Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification

Abstract

Microorganisms play important roles in the nitrogen cycles of various ecosystems. Research has revealed that a greater diversity of microorganisms is involved in the nitrogen cycle than previously understood. It is becoming clear that denitrifying fungi, nitrifying archaea, anammox bacteria, aerobic denitrifying bacteria and heterotrophic nitrifying microorganisms are key players in the nitrogen cycle. Studies have revealed a major contribution by fungi in the production of N2O and N2 in grasslands, semiarid regions and forest soils. Some fungi can grow under various O2 conditions by using three types of energy-yielding metabolism: O2 respiration, denitrification (nitrite respiration) and ammonia fermentation. The amoA-like gene copies of Crenarchaeota were shown to be more abundant in soils than in autotrophic ammonia-oxidizing bacteria, and the gene was expressed at higher levels in soil to which ammonia was added. There are some contradictory findings, however, regarding archaeal and bacterial nitrification. Anammox bacteria have been shown to be widely distributed and to play an important role in both artificial and natural environments. The contribution of heterotrophic microorganisms to nitrification has been recognized in soil, and the biochemical mechanisms of several bacteria are becoming clear. A wide variety of bacteria have been found to be able to carry out aerobic denitrification and to be distributed across diverse environments. Using molecular biological techniques for soil bacteria, Nitrosospira species of clusters 2, 3 and 4 have been shown to be the dominant group in soils. Genome analyses of autotrophic nitrifying bacteria are providing new insights into their ecology and functions in soils.