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Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification

Hemp, James and Lücker, Sebastian and Schott, Joachim and Pace, Laura A. and Johnson, Jena E. and Schink, Bernhard and Daims, Holger and Fischer, Woodward W. (2016) Genomics of a phototrophic nitrite oxidizer: insights into the evolution of photosynthesis and nitrification. ISME Journal, 10 (11). pp. 2669-2678. ISSN 1751-7362. PMCID PMC5113846. doi:10.1038/ismej.2016.56.

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Oxygenic photosynthesis evolved from anoxygenic ancestors before the rise of oxygen ~2.32 billion years ago; however, little is known about this transition. A high redox potential reaction center is a prerequisite for the evolution of the water-oxidizing complex of photosystem II. Therefore, it is likely that high-potential phototrophy originally evolved to oxidize alternative electron donors that utilized simpler redox chemistry, such as nitrite or Mn. To determine whether nitrite could have had a role in the transition to high-potential phototrophy, we sequenced and analyzed the genome of Thiocapsa KS1, a Gammaproteobacteria capable of anoxygenic phototrophic nitrite oxidation. The genome revealed a high metabolic flexibility, which likely allows Thiocapsa KS1 to colonize a great variety of habitats and to persist under fluctuating environmental conditions. We demonstrate that Thiocapsa KS1 does not utilize a high-potential reaction center for phototrophic nitrite oxidation, which suggests that this type of phototrophic nitrite oxidation did not drive the evolution of high-potential phototrophy. In addition, phylogenetic and biochemical analyses of the nitrite oxidoreductase (NXR) from Thiocapsa KS1 illuminate a complex evolutionary history of nitrite oxidation. Our results indicate that the NXR in Thiocapsa originates from a different nitrate reductase clade than the NXRs in chemolithotrophic nitrite oxidizers, suggesting that multiple evolutionary trajectories led to modern nitrite-oxidizing bacteria.

Item Type:Article
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URLURL TypeDescription CentralArticle ReadCube access
Hemp, James0000-0001-7193-0553
Lücker, Sebastian0000-0003-2935-4454
Pace, Laura A.0000-0002-3311-8342
Johnson, Jena E.0000-0001-8842-100X
Daims, Holger0000-0002-4195-0913
Fischer, Woodward W.0000-0002-8836-3054
Additional Information:© 2016 International Society for Microbial Ecology. Received 18 June 2015; revised 24 February 2016; accepted 4 March 2016; Advance online publication 19 April 2016. We are grateful to LABGeM and the National Infrastructure ‘France Genomique’ for annotation support within the MicroScope platform. Support for this work was provided by the Caltech Center for Environmental Microbial Interactions (WWF), the David and Lucile Packard Foundation (WWF), the National Science Foundation Graduate Research Fellowship program (JEJ), the Austrian Science Fund (FWF, grant P24101-B22), the Radboud Excellence Initiative and the Netherlands Organization for Scientific Research (NWO, VENI grand 863.14.019 to SL), the Deutsche Forschungsgemeinschaft, Bonn, Germany, grant Schi 180/12 (BS) and the Agouron Institute (JH and WWF). JH is an Agouron Postdoctoral Scholar. The authors declare no conflict of interest.
Group:Caltech Center for Environmental Microbial Interactions (CEMI)
Funding AgencyGrant Number
Caltech Center for Environmental Microbial Interactions (CEMI)UNSPECIFIED
David and Lucile Packard FoundationUNSPECIFIED
NSF Graduate Research FellowshipUNSPECIFIED
FWF Der WissenschaftsfondsP24101-B22
Radboud Excellence InitiativeUNSPECIFIED
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)863.14.019
Deutsche Forschungsgemeinschaft (DFG)Schi 180/12
Agouron InstituteUNSPECIFIED
Issue or Number:11
PubMed Central ID:PMC5113846
Record Number:CaltechAUTHORS:20160425-075949394
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66434
Deposited By: Tony Diaz
Deposited On:02 May 2016 23:04
Last Modified:28 Apr 2022 18:07

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