via the same pathway.

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Isolation and Characterization of Nitrate Reducing Bacteria for Conversion of Vegetable-Derived Nitrate to ‘Natural Nitrite’

Applied Microbiology ◽

10.3390/applmicrobiol1010002 ◽

2021 ◽

Vol 1 (1) ◽

pp. 11-23

Author(s):

Arjun Bhusal ◽

Peter M. Muriana

Keyword(s):

Nitrate Reduction ◽

High Performance ◽

Limit Of Detection ◽

Reversed Phase ◽

Test Tube ◽

Screening Assay ◽

Isolation And Characterization ◽

The Us ◽

Reducing Bacteria ◽

Nitrate Reducing Bacteria

In the US, sodium nitrate is used as a preservative and curing agent in processed meats and is therefore a regulated ingredient. Nitrate reducing bacteria (NRB) can convert vegetable nitrate into nitrite allowing green/clean label status in the US as per the USDA-FSIS definition of ‘natural nitrite’. The current ‘in-liquid’ test tube assay for detecting nitrite is not suitable for screening mixtures of bacteria nor is commercial nitrate broth suitable for growth of many Gram (+) bacteria. M17 broth was therefore used to develop M17-nitrate broth to be inclusive of Gram (+) bacteria. An ‘on-agar’ colony-screening assay was developed to detect the conversion of nitrate to nitrite on agar plates and could detect one NRB+ colony among ~300–500 colonies on a single plate. Samples that might have NRB were spread-plated on M17 agar plates, sandwiched with nitrate agar, and after incubation followed with sequential agar overlays containing the reagents used in the nitrate reduction assay; the appearance of red color zones above colonies indicated the presence of nitrite. NRB derived from various samples were confirmed for nitrate conversion and both nitrate and nitrite were quantified by C8 reversed-phase (RP) ion-pairing high performance liquid chromatography (HPLC) analysis (1 ppm limit of detection). Staphylococcus carnosus, a strain commonly used for nitrate reduction, was able to convert 1100 ppm M17-nitrate broth to 917 ppm nitrite. Staphylococcus caprae and Panteoa agglomerans, NRB isolated using the M17-nitrate agar assay, were also able to ferment the same broth to 916 ppm and 867 ppm nitrite, respectively. This is the first report of an on-agar colony screening assay for the detection and isolation of nitrite reducing bacteria allowing NRB to be readily isolated. This may allow for the identification of new bacteria that may have a more efficient process to generate nitrite, and possibly concomitant with production of additional natural antimicrobials, as vegetable nitrite becomes more widely used to prevent spore germination.

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Activation of short-chain ketones and isopropanol in sulfate-reducing bacteria

BMC Microbiology ◽

10.1186/s12866-021-02112-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jasmin Frey ◽

Sophie Kaßner ◽

Dieter Spiteller ◽

Mario Mergelsberg ◽

Matthias Boll ◽

...

Keyword(s):

Sulfate Reducing Bacteria ◽

Short Chain ◽

Enzyme Assays ◽

Protein Patterns ◽

Sulfate Reducing ◽

Protein Gel ◽

Branched Chain ◽

Reducing Bacteria ◽

Coenzyme B ◽

Nitrate Reducing Bacteria

Abstract Background Degradation of acetone by aerobic and nitrate-reducing bacteria can proceed via carboxylation to acetoacetate and subsequent thiolytic cleavage to two acetyl residues. A different strategy was identified in the sulfate-reducing bacterium Desulfococcus biacutus that involves formylation of acetone to 2-hydroxyisobutyryl-CoA. Results Utilization of short-chain ketones (acetone, butanone, 2-pentanone and 3-pentanone) and isopropanol by the sulfate reducer Desulfosarcina cetonica was investigated by differential proteome analyses and enzyme assays. Two-dimensional protein gel electrophoresis indicated that D. cetonica during growth with acetone expresses enzymes homologous to those described for Desulfococcus biacutus: a thiamine diphosphate (TDP)-requiring enzyme, two subunits of a B12-dependent mutase, and a NAD+-dependent dehydrogenase. Total proteomics of cell-free extracts confirmed these results and identified several additional ketone-inducible proteins. Acetone is activated, most likely mediated by the TDP-dependent enzyme, to a branched-chain CoA-ester, 2-hydroxyisobutyryl-CoA. This compound is linearized to 3-hydroxybutyryl-CoA by a coenzyme B12-dependent mutase followed by oxidation to acetoacetyl-CoA by a dehydrogenase. Proteomic analysis of isopropanol- and butanone-grown cells revealed the expression of a set of enzymes identical to that expressed during growth with acetone. Enzyme assays with cell-free extract of isopropanol- and butanone-grown cells support a B12-dependent isomerization. After growth with 2-pentanone or 3-pentanone, similar protein patterns were observed in cell-free extracts as those found after growth with acetone. Conclusions According to these results, butanone and isopropanol, as well as the two pentanone isomers, are degraded by the same enzymes that are used also in acetone degradation. Our results indicate that the degradation of several short-chain ketones appears to be initiated by TDP-dependent formylation in sulfate-reducing bacteria.

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