Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
- Publication Date:
- Research Org.:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1619546
- Alternate Identifier(s):
- OSTI ID: 1558875; OSTI ID: 1559237
- Report Number(s):
- LLNL-JRNL-744481
Journal ID: ISSN 2045-2322; 10370; PII: 46663
- Grant/Contract Number:
- AC52-07NA27344; AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Name: Scientific Reports Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- Environmental sciences, Biological and medical sciences, Chemistry; 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Mailloux, Brian J., Kim, Carol, Kichuk, Tess, Nguyen, Khue, Precht, Chandler, Wang, Shi, Jewell, Talia N. M., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., Beller, Harry R., and Buchholz, Bruce A. Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. United Kingdom: N. p., 2019.
Web. doi:10.1038/s41598-019-46663-1.
Mailloux, Brian J., Kim, Carol, Kichuk, Tess, Nguyen, Khue, Precht, Chandler, Wang, Shi, Jewell, Talia N. M., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., Beller, Harry R., & Buchholz, Bruce A. Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. United Kingdom. https://doi.org/10.1038/s41598-019-46663-1
Mailloux, Brian J., Kim, Carol, Kichuk, Tess, Nguyen, Khue, Precht, Chandler, Wang, Shi, Jewell, Talia N. M., Karaoz, Ulas, Brodie, Eoin L., Williams, Kenneth H., Beller, Harry R., and Buchholz, Bruce A. Wed .
"Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer". United Kingdom. https://doi.org/10.1038/s41598-019-46663-1.
@article{osti_1619546,
title = {Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer},
author = {Mailloux, Brian J. and Kim, Carol and Kichuk, Tess and Nguyen, Khue and Precht, Chandler and Wang, Shi and Jewell, Talia N. M. and Karaoz, Ulas and Brodie, Eoin L. and Williams, Kenneth H. and Beller, Harry R. and Buchholz, Bruce A.},
abstractNote = {},
doi = {10.1038/s41598-019-46663-1},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United Kingdom},
year = {2019},
month = {7}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41598-019-46663-1
https://doi.org/10.1038/s41598-019-46663-1
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 1 work
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Magnesium Perchlorate as an Alternative Water Trap in AMS Graphite Sample Preparation: A Report On Sample Preparation at Kccams at the University of California, Irvine
journal, January 2004
- Santos, G. M.; Southon, J. R.; Druffel-Rodriguez, K. C.
- Radiocarbon, Vol. 46, Issue 1
A carbon free filter for collection of large volume samples of cellular biomass from oligotrophic waters
journal, September 2012
- Mailloux, Brian J.; Dochenetz, Audra; Bishop, Michael
- Journal of Microbiological Methods, Vol. 90, Issue 3
Microbial carbon cycling in oligotrophic regional aquifers near the Tono Uranium Mine, Japan as inferred from δ13C and Δ14C values of in situ phospholipid fatty acids and carbon sources
journal, July 2010
- Mills, Christopher T.; Amano, Yuki; Slater, Gregory F.
- Geochimica et Cosmochimica Acta, Vol. 74, Issue 13
Advection of surface-derived organic carbon fuels microbial reduction in Bangladesh groundwater
journal, March 2013
- Mailloux, B. J.; Trembath-Reichert, E.; Cheung, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 14
Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas denitrificans
journal, December 2007
- Sievert, S. M.; Scott, K. M.; Klotz, M. G.
- Applied and Environmental Microbiology, Vol. 74, Issue 4
Sulfuricella denitrificans gen. nov., sp. nov., a sulfur-oxidizing autotroph isolated from a freshwater lake
journal, January 2010
- Kojima, H.; Fukui, M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 12
Physico-Chemical Heterogeneity of Organic-Rich Sediments in the Rifle Aquifer, CO: Impact on Uranium Biogeochemistry
journal, December 2015
- Janot, Noémie; Lezama Pacheco, Juan S.; Pham, Don Q.
- Environmental Science & Technology, Vol. 50, Issue 1
Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: a molecule for phylogenetic and enzymological investigation
journal, January 1997
- Watson, G.
- FEMS Microbiology Letters, Vol. 146, Issue 1
Catalyst and binder effects in the use of filamentous graphite for AMS
journal, November 1987
- Vogel, John S.; Southon, John R.; Nelson, D. Erle
- Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 29, Issue 1-2
Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer
journal, March 2016
- Jewell, Talia N. M.; Karaoz, Ulas; Brodie, Eoin L.
- The ISME Journal, Vol. 10, Issue 9
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013
- Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
- The ISME Journal, Vol. 7, Issue 11
Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids
journal, July 2016
- Whaley-Martin, K. J.; Mailloux, B. J.; van Geen, A.
- Environmental Science & Technology, Vol. 50, Issue 14
Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry
journal, January 1991
- McMahon, Peter B.; Chapelle, Francis H.
- Nature, Vol. 349, Issue 6306
Quantifying Microbial Utilization of Petroleum Hydrocarbons in Salt Marsh Sediments by Using the 13C Content of Bacterial rRNA
journal, December 2007
- Pearson, A.; Kraunz, K. S.; Sessions, A. L.
- Applied and Environmental Microbiology, Vol. 74, Issue 4
Natural organic matter in sedimentary basins and its relation to arsenic in anoxic ground water: the example of West Bengal and its worldwide implications
journal, August 2004
- McArthur, J. M.; Banerjee, D. M.; Hudson-Edwards, K. A.
- Applied Geochemistry, Vol. 19, Issue 8
Characterization and Origin of Dissolved Organic Carbon in Yegua Ground Water in Brazos County, Texas
journal, September 2001
- Routh, Joyanto; Grossman, Ethan L.; Murphy, Ellyn M.
- Ground Water, Vol. 39, Issue 5
Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment
journal, March 2012
- Lomstein, Bente Aa.; Langerhuus, Alice T.; D’Hondt, Steven
- Nature, Vol. 484, Issue 7392
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
journal, May 2011
- Miller, Christopher S.; Baker, Brett J.; Thomas, Brian C.
- Genome Biology, Vol. 12, Issue 5
Retrospective Birth Dating of Cells in Humans
journal, July 2005
- Spalding, Kirsty L.; Bhardwaj, Ratan D.; Buchholz, Bruce A.
- Cell, Vol. 122, Issue 1
Thiobacillus thiophilus sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments
journal, March 2009
- Kellermann, C.; Griebler, C.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 3
The radiocarbon signature of microorganisms in the mesopelagic ocean
journal, April 2009
- Hansman, R. L.; Griffin, S.; Watson, J. T.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 16
Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer
journal, August 2012
- Campbell, K. M.; Kukkadapu, R. K.; Qafoku, N. P.
- Applied Geochemistry, Vol. 27, Issue 8
Persistence of soil organic matter as an ecosystem property
journal, October 2011
- Schmidt, Michael W. I.; Torn, Margaret S.; Abiven, Samuel
- Nature, Vol. 478, Issue 7367
Assessing sources and ages of organic matter supporting river and estuarine bacterial production: A multiple-isotope (Δ14C, 㬔C, and δ15N) approach
journal, September 2004
- McCallister, S. Leigh; Bauer, James E.; Cherrier, Jennifer E.
- Limnology and Oceanography, Vol. 49, Issue 5
Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain
journal, March 2017
- Yabusaki, Steven B.; Wilkins, Michael J.; Fang, Yilin
- Environmental Science & Technology, Vol. 51, Issue 6
Spatial and Temporal Variations of Groundwater Arsenic in South and Southeast Asia
journal, May 2010
- Fendorf, S.; Michael, H. A.; van Geen, A.
- Science, Vol. 328, Issue 5982
O 2 reduction and denitrification rates in shallow aquifers : O
journal, December 2011
- Tesoriero, Anthony J.; Puckett, Larry J.
- Water Resources Research, Vol. 47, Issue 12
Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: Genetic insights into the sulfur oxidation pathway of betaproteobacteria
journal, September 2014
- Watanabe, Tomohiro; Kojima, Hisaya; Fukui, Manabu
- Systematic and Applied Microbiology, Vol. 37, Issue 6
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans
journal, February 2006
- Beller, H. R.; Chain, P. S. G.; Letain, T. E.
- Journal of Bacteriology, Vol. 188, Issue 4
Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria
journal, January 2017
- Hutt, Lee P.; Huntemann, Marcel; Clum, Alicia
- Standards in Genomic Sciences, Vol. 12, Issue 1
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012
- Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver
- Bioinformatics, Vol. 28, Issue 14
Biodegradable Organic Carbon in Sediments of an Arsenic-Contaminated Aquifer in Bangladesh
journal, March 2014
- Neumann, Rebecca B.; Pracht, Lara E.; Polizzotto, Matthew L.
- Environmental Science & Technology Letters, Vol. 1, Issue 4
Characterization and isotopic composition of organic and inorganic carbon in the Milk River Aquifer
journal, August 1989
- Murphy, Ellyn M.; Davis, Stanley N.; Long, Austin
- Water Resources Research, Vol. 25, Issue 8
A versatile method for simultaneous stable carbon isotope analysis of DNA and RNA nucleotides by liquid chromatography/isotope ratio mass spectrometry: Stable carbon isotope analysis of DNA and RNA nucleotides by LC/IRMS
journal, May 2014
- Moerdijk-Poortvliet, Tanja C. W.; Brasser, Jurian; de Ruiter, Gerjan
- Rapid Communications in Mass Spectrometry, Vol. 28, Issue 12
Acetate Availability and its Influence on Sustainable Bioremediation of Uranium-Contaminated Groundwater
journal, June 2011
- Williams, Kenneth H.; Long, Philip E.; Davis, James A.
- Geomicrobiology Journal, Vol. 28, Issue 5-6
Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Groundwater and Aquifer Microorganisms
journal, June 2003
- Alfreider, A.; Vogt, C.; Hoffmann, D.
- Microbial Ecology, Vol. 45, Issue 4
Origins of lipid biomarkers in Santa Monica Basin surface sediment: a case study using compound-specific Δ 14 C analysis
journal, September 2001
- Pearson, A.; McNichol, A. P.; Benitez-Nelson, B. C.
- Geochimica et Cosmochimica Acta, Vol. 65, Issue 18
Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks
journal, September 2012
- Huson, Daniel H.; Scornavacca, Celine
- Systematic Biology, Vol. 61, Issue 6
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
journal, December 2016
- Carini, Paul; Marsden, Patrick J.; Leff, Jonathan W.
- Nature Microbiology, Vol. 2, Issue 3
The complete genome sequence for putative H 2 - and S-oxidizer C andidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome : Complete genome of
journal, April 2014
- Handley, Kim M.; Bartels, Daniela; O'Loughlin, Edward J.
- Environmental Microbiology, Vol. 16, Issue 11
Large Fractions of CO 2 -Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds
journal, January 2015
- Herrmann, Martina; Rusznyák, Anna; Akob, Denise M.
- Applied and Environmental Microbiology, Vol. 81, Issue 7
Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes
journal, April 2009
- Alfreider, Albin; Vogt, Carsten; Geiger-Kaiser, Margot
- Systematic and Applied Microbiology, Vol. 32, Issue 2
Microbial CO2 fixation potential in a tar-oil-contaminated porous aquifer
journal, April 2012
- Kellermann, Claudia; Selesi, Draženka; Lee, Natuschka
- FEMS Microbiology Ecology, Vol. 81, Issue 1
Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO 2 and N 2
journal, March 2018
- Newcomer, Michelle E.; Hubbard, Susan S.; Fleckenstein, Jan H.
- Journal of Geophysical Research: Biogeosciences, Vol. 123, Issue 3
Variations in microbial carbon sources and cycling in the deep continental subsurface
journal, January 2016
- Simkus, Danielle N.; Slater, Greg F.; Lollar, Barbara Sherwood
- Geochimica et Cosmochimica Acta, Vol. 173
Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics
journal, January 2013
- Emerson, David; Field, Erin K.; Chertkov, Olga
- Frontiers in Microbiology, Vol. 4
Genetic Evidence for Bacterial Chemolithoautotrophy Based on the Reductive Tricarboxylic Acid Cycle in Groundwater Systems
journal, January 2012
- Alfreider, Albin; Vogt, Carsten
- Microbes and Environments, Vol. 27, Issue 2
Diversity of iron oxidizers in wetland soils revealed by novel 16S rRNA primers targeting Gallionella-related bacteria
journal, February 2009
- Wang, Juanjuan; Muyzer, Gerard; Bodelier, Paul L. E.
- The ISME Journal, Vol. 3, Issue 6
Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds
journal, October 2017
- Trembath-Reichert, Elizabeth; Morono, Yuki; Ijiri, Akira
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 44
Determination of Microbial Carbon Sources and Cycling during Remediation of Petroleum Hydrocarbon Impacted Soil Using Natural Abundance 14 C Analysis of PLFA
journal, April 2010
- Cowie, Benjamin R.; Greenberg, Bruce M.; Slater, Gregory F.
- Environmental Science & Technology, Vol. 44, Issue 7
Bomb pulse biology
journal, January 2013
- Falso, Miranda J. Sarachine; Buchholz, Bruce A.
- Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, Vol. 294
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
Assessing Microbial Uptake of Petroleum Hydrocarbons in Groundwater Systems Using Natural Abundance Radiocarbon
journal, July 2010
- Ahad, Jason M. E.; Burns, Leanne; Mancini, Silvia
- Environmental Science & Technology, Vol. 44, Issue 13
Silicone lubricant enhances recovery of nucleic acids after phenol-chloroform extraction
journal, January 1993
- Mukhopadhyay, Tapas; Roth, Jack A.
- Nucleic Acids Research, Vol. 21, Issue 3
Discussion Reporting of 14 C Data
journal, January 1977
- Stuiver, Minze; Polach, Henry A.
- Radiocarbon, Vol. 19, Issue 3
14C-Dead Living Biomass: Evidence for Microbial Assimilation of Ancient Organic Carbon During Shale Weathering
journal, March 2001
- Petsch, S. T.
- Science, Vol. 292, Issue 5519
Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
journal, April 1987
- Chomczynski, Piotr; Sacchi, Nicoletta
- Analytical Biochemistry, Vol. 162, Issue 1