Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
Year: 2019
Type: article
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.
Source: Scientific Reports
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $1,790
Funders: National Science Foundation, U.S. Department of Energy, U.S. Department of Health and Human Services, University of California Berkeley, National Institutes of Health, Office of Science, National Institute of General Medical Sciences, National Institute of Environmental Health Sciences, National Center for Research Resources, Biological and Environmental Research, Laboratory Directed Research and Development, Lawrence Livermore National Laboratory, Lawrence Berkeley National Laboratory
Awards: G1079818582, G1088636562, G1143651532, G1216544436, G1286236842, G1337544421, G1356433355, G14554683, G1460240928, G1474850823, G1716777315, G1737889641, G1863003419, G2145270357, G223002938, G2539837713, G2812390658, G3083819904, Genome Sequencer FLX, G3571461640, G3669113783, G382641700, G419881185, G42916606, G4343739756, G4501827968, G498139845, Health Effects and Geochemistry of Arsenic, G5453794400, G5630301777, G574795485, G6019455411, G6163473734, G6652958823, G69709960, G7354628648, G7787287669, Collaborative Research: Changes in river-aquifer exchange induced by groundwater pumping, and their effect on arsenic contamination in the Red River Delta, Vietnam, G8326222658, Illumina Sequencer to Facilitate Functional Genomics at Berkeley, G8807659652, Resource for the Development of Biomedical Accelerator Mass Spectrometry (AMS), G895790057, G9000217211, G969889393, G991281326
OpenAlex ID: W2958541674