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

TL;DR

A nitrite-oxidizing bacterium helps acid-loving soil microbes grow better by removing harmful compounds under acidic conditions.

Contribution

Discovery of a novel acidotolerant nitrite oxidizer that enhances ammonia oxidizer growth in acidic soils through metabolic interactions.

Findings

NHB1 grows optimally at pH 6.0 but extends to pH 3.5 at low nitrite concentrations.

Coculture with NHB1 allows acidophilic AOA to oxidize up to ~3 mM ammonia.

NHB1's cyanase enables cross-feeding with AOA via cyanate-derived ammonia.

Abstract

Nitrobacter 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 (NO2−) 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 NO2− concentration of 500 μM. However, at lower NO2− 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 Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2, which are highly sensitive to NO2-derived compounds and typically oxidize only ~200 to 300 μM ammonia (NH3) when grown in batch cultures as isolates. However, in coculture with NHB1, both strains oxidized up to ~3 mM NH3, 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 NH3 production while utilizing AOA-derived NO2−. These findings suggest that NO2− 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 “Nitrobacter laanbroekii.”

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