Ecological perspectives on microbes involved in N-cycling

Abstract

Nitrogen (N) cycles have been directly linked to the functional stability of ecosystems because N is an essential element for life. Furthermore, the supply of N to organisms regulates primary productivity in many natural ecosystems. Microbial communities have been shown to significantly contribute to N cycles because many N-cycling processes are microbially mediated. Only particular groups of microbes were implicated in N-cycling processes, such as nitrogen fixation, nitrification, and denitrification, until a few decades ago. However, recent advances in high-throughput sequencing technologies and sophisticated isolation techniques have enabled microbiologists to discover that N-cycling microbes are unexpectedly diverse in their functions and phylogenies. Therefore, elucidating the link between biogeochemical N-cycling processes and microbial community dynamics can provide a more mechanistic understanding of N cycles than the direct observation of N dynamics. In this review, we summarized recent findings that characterized the microbes governing novel N-cycling processes. We also discussed the ecological role of N-cycling microbial community dynamics, which is essential for advancing our understanding of the functional stability of ecosystems.

Fig. 1

Schematic representation highlighting the main processes in the microbial N cycle, with a focus on (A, gray) the classical processes and (B, black) recently discovered processes discussed in the text. Processes mainly occurring under oxic and anoxic conditions are shown as solid and dashed arrows, respectively. Detailed reactions of recently discovered processes are described in Table 1. Note: denitrification (A), denitrification coupled to the oxidation of organic matter, hydrogen, reduced iron, or reduced sulfur species; nitrite oxidation (A), aerobic chemolithotrophic nitrite oxidation; N₂ fixation(B), N₂ fixation by unicellular cyanobacteria; N₂O reduction (B), N₂O reduction by non-denitrifying bacteria. Abbreviations: DON, dissolved organic N; DNRA, dissimilatory nitrate reduction to ammonia.

Fig. 2

Representative reactions that have been confirmed with bacterial isolates of nitrate reduction to N₂ or NH₃ coupled with the oxidation of reductants ranging from organic carbon to Fe (II) along the redox tower.

Fig. 3

Schematic outline of N flows and microbial involvements at the ecosystem level, as discussed in this review. (1) bioavailable N is microbially supplied through the mineralization of organic N including microbe-derived N, (2) supplied bioavailable N is dissimilatorily transformed in the redox reaction with other oxidants/reductants to yield energy, and (3) the storage of N in an ecosystem through microbial N assimilation using this energy contributes to the stability of the ecosystem. A: depolymerization; B: ammonification.