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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Microbiol. | doi: 10.3389/fmicb.2019.02682

Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope nanoSIP

  • 1Stanford University, United States
  • 2Lawrence Livermore National Laboratory, United States Department of Energy (DOE), United States
  • 3University of Southern California, United States

Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle—chemoautotrophic or heterotrophic—of each cell. Most cells (>90%) were anabolically active during the incubation, and 4-17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that these Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.

Keywords: NanoSIMS, chemoautotrophy, single cell, Stable isotope probing (SIP), Marine Group I Thaumarchaeota, Microbial actiity

Received: 18 Feb 2019; Accepted: 05 Nov 2019.

Copyright: © 2019 Dekas, Parada, Mayali, Fuhrman, Wollard, Weber and Pett-Ridge. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Anne E. Dekas, Stanford University, Stanford, United States,