Heterotrophic nitrification – An eternal mystery in the nitrogen cycle

Despite the fact that heterotrophic nitrification was identified more than 100 years ago, the biochemistry of heterotrophic nitrifiers is poorly known and their contribution to nitrification in soil is still speculative. Heterotrophic nitrifiers need organic compounds as their energy source in contrast to the chemolithotrophic nitrifiers. Most of the potential pathways for nitrite/nitrate production by heterotrophs can be considered as secondary metabolism. Only nitrification and simultaneous denitrification by some heterotrophic bacteria is known to have connection to the energy metabolism. Evidently, the nitrification pathways of bacteria and fungi differ. Some heterotrophic bacteria oxidizing ammonia have ammonia monooxygenase (AMO), but there are also heterotrophic bacteria oxidizing ammonia without AMO. The structure of AMO of chemolithotrophic ammonia oxidizers and heterotrophs differs. AMO has not been found in nitrifying fungi. The conditions for heterotrophic nitrification in soil highly differ from those in waste waters where heterotrophic nitrification activity can be high. Heterotrophic nitrification in soil is limited by the low availability of easily decomposable organic substrates. Possible nitrification by heterotrophs in the rhizosphere and endophytic root microbes gaining a good supply of substrates from plants is not known. Fungi are of special interest in heterotrophic nitrification in soil because fungi can evidently nitrify not only easily decomposable substrates but also when decomposing recalcitrant organic compounds (like lignin) which are abundant in soil. Nitrite/nitrate production from easily decomposable nitrogenous organic compounds, such as amino acids, is common among heterotrophic bacteria and fungi. The general conclusion that heterotrophs use solely an “organic pathway” in their nitrification is, however, not valid because also ammonia can be oxidized. Owing to the diverse, poorly known biochemistry of heterotrophic nitrification and methodological difficulties to differentiate heterotrophic and chemolithotrophic nitrification in soil, the role of heterotrophic nitrification in soil nitrogen cycle remains uncertain.