skip to main content


Title: Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
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 asThiobacillusandGallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on thein-situcarbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.

 
more » « less
NSF-PAR ID:
10153512
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
Nature Publishing Group
Date Published:
Journal Name:
Scientific Reports
Volume:
9
Issue:
1
ISSN:
2045-2322
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Fractured rock aquifers cover much of Earth's surface and are important mountain sites for groundwater recharge but are poorly understood. To investigate groundwater systematics of a fractured‐dominated aquifer in Baja California Sur, Mexico, we examined the spatial patterns of aquifer recharge and connectivity using the geochemistry of springs. We evaluate a range of geochemical data within the context of two endmember hypotheses describing spatial recharge patterns and fracture connectivity. Hypothesis 1 is that the aquifer system is segmented, and springs are fed by local recharge. Hypothesis 2 is that the aquifer system is well connected, with dominant recharge occurring in the higher elevations. The study site is a small <15 km2catchment. Thirty‐four distinct springs and two wells were identified in the study area, and 24 of these sites were sampled for geochemical analyses along an elevation gradient and canyon transect. These analyses included major ion composition, trace element and strontium isotopes, δ18O and δ2H isotopes, radiocarbon, and tritium. δ18O and δ2H isotopes suggest that the precipitation feeding the groundwater system has at least two distinct sources. Carbon isotopes showed a change along the canyon transect, suggesting that shorter flowpaths feed springs in the top of the transect, and longer flowpaths discharge near the bottom. Geochemical interpretations support a combination of the two proposed hypotheses. Understanding of the connectivity and provenance of these springs is significant as they are the primary source of water for the communities that inhabit this region and may be impacted by changes in recharge and use.

     
    more » « less
  2. null (Ed.)
    Beach aquifers, located in the subsurface of sandy beaches, are unique ecosystems with steep chemical and physical gradients resulting from the mixing of terrestrial fresh groundwater and saline groundwater from the sea. While work has rapidly progressed to understand the physics and chemistry in this environment, much less is known about the microorganisms present despite the fact that they are responsible for vital biogeochemical processes. This paper presents a review of the current state of knowledge of microbes within beach aquifers and the mechanisms that control the beach aquifer microbiome. We review literature describing the distribution and diversity of microorganisms in the freshwater-saltwater mixing zone of beach aquifers, and identify just 12 papers. We highlight knowledge gaps, as well as future research directions: The understanding of beach aquifer microorganisms is informed primarily by 16S ribosomal RNA gene sequences. Metagenomics and metatranscriptomics have not yet been applied but are promising approaches for elucidating key metabolic and ecological roles of microbes in this environment. Additionally, variability in field sampling and analytical methods restrict comparison of data across studies and geographic locations. Further, documented evidence on the migration of microbes within the beach aquifer is limited. Taking into account the physical transport of microbes through sand by flowing groundwater may be critical for understanding the structure and dynamics of microbial communities. Quantitative measurements of rates of elemental cycling in the context of microbial diversity need further investigation, in order to understand the roles of microbes in mediating biogeochemical fluxes from the beach aquifer to the coastal ocean. Lastly, understanding the current state of beach aquifers in regulating carbon stocks is critical to foster a better understanding of the contribution of the beach aquifer microbiome to global climate models. 
    more » « less
  3. Abstract

    Widespread contamination of groundwater with geogenic arsenic is attributed to microbial dissolution of arsenic‐bearing iron (oxyhydr)oxides minerals coupled to the oxidation of organic carbon. The recharge sources to an aquifer can influence groundwater arsenic concentrations by transport of dissolved arsenic or reactive constituents that affect arsenic mobilization. To understand how different recharge sources affect arsenic contamination—in particular through their influence on organic carbon and sulfate cycling—we delineated and quantified recharge sources in the arsenic affected region around Hanoi, Vietnam. We constrained potential end‐member compositions and employed a novel end‐member mixing model using an ensemble approach to apportion recharge sources. Groundwater arsenic and dissolved organic carbon concentrations are controlled by the dominant source of recharge. High arsenic concentrations are prevalent regardless of high dissolved organic carbon or ammonium levels, indicative of organic matter decomposition, where the dominant recharge source is riverine. In contrast, high dissolved organic carbon and significant organic matter decomposition are required to generate elevated groundwater arsenic where recharge is largely nonriverine. These findings suggest that in areas of riverine recharge, arsenic may be efficiently mobilized from reactive surficial environments and carried from river‐aquifer interfaces into groundwater. In groundwaters derived from nonriverine recharge areas, significantly more organic carbon mineralization is required to obtain equivalent levels of arsenic mobilization within inland sediments. This method can be broadly applied to examine the connection between hydrology, geochemistry and groundwater quality.

     
    more » « less
  4. Abstract

    Mountain‐front recharge (MFR), or all inflow to a basin‐fill aquifer with its source in the mountain block, is an important component of recharge to basin‐fill aquifer systems. Distinguishing and quantifying the surface from subsurface components of MFR is necessary for water resource planning and management, particularly as climate change may impact these components in distinct ways. This study tests the hypothesis that MFR components can be distinguished in long‐screened, basin‐fill production wells by (1) groundwater age and (2) the median elevation of recharge. We developed an MFR characterization approach by combining age distributions in six wells using tritium, krypton‐85, argon‐39, and radiocarbon, and median recharge elevations from noble gas thermometry combined with numerical experiments to determine recharge temperature lapse rates using flow and energy transport modeling. We found that groundwater age distributions provided valuable information for characterizing the dominant flow system behavior captured by the basin‐fill production wells. Tracers indicated the presence of old (i.e., no detectable tritium) water in a well completed in weathered bedrock located close to the mountain front. Two production wells exhibited age distributions of binary mixing between modern and a small fraction of old water, whereas the remaining wells captured predominantly modern flow paths. Noble gas thermometry provided important complementary information to the age distributions; however, assuming constant recharge temperature lapse rates produced improbable recharge elevations. Numerical experiments suggest that surface MFR, if derived from snowmelt, can locally suppress water table temperatures in the basin‐fill aquifer, with implications for recharge elevations estimated from noble gas thermometry.

     
    more » « less
  5. Abstract

    For a large part of earth's history, cyanobacterial mats thrived in low‐oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment–water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment–mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low‐oxygen, sulfidic environment in which a microbial mat dominated byPhormidiumandPlanktothrixthat is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic‐rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low‐throughput or shotgun metagenomic approaches, our high‐throughput 16SrRNAgene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate‐reducing taxa ofDeltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in theMISwere distinctly different from those in typicalLHsediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related toMISmicrobial community composition, whileLHcommunities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling.

     
    more » « less