• Altmetrics
  • Sign-up for PNAS eTOC Alerts

Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway

  1. John D. Coatesa,2
  1. aDepartment of Plant and Microbial Biology, University of California, Berkeley, CA 94720
  1. Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved November 2, 2017 (received for review September 5, 2017)


Phosphite (HPO32?) is the most energetically favorable biological electron donor known, but only one organism capable of growing by phosphite oxidation has been previously identified. Here, we describe a phosphite-oxidizing bacterium that can grow with CO2 as its sole electron acceptor, and we propose a metabolic model in which inorganic carbon is assimilated via the reductive glycine pathway. Although the reductive glycine pathway has previously been identified as a “synthetic” carbon fixation pathway, this study provides evidence that it may actually function as a natural autotrophic pathway. Our results suggest that phosphite may serve as a driver of microbial growth and carbon fixation in energy-limited environments, particularly in aphotic environments lacking alternative terminal electron acceptors.


Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO32?) is oxidized to phosphate (PO43?), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax (Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria, which has no known cultured isolates. Genes for phosphite oxidation and for CO2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway.


  • ?1Present address: Institute for Microbiology, ETH Zürich, Zürich, Switzerland.

  • ?2To whom correspondence should be addressed. Email: jdcoates{at}berkeley.edu.
  • Author contributions: I.A.F. and J.D.C. designed research; I.A.F. and P.Y.S. performed research; T.P.B., C.I.C., and A.L.E. contributed new reagents/analytic tools; I.A.F. and J.D.C. analyzed data; and I.A.F., T.P.B., A.L.E., and J.D.C. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • Data deposition: The full 16S rRNA gene sequence of Ca. Phosphitivorax anaerolimi Phox-21 has been deposited in the GenBank (GB) database (accession no. KU898264). MiSeq reads from community 16S rRNA gene amplicon sequencing have been deposited in the National Center for Biotechnology Information Sequence Read Archive (accession no. SRP071909). The combined metagenomic assembly of all four enrichment community samples has been deposited in the Integrated Microbial Genomes (IMG) database (accession no. Ga0100964). Individual genomes recovered from the combined assembly are available in the IMG and GB databases under the following accession nos.: Ca. Phosphitivorax anaerolimi Phox-21, Ga0115057 (IMG), MPOS00000000 (GB); Tepidanaerobacter sp. EBM-38, Ga0115060 (IMG), MPOT00000000 (GB); unclassified bacterium EBM-40, Ga0115061 (IMG), MPOU00000000 (GB); Proteiniphilum sp. EBM-39, Ga0115062 (IMG), MPOV00000000 (GB); Thermotogales bacterium EBM-19, Ga0115064 (IMG), MPOW00000000 (GB); Proteiniphilum sp. EBM-41, Ga0115065 (IMG), MPOX00000000 (GB); Methanoculleus sp. EBM-46, Ga0115067 (IMG), MPOY00000000 (GB); Coprothermobacter sp. EBM-25, Ga0115069 (IMG), MPOZ00000000 (GB); Methanococcoides sp. EBM-47, Ga0115071 (IMG), MPPA00000000 (GB); Spirochaeta sp. EBM-43, Ga0115073 (IMG), MPPB00000000 (GB); Aminobacterium sp. EBM-42, Ga0115070 (IMG), MPPC00000000 (GB); Thermotogales bacterium EBM-38, Ga0115076 (IMG), MPPD00000000 (GB); Tepidanaerobacter sp. EBM-49, Ga0115075 (IMG), MPPE00000000 (GB).

  • This article contains supporting information online at www.danielhellerman.com/lookup/suppl/doi:10.1073/pnas.1715549114/-/DCSupplemental.

Published under the PNAS license.

Online Impact

                          1. 8479981288 2018-02-19
                          2. 4088241287 2018-02-19
                          3. 6348191286 2018-02-19
                          4. 4338491285 2018-02-19
                          5. 2501641284 2018-02-19
                          6. 2783851283 2018-02-19
                          7. 6592651282 2018-02-19
                          8. 1195271281 2018-02-19
                          9. 4085021280 2018-02-19
                          10. 5744491279 2018-02-19
                          11. 436941278 2018-02-19
                          12. 9816021277 2018-02-19
                          13. 82451276 2018-02-19
                          14. 8189251275 2018-02-18
                          15. 6298941274 2018-02-18
                          16. 8345181273 2018-02-18
                          17. 207841272 2018-02-18
                          18. 2683681271 2018-02-18
                          19. 5067491270 2018-02-18
                          20. 2051721269 2018-02-18