Title
Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia
Author
Sorokin, Dimitry Y. (TU Delft BT/Environmental Biotechnology; Russian Academy of Sciences) 
Tikhonova, Tamara V. (Russian Academy of Sciences)
Koch, Hanna (Radboud Universiteit Nijmegen)
van den Berg, E.M. (TU Delft BT/Industriele Microbiologie)
Hinderks, Renske S. (Student TU Delft)
Pabst, Martin (TU Delft BT/Environmental Biotechnology)
Kuenen, J.G. (TU Delft BT/Environmental Biotechnology)
van Loosdrecht, Mark C.M. (TU Delft BT/Environmental Biotechnology)
Lücker, Sebastian (Radboud Universiteit Nijmegen)
Date
2023
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H2 can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.
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DOI
https://doi.org/10.1038/s41396-023-01473-2
Embargo date
2024-01-14
ISSN
1751-7362
Source
The ISME Journal: multidisciplinary journal of microbial ecology, 17 (10), 1639-1648
Bibliographical note
Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.
Part of collection
Institutional Repository
Document type
journal article
Rights
© 2023 Dimitry Y. Sorokin, Tamara V. Tikhonova, Hanna Koch, E.M. van den Berg, Renske S. Hinderks, Martin Pabst, J.G. Kuenen, Mark C.M. van Loosdrecht, Sebastian Lücker, More Authors