Acidotolerant soil nitrite oxidizer “ <i>Candidatus</i> Nitrobacter laanbroekii” NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidizers

<i>Nitrobacter</i> strain NHB1 is a nitrite-oxidizing bacterium previously demonstrated to form a consortium capable of nitrification under acidic conditions when cocultivated with a neutrophilic ammonia-oxidizing bacterium. Here, we characterize the growth of isolated NHB1 under different pH and nitrite (NO<sub>2</sub> <sup>-</sup>) concentrations, as well as its influence on the activity of obligately acidophilic soil ammonia-oxidizing archaea (AOA) isolated from acidic soils when grown in coculture. NHB1 is acidotolerant with optimal growth at pH 6.0 (range: 5.0-7.5) at an initial NO<sub>2</sub> <sup>-</sup> concentration of 500 μM. However, at lower NO<sub>2</sub> <sup>-</sup> concentrations, closer to those found in soil, its pH optimum decreases to 5.0 and with detectable growth extended to pH 3.5. In coculture, NHB1 enhances the growth of the acidophilic AOA <i>Nitrosotalea devaniterrae</i> Nd1 and <i>Nitrosotalea sinensis</i> Nd2, which are highly sensitive to NO<sub>2</sub> <sup>-</sup>derived compounds and typically oxidize only ~200 to 300 μM ammonia (NH<sub>3</sub>) when grown in batch cultures as isolates. However, in coculture with NHB1, both strains oxidized up to ~3 mM NH<sub>3</sub>, limited only by the buffering capacity of the medium, and their pH range was also extended downward by ~0.5 units. NHB1 also possesses a cyanase, enabling reciprocal cross-feeding through cyanate-derived NH<sub>3</sub> production while utilizing AOA-derived NO<sub>2</sub> <sup>-</sup>. These findings suggest that NO<sub>2</sub> <sup>-</sup> removal is essential for ammonia oxidizer growth in acidic soils and emphasize the importance of considering substrate and metabolic product concentrations when characterizing ecophysiology. Genome analysis reveals that NHB1 is distinct from validated species, and we propose the name <i>"Nitrobacter laanbroekii."</i>

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Journal
ISME Communications
Published
2025-12-21
DOI
https://doi.org/10.1093/ismeco/ycaf244
Primary Topic
Wastewater Treatment and Nitrogen Removal
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article
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article

Acidotolerant soil nitrite oxidizer “ Candidatus Nitrobacter laanbroekii” NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidizers

Holger Daims, Eleftheria Bachtsevani, James I. Prosser, Wietse de Boer et al.
ISME Communications
Wastewater Treatment and Nitrogen Removal
article

Acidotolerant soil nitrite oxidizer “ Candidatus Nitrobacter laanbroekii” NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidizers

Holger Daims, Eleftheria Bachtsevani, James I. Prosser, Wietse de Boer, Yiyu Meng, Linda Hink, Christopher J. Sedlacek, M. Wagner, Christina Hazard, Sungeun Lee, Graeme W Nicol, Cécile Gubry-Rangin
article en

Abstract

<i>Nitrobacter</i> strain NHB1 is a nitrite-oxidizing bacterium previously demonstrated to form a consortium capable of nitrification under acidic conditions when cocultivated with a neutrophilic ammonia-oxidizing bacterium. Here, we characterize the growth of isolated NHB1 under different pH and nitrite (NO<sub>2</sub> <sup>-</sup>) concentrations, as well as its influence on the activity of obligately acidophilic soil ammonia-oxidizing archaea (AOA) isolated from acidic soils when grown in coculture. NHB1 is acidotolerant with optimal growth at pH 6.0 (range: 5.0-7.5) at an initial NO<sub>2</sub> <sup>-</sup> concentration of 500 μM. However, at lower NO<sub>2</sub> <sup>-</sup> concentrations, closer to those found in soil, its pH optimum decreases to 5.0 and with detectable growth extended to pH 3.5. In coculture, NHB1 enhances the growth of the acidophilic AOA <i>Nitrosotalea devaniterrae</i> Nd1 and <i>Nitrosotalea sinensis</i> Nd2, which are highly sensitive to NO<sub>2</sub> <sup>-</sup>derived compounds and typically oxidize only ~200 to 300 μM ammonia (NH<sub>3</sub>) when grown in batch cultures as isolates. However, in coculture with NHB1, both strains oxidized up to ~3 mM NH<sub>3</sub>, limited only by the buffering capacity of the medium, and their pH range was also extended downward by ~0.5 units. NHB1 also possesses a cyanase, enabling reciprocal cross-feeding through cyanate-derived NH<sub>3</sub> production while utilizing AOA-derived NO<sub>2</sub> <sup>-</sup>. These findings suggest that NO<sub>2</sub> <sup>-</sup> removal is essential for ammonia oxidizer growth in acidic soils and emphasize the importance of considering substrate and metabolic product concentrations when characterizing ecophysiology. Genome analysis reveals that NHB1 is distinct from validated species, and we propose the name <i>"Nitrobacter laanbroekii."</i>

ISME CommunicationsVol. 6(1)
Université Claude Bernard Lyon 1 (FR), Leibniz University Hannover (DE), University of Southern Indiana (US), Centre National de la Recherche Scientifique (FR), University of Vienna (AT), University of Aberdeen (GB), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), VetAgro Sup (FR)
European Commission, Agence Nationale de la Recherche, Institut National de la Santé et de la Recherche Médicale, AXA Research Fund, Hebrew University of Jerusalem, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1
Life in Land
Openalex Percentile: Top 50%
Wastewater Treatment and Nitrogen Removal
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