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Title: Geochemical Rate/RNA Integration Study (GRIST): A Pilot Field Experiment for Inter-Calibration of Biogeochemistry and Nucleic Acid Measurements Final Report

Abstract

The Geochemical Rate/RNA Integration Study (GRIST) project sought to correlate biogeochemical flux rates with measurements of gene expression and mRNA abundance to demonstrate the application of molecular approaches to estimate the presence and magnitude of a suite of biogeochemical processes. The study was headed by Lee Kerkhoff of Rutgers University. In this component of the GRIST study, we characterized ambient nutrient concentrations and measured uptake rates for dissolved inorganic nitrogen (DIN, ammonium, nitrate and nitrite) and dissolved organic nitrogen (urea and dissolved free amino acids) during two diel studies at the Long-Term Ecosystem Observatory (LEO-15) on the New Jersey continental shelf.

Authors:
Publication Date:
Research Org.:
Virginia Institute of Marine Sciecne
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
920499
Report Number(s):
DOE/FG020- Final Report
DOE Contract Number:
FG02-02ER63402
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Bronk, Deborah. Geochemical Rate/RNA Integration Study (GRIST): A Pilot Field Experiment for Inter-Calibration of Biogeochemistry and Nucleic Acid Measurements Final Report. United States: N. p., 2007. Web. doi:10.2172/920499.
Bronk, Deborah. Geochemical Rate/RNA Integration Study (GRIST): A Pilot Field Experiment for Inter-Calibration of Biogeochemistry and Nucleic Acid Measurements Final Report. United States. doi:10.2172/920499.
Bronk, Deborah. Mon . "Geochemical Rate/RNA Integration Study (GRIST): A Pilot Field Experiment for Inter-Calibration of Biogeochemistry and Nucleic Acid Measurements Final Report". United States. doi:10.2172/920499. https://www.osti.gov/servlets/purl/920499.
@article{osti_920499,
title = {Geochemical Rate/RNA Integration Study (GRIST): A Pilot Field Experiment for Inter-Calibration of Biogeochemistry and Nucleic Acid Measurements Final Report},
author = {Bronk, Deborah},
abstractNote = {The Geochemical Rate/RNA Integration Study (GRIST) project sought to correlate biogeochemical flux rates with measurements of gene expression and mRNA abundance to demonstrate the application of molecular approaches to estimate the presence and magnitude of a suite of biogeochemical processes. The study was headed by Lee Kerkhoff of Rutgers University. In this component of the GRIST study, we characterized ambient nutrient concentrations and measured uptake rates for dissolved inorganic nitrogen (DIN, ammonium, nitrate and nitrite) and dissolved organic nitrogen (urea and dissolved free amino acids) during two diel studies at the Long-Term Ecosystem Observatory (LEO-15) on the New Jersey continental shelf.},
doi = {10.2172/920499},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Jan 08 00:00:00 EST 2007},
month = {Mon Jan 08 00:00:00 EST 2007}
}

Technical Report:

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  • Our understanding of subsurface microbiology is hindered by the inaccessibility of this environment, particularly when the hydrogeologic medium is contaminated with toxic substances. Research in our labs indicated that the composition of the growth medium (e.g., bicarbonate complexation of U(VI)) and the underlying mineral phase (e.g., hematite) significantly affects the rate and extent of U(VI) reduction and immobilization through a variety of effects. Our research was aimed at elucidating those effects to a much greater extent, while exploring the potential for U(IV) reoxidation and subsequent re-mobilization, which also appears to depend on the mineral phases present in the system. Inmore » situ coupons with a variety of mineral phases were placed in monitoring wells at the NABIR FRC. These coupons showed that the mineral phase composition significantly affected the resulting attached phase microbial community. Our comparative use of both batch and open flow reactors (more representative of field conditions) indicates that hydrodynamics and continual influx of substrate and contaminants can also yield significantly different results than those obtained with closed serum bottles. To this end, the following overall experimental hypothesis tested was the following: On a mineral surface under anaerobic conditions, accumulations of secondary inorganic precipitates are controlled by a) the bacteria associated with the mineral surface, b) the electron acceptors available for anaerobic bacterial respiration, and c) local hydrodynamics and pH buffers govern micro- and meso-scale interaction of U in the presence of electron donors and acceptors, and nutrients.« less
  • Our understanding of subsurface microbiology is hindered by the inaccessibility of this environment, particularly when the hydrogeologic medium is contaminated with toxic substances. Past research in our labs indicated that the composition of the growth medium (e.g., bicarbonate complexation of U(VI)) and the underlying mineral phase (e.g., hematite) significantly affects the rate and extent of U(VI) reduction and immobilization through a variety of effects. Our research was aimed at elucidating those effects to a much greater extent, while exploring the potential for U(IV) reoxidation and subsequent re-mobilization, which also appears to depend on the mineral phases present in the system.more » The project reported on here was an extension ($20,575) of the prior (much larger) project. This report is focused only on the work completed during the extension period. Further information on the larger impacts of our research, including 28 publications, can be found in the final report for the following projects: 1) Biogeochemistry of Uranium Under Reducing and Re-oxidizing Conditions: An Integrated Laboratory and Field Study Grant # DE-FG03-01ER63270, and 2) Acceptable Endpoints for Metals and Radionuclides: Quantifying the Stability of Uranium and Lead Immobilized Under Sulfate Reducing Conditions Grant # DE-FG03-98ER62630/A001 In this Phase II project, the toxic effects of uranium(VI) were studied using Desulfovibrio desulfuricans G20 in a medium containing bicarbonate or 1, 4-piperazinediethane sulfonic acid disodium salt monohydrate (PIPES) buffer (each at 30 mM, pH 7). The toxicity of uranium(VI) was dependent on the medium buffer and was observed in terms of longer lag times and in some cases, no measurable growth. The minimum inhibiting concentration (MIC) was 140 M U(VI) in PIPES buffered medium. This is 36 times lower than previously reported for D. desulfuricans. These results suggest that U(VI) toxicity and the detoxification mechanisms of G20 depend greatly on the chemical forms of U(VI) present and the buffer present in a system. Phase II of this project was supported at a cost of $20,575 with most funds expended to support Rajesh Sani salary and benefits. Results have been published in a peer reviewed journal article.« less
  • This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Areamore » 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.« less
  • Design calculations concerning the collector field foundations of the Barstow Solar Pilot Plant are presented. The calculations include computer printouts for heliostat foundations, input requirements, heliostat foundation design, and miscellaneous collector field foundations design.
  • The existence of an intricate interplay of nucleic acids and nucleotides in the chain of events leading from free amino acid to completed polypeptide chain has been determined. To this was added another participant to the nucleotides in protein synthesis - diadenosine-5', 5''', p'p/sup 4/-tetraphosphate (Ap4A). Ap/sub 4/A serves as an initiation primer for DNA synthesis in a eukaryotic system catalyzed by DNA polymerase ..cap alpha... Thus the initial step in protein synthesis is linked to the first step in DNA synthesis by a small molecular weight, unique dinucleotide signal. Advances in the methodology of nucleic acid sequencing have mademore » it possible to examine the relationship between specific short segments of DNA and RNA and their function in the metabolism of the living cell. The triester method of synthesizing deoxynucleotide polymers has made it feasible to synthesize and use specific oligomeric deoxynucleotide sequences as probes of genetic function and potential viral inhibitors. The synthesis of ribonucleotide polymers has been more difficult, due almost entirely to the presence of the 2' ribosyl hydroxyl group. The possibility is now emerging, however, of employing ribonucleotide polymers as specific RNA-virus inhibitors.« less