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Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer.
Sci Rep 2019; 9(1):10370SR

Abstract

Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.

Authors+Show Affiliations

Environmental Science Department, Barnard College, NY, NY, 10027, New York, USA. bmaillou@barnard.edu.Environmental Science Department, Barnard College, NY, NY, 10027, New York, USA.Environmental Science Department, Barnard College, NY, NY, 10027, New York, USA.Environmental Science Department, Barnard College, NY, NY, 10027, New York, USA.Environmental Science Department, Barnard College, NY, NY, 10027, New York, USA.Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, 94551-9900, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31316095

Citation

Mailloux, Brian J., et al. "Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer." Scientific Reports, vol. 9, no. 1, 2019, p. 10370.
Mailloux BJ, Kim C, Kichuk T, et al. Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. Sci Rep. 2019;9(1):10370.
Mailloux, B. J., Kim, C., Kichuk, T., Nguyen, K., Precht, C., Wang, S., ... Buchholz, B. A. (2019). Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. Scientific Reports, 9(1), p. 10370. doi:10.1038/s41598-019-46663-1.
Mailloux BJ, et al. Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. Sci Rep. 2019 Jul 17;9(1):10370. PubMed PMID: 31316095.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer. AU - Mailloux,Brian J, AU - Kim,Carol, AU - Kichuk,Tess, AU - Nguyen,Khue, AU - Precht,Chandler, AU - Wang,Shi, AU - Jewell,Talia N M, AU - Karaoz,Ulas, AU - Brodie,Eoin L, AU - Williams,Kenneth H, AU - Beller,Harry R, AU - Buchholz,Bruce A, Y1 - 2019/07/17/ PY - 2019/02/15/received PY - 2019/07/01/accepted PY - 2019/7/19/entrez PY - 2019/7/19/pubmed PY - 2019/7/19/medline SP - 10370 EP - 10370 JF - Scientific reports JO - Sci Rep VL - 9 IS - 1 N2 - Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/31316095/Paired_RNA_Radiocarbon_and_Sequencing_Analyses_Indicate_the_Importance_of_Autotrophy_in_a_Shallow_Alluvial_Aquifer_ L2 - http://dx.doi.org/10.1038/s41598-019-46663-1 DB - PRIME DP - Unbound Medicine ER -