Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP

Dekas, Anne E.; Parada, Alma E.; Mayali, Xavier; Fuhrman, Jed A.; Wollard, Jessica; Weber, Peter K.; Pett-Ridge, Jennifer

doi:10.3389/fmicb.2019.02682

Title: Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP

Journal Article · Tue Dec 17 00:00:00 EST 2019 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2019.02682· OSTI ID:1579574

Dekas, Anne E.; Parada, Alma E.; Mayali, Xavier; Fuhrman, Jed A.; Wollard, Jessica; Weber, Peter K.; Pett-Ridge, Jennifer

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 some 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.

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

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Laboratory Directed Research and Development (LDRD) Program; National Science Foundation (NSF); Gordon and Betty Moore Foundation

Grant/Contract Number:: AC52-07NA27344; 13-LW-032; SCW1039; 1136818; GBMF3779

OSTI ID:: 1579574

Alternate ID(s):: OSTI ID: 1660502

Report Number(s):: LLNL-JRNL-772256; 2682

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 10; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: Switzerland

Language:: English

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Cited by: 29 works

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59 BASIC BIOLOGICAL SCIENCES
thaumarchaeota
archaea
nanoSIMS
chemoautotrophy
mixotrophy
single cell
deep sea
stable isotope probing
13C
15N

Title: Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP

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