Quantitative substrate utilization in microbial ecology using stable isotope probing

Hungate, Bruce; Schwartz, Egbert; Mau, Rebecca; Marks, Jane

Quantitative substrate utilization in microbial ecology using stable isotope probing

Patent · 12 November 2019

OSTI ID:1600267

Hungate, Bruce; Schwartz, Egbert; Mau, Rebecca; Marks, Jane

Methods modifying conventional SIP so that isotopic incorporation into the genomes of individual microbial taxa can be quantified are described. Further, methods to quantify the baseline densities of the DNA of individual microbial taxa without exposure to isotope tracers and then to quantify the change in DNA density of each taxon caused by isotope incorporation are described. The distribution of DNA of each taxon along a density gradient reflects the influence of isotope incorporation only, without reflecting the guanine-plus-cytosine content.

Research Organization:: Northern Arizona Univ., Flagstaff, AZ (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: SC0010579

Assignee:: Arizona Board of Regents on Behalf of Northern Arizona University (Flagstaff, AZ)

Patent Number(s):: 10,472,670

Application Number:: 15/640,028

OSTI ID:: 1600267

Country of Publication:: United States

Language:: English

References (12)

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Methodological Considerations for the Use of Stable Isotope Probing in Microbial Ecology Neufeld, Josh D.; Dumont, Marc G.; Vohra, Jyotsna Microbial Ecology, Vol. 53, Issue 3 https://doi.org/10.1007/s00248-006-9125-x	journal	October 2006
Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients: Quantitative analysis of SIP gradients Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W. Environmental Microbiology, Vol. 6, Issue 1 https://doi.org/10.1046/j.1462-2920.2003.00536.x	journal	December 2003
Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples Schwartz, Egbert; Hayer, Michaela; Hungate, Bruce A. Current Opinion in Biotechnology, Vol. 41 https://doi.org/10.1016/j.copbio.2016.03.003	journal	October 2016
Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil: SIP of methylotrophs in rice field soil Lueders, Tillmann; Wagner, Bianca; Claus, Peter Environmental Microbiology, Vol. 6, Issue 1 https://doi.org/10.1046/j.1462-2920.2003.00535.x	journal	December 2003
Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers Štursová, Martina; Žifčáková, Lucia; Leigh, Mary Beth FEMS Microbiology Ecology, Vol. 80, Issue 3 https://doi.org/10.1111/j.1574-6941.2012.01343.x	journal	March 2012
Identification of Nitrogen-Incorporating Bacteria in Petroleum-Contaminated Arctic Soils by Using [ ¹⁵ N]DNA-Based Stable Isotope Probing and Pyrosequencing Bell, Terrence H.; Yergeau, Etienne; Martineau, Christine Applied and Environmental Microbiology, Vol. 77, Issue 12 https://doi.org/10.1128/AEM.00172-11	journal	April 2011
Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms Radajewski, Stefan; McDonald, Ian R.; Murrell, J. Colin Current Opinion in Biotechnology, Vol. 14, Issue 3, p. 296-302 https://doi.org/10.1016/S0958-1669(03)00064-8	journal	June 2003
Quantitative Microbial Ecology through Stable Isotope Probing Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert Applied and Environmental Microbiology, Vol. 81, Issue 21 https://doi.org/10.1128/AEM.02280-15	journal	August 2015
Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density Buckley, D. H.; Huangyutitham, V.; Hsu, S. -F. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.02609-06	journal	March 2007
Characterization of Growing Microorganisms in Soil by Stable Isotope Probing with H218O Schwartz, E. Applied and Environmental Microbiology, Vol. 73, Issue 8 https://doi.org/10.1128/AEM.02021-06	journal	February 2007
Linking Microbial Community Function to Phylogeny of Sulfate-Reducing Deltaproteobacteria in Marine Sediments by Combining Stable Isotope Probing with Magnetic-Bead Capture Hybridization of 16S rRNA Miyatake, Tetsuro; MacGregor, Barbara J.; Boschker, Henricus T. S. Applied and Environmental Microbiology, Vol. 75, Issue 15 https://doi.org/10.1128/AEM.00652-09	journal	August 2009

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