Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer

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.

doi:10.1038/s41598-019-46663-1

Title: Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer

Journal Article · 17 July 2019 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-019-46663-1 · OSTI ID:1619546

Mailloux, Brian J.; Kim, Carol; Kichuk, Tess; Nguyen, Khue; Precht, Chandler;

; Jewell, Talia N. M.; Karaoz, Ulas;

; Williams, Kenneth H.;

;

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 (Δ ¹⁴ C) 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; AC52-07NA27344; SC0006796

OSTI ID:: 1619546

Report Number(s):: LLNL-JRNL-744481; 10370; PII: 46663

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 9; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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