Emily R. Paris

All Publications

• Single-cell analysis in hypersaline brines predicts a water-activity limit of microbial anabolic activity. Science advances Paris, E. R., Arandia-Gorostidi, N., Klempay, B., Bowman, J. S., Pontefract, A., Elbon, C. E., Glass, J. B., Ingall, E. D., Doran, P. T., Som, S. M., Schmidt, B. E., Dekas, A. E. 2023; 9 (51): eadj3594

  Abstract

  Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the 0.409-aw brine (an MgCl2-dominated site) despite the presence of cell-like structures. Extrapolating our data, we predict an aw limit for detectable anabolic activity of 0.540, which is beyond the currently accepted limit of life based on cell division. This work demonstrates the utility of single-cell, metabolism-based techniques for detecting active life and expands the potential habitable space on Earth and beyond.

  View details for DOI 10.1126/sciadv.adj3594

  View details for PubMedID 38134283

  View details for PubMedCentralID PMC10745694

• Abundance, Identity, and Potential Diazotrophic Activity of nifH-Containing Organisms at Marine Cold Seeps. Environmental microbiology Semler, A. C., Paris, E. R., Salvador, M., Dekas, A. E. 2025; 27 (3): e70058

  Abstract

  Diazotrophic microorganisms alleviate nitrogen limitation at marine cold seeps using nitrogenase, encoded in part by the gene nifH. Here, we investigated nifH-containing organisms (NCOs) inside and outside six biogeochemically heterogeneous seeps using amplicon sequencing and quantitative real-time PCR (qPCR) of nifH genes and transcripts. We detected nifH genes affiliated with phylogenetically and metabolically diverse organisms spanning 18 bacterial and archaeal phyla (17 within seeps). Detected NCOs included methane-oxidising ANME-2 archaea and sulfate-reducing Desulfobacteraceae, which have been shown to fix nitrogen at seeps previously, as well as Desulfuromonadales and putatively hydrocarbon-oxidising Desulfoglaeba and Candidatus Methanoliparia. We detected nifH transcripts at five of the six seeps, suggesting widespread diazotrophic activity. We corrected our qPCR data based on our amplicon results, which found that 71% of recovered sequences were not bona fide nifH, and we recommend a similar correction in future qPCR studies that use broad nifH primers. NifH abundance was up to three orders of magnitude higher within seeps, was correlated with mcrA abundance, and, when corrected, was negatively correlated with porewater ammonium < 25 μM, consistent with the inhibition of diazotrophy by ammonium. Our findings expand the known diversity of NCOs at seeps and emphasise seeps as hotspots for deep-sea diazotrophy.

  View details for DOI 10.1111/1462-2920.70058

  View details for PubMedID 40065596

• Biosignature Molecules Accumulate and Persist in Evaporitic Brines: Implications for Planetary Exploration. Astrobiology Pozarycki, C., Seaton, K. M., C Vincent, E., Novak Sanders, C., Nuñez, N., Castillo, M., Ingall, E., Klempay, B., Pontefract, A., Fisher, L. A., Paris, E. R., Buessecker, S., Alansson, N. B., Carr, C. E., Doran, P. T., Bowman, J. S., Schmidt, B. E., Stockton, A. M. 2024; 24 (8): 795-812

  Abstract

  The abundance of potentially habitable hypersaline environments in our solar system compels us to understand the impacts of high-salt matrices and brine dynamics on biosignature detection efforts. We identified and quantified organic compounds in brines from South Bay Salt Works (SBSW), where evapoconcentration of ocean water enables exploration of the impact of NaCl- and MgCl2-dominated brines on the detection of potential biosignature molecules. In SBSW, organic biosignature abundance and distribution are likely influenced by evapoconcentration, osmolyte accumulation, and preservation effects. Bioluminescence assays show that adenosine triphosphate (ATP) concentrations are higher in NaCl-rich, low water activity (aw) samples (<0.85) from SBSW. This is consistent with the accumulation and preservation of ATP at low aw as described in past laboratory studies. The water-soluble small organic molecule inventory was determined by using microchip capillary electrophoresis paired with high-resolution mass spectrometry (µCE-HRMS). We analyzed the relative distribution of proteinogenic amino acids with a recently developed quantitative method using CE-separation and laser-induced fluorescence (LIF) detection of amino acids in hypersaline brines. Salinity trends for dissolved free amino acids were consistent with amino acid residue abundance determined from the proteome of the microbial community predicted from metagenomic data. This highlights a tangible connection up and down the "-omics" ladder across changing geochemical conditions. The detection of water-soluble organic compounds, specifically proteinogenic amino acids at high abundance (>7 mM) in concentrated brines, demonstrates that potential organic biomarkers accumulate at hypersaline sites and suggests the possibility of long-term preservation. The detection of such molecules in high abundance when using diverse analytical tools appropriate for spacecraft suggests that life detection within hypersaline environments, such as evaporates on Mars and the surface or subsurface brines of ocean world Europa, is plausible and argues such environments should be a high priority for future exploration. Key Words: Salts-Analytical chemistry-Amino acids-Biosignatures-Capillary electrophoresis-Preservation. Astrobiology 24, 795-812.

  View details for DOI 10.1089/ast.2023.0122

  View details for PubMedID 39159437

• Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments Frontiers in Microbiology Raut, Y., Barr, C. R., Paris, E. R., Kapili, B. J., Dekas, A. E., Capone, D. G. 2024; 14

  View details for DOI 10.3389/fmicb.2023.1312843