Title: Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo ¹³C and ²H metabolic network mapping

Abstract

Anaerobic ammonium-oxidizing (anammox) bacteria mediate a key step in the biogeochemical nitrogen cycle and have been applied worldwide for the energy-efficient removal of nitrogen from wastewater. However, outside their core energy metabolism, little is known about the metabolic networks driving anammox bacterial anabolism and use of different carbon and energy substrates beyond genome-based predictions. Here, we experimentally resolved the central carbon metabolism of the anammox bacterium Candidatus ‘Kuenenia stuttgartiensis’ using time-series ¹³C and ²H isotope tracing, metabolomics, and isotopically nonstationary metabolic flux analysis. Our findings confirm predicted metabolic pathways used for CO₂ fixation, central metabolism, and amino acid biosynthesis in K. stuttgartiensis, and reveal several instances where genomic predictions are not supported by in vivo metabolic fluxes. This includes the use of the oxidative branch of an incomplete tricarboxylic acid cycle for alpha-ketoglutarate biosynthesis, despite the genome not having an annotated citrate synthase. We also demonstrate that K. stuttgartiensis is able to directly assimilate extracellular formate via the Wood–Ljungdahl pathway instead of oxidizing it completely to CO₂ followed by reassimilation. In contrast, our data suggest that K. stuttgartiensis is not capable of using acetate as a carbon or energy source in situ and that acetate oxidation occurred via the metabolicmore » activity of a low-abundance microorganism in the bioreactor’s side population. Together, these findings provide a foundation for understanding the carbon metabolism of anammox bacteria at a systems-level and will inform future studies aimed at elucidating factors governing their function and niche differentiation in natural and engineered ecosystems.« less

Authors:

Lawson, Christopher E.  ^[1];

• Search DOE PAGES for author "Lawson, Christopher E."
• Search DOE PAGES for ORCID "0000-0002-3473-1640"

Nuijten, Guylaine L. ^[2]; de Graaf, Rob M. ^[2]; Jacobson, Tyler B. ^[3]; Pabst, Martin ^[4]; Stevenson, David. M. ^[3]; Jetten, Mike S. M. ^[2]; Noguera, Daniel R.  ^[3];

• Search DOE PAGES for author "Noguera, Daniel R."
• Search DOE PAGES for ORCID "0000-0003-0372-3063"

McMahon, Katherine D. ^[1]; Amador-Noguez, Daniel  ^[3];

• Search DOE PAGES for author "Amador-Noguez, Daniel"
• Search DOE PAGES for ORCID "0000-0002-3568-3070"

Lücker, Sebastian  ^[2]

• Search DOE PAGES for author "Lücker, Sebastian"
• Search DOE PAGES for ORCID "0000-0003-2935-4454"

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+ Show Author Affiliations

1. Univ. of Wisconsin, Madison, WI (United States)
2. Radboud Univ., Nijmegen (Netherlands)
3. Univ. of Wisconsin, Madison, WI (United States); Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
4. Delft Univ. of Technology (Netherlands)

Publication Date:

Tue Oct 20 00:00:00 EDT 2020

Research Org.:

Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); Netherlands Organization for Scientific Research (NWO); European Research Council (ERC)

OSTI Identifier:

1804720

Grant/Contract Number:  

SC0018998; CBET-1435661; CBET-1803055; MCB-1518130; 016.Vidi.189.050; 024.002.002; 339880

Resource Type:

Accepted Manuscript

Journal Name:

The ISME Journal

Additional Journal Information:

Journal Volume: 15; Journal Issue: 3; Journal ID: ISSN 1751-7362

Publisher:

Nature Publishing Group

Country of Publication:

United States

Language:

English

Subject:

54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES