A paradigm shift towards low-nitrifying production systems: the role of biological nitrification inhibition (BNI)

Abstract

Background: Agriculture is the single largest geo-engineering initiative that humans have initiated on planet Earth, largely through the introduction of unprecedented amounts of reactive nitrogen (N) into ecosystems. A major portion of this reactive N applied as fertilizer leaks into the environment in massive amounts, with cascading negative effects on ecosystem health and function. Natural ecosystems utilize many of the multiple pathways in the N cycle to regulate N flow. In contrast, the massive amounts of N currently applied to agricultural systems cycle primarily through the nitrification pathway, a single inefficient route that channels much of this reactive N into the environment. This is largely due to the rapid nitrifying soil environment of present-day agricultural systems.

Scope: In this Viewpoint paper, the importance of regulating nitrification as a strategy to minimize N leakage and to improve N-use efficiency (NUE) in agricultural systems is highlighted. The ability to suppress soil nitrification by the release of nitrification inhibitors from plant roots is termed 'biological nitrification inhibition' (BNI), an active plant-mediated natural function that can limit the amount of N cycling via the nitrification pathway. The development of a bioassay using luminescent Nitrosomonas to quantify nitrification inhibitory activity from roots has facilitated the characterization of BNI function. Release of BNIs from roots is a tightly regulated physiological process, with extensive genetic variability found in selected crops and pasture grasses. Here, the current status of understanding of the BNI function is reviewed using Brachiaria forage grasses, wheat and sorghum to illustrate how BNI function can be utilized for achieving low-nitrifying agricultural systems. A fundamental shift towards ammonium (NH4(+))-dominated agricultural systems could be achieved by using crops and pastures with high BNI capacities. When viewed from an agricultural and environmental perspective, the BNI function in plants could potentially have a large influence on biogeochemical cycling and closure of the N loop in crop-livestock systems.

Keywords: AMO; BNI; BNI capacity; HAO; Nitrosomonas; ammonia mono-oxygenase; biological nitrification inhibition; brachialactone; fatty acids; high-nitrifying production systems; hydroxylamine oxidoreductase; low-nitrifying production systems; nitrate leaching; nitrification; nitrous oxide emissions; sustainability; synthetic nitrification inhibitors.

Fig. 1.

The nitrogen cycle in a typical agricultural system (i.e. upland aerobic soil with neutral reaction) dominated by the nitrification pathway in which >95 % of the N flows through, and NO₃⁻ remains the major inorganic N form for absorption and assimilation by plants (adapted from Subbarao et al., 2012a).

Fig. 2.

Schematic representation of the biological nitrification inhibition (BNI) interfaces with the N cycle. The BNI exuded by the root inhibits nitrification that converts NH₄⁺ to NO₂⁻. In ecosystems with large amounts of BNI (e.g. brachialactone) such as Brachiaria grasses, the flow of nitrogen from NH₄⁺ to NO₃⁻ is restricted, and it is NH₄⁺ and microbial N rather than NO₃⁻ that accumulates in the soil and root systems. In systems with little or no BNI, such as modern agricultural systems, nitrification occurs at a rapid rate, converting NH₄⁺ to NO₃⁻, which is highly susceptible to loss by denitrification and leaching from the system (adapted from Subbarao et al., 2012a).

Fig. 3.

Map of recombinant luminous Nitrosomonas europaea (pHLUX20) developed to detect and quantify nitrification inhibitors in the plant–soil system (redrawn from Iizumi et al., 1998).

Fig. 4.

(A) Soil ammonium oxidation rates (mg of NO₂⁻ N kg⁻¹ soil d⁻¹) in field plots planted to tropical pasture grasses (differing in BNI capacity) and soybean (lacking BNI capacity in roots) [covering 3 years from establishment of pastures (September 2004–November 2007); for soybean, two planting seasons every year and after six seasons of cultivation]. CON, control (plant-free) plots; SOY, soybean; PM, P. maximum; BHM, Brachiaria hybrid ‘Mulato’; BH-679, B. humidicola CIAT 679 (standard cultivar); BH-16888, B. humidicola accession CIAT 16888 (a germplasm accession). Values are means ± s.e. of three replications (adapted from Subbarao et al., 2009a). (B) Cumulative N₂O emissions (mg of N₂O N m⁻² year⁻¹) from field plots of tropical pasture grasses (monitored monthly over a 3-year period, from September 2004 to November 2007). Values are means ± s.e. of three replications (adapted from Subbarao et al., 2009a).

Fig. 5.

Relationships of the BNI capacity of plant species to N₂O emissions from field plots (based on data from Fig. 4B). The N₂O emissions were monitored over a period of 3 years (adapted from Subbarao et al., 2012a; see Fig. 4 for abbreviations and treatment details).

Fig. 6.

(A) BNI activity released from B. humidicola roots during a 10 d period (adapted from Subbarao et al., 2007a). (B) The BNI activity in the root tissue (ATU g⁻¹ root d. wt) at the end of the 10 d root exudate collection (redrawn from Subbarao et al., 2007a).

Fig. 7.

Chemical structure of BNIs belonging to different chemical functional groups isolated from plant tissues or root exudates.

Fig. 8.

Chemical structure of linoleic acid and α-linolenic acid, the BNIs isolated from the aerial parts of B. humidicola.

Fig. 9.

Chemical structure of isothiocyanates (mostly found in crucifer tissues) that show BNI function (based on Fenwick et al., 1983; Bending and Lincoln, 2000).

Fig. 10.

Chemical structure of brachialactone, the major nitrification inhibitor isolated from root exudates of B. humidicola (from Subbarao et al., 2009a).

Fig. 11.

Inhibition of nitrification by brachialactone and the contribution of brachialactone to the BNI activity released from roots. (A) Inhibitory effect of brachialactone on N. europaea in an in vitro assay. (B) Contribution of brachialactone to the BNI activity released from roots (i.e. in root exudates) of B. humidicola. Root exudates were collected from intact plants using 1 L of aerated solution of 1 mm NH₄Cl with 200 µm CaCl₂ over 24 h. Each data point represents root exudates collected from hydroponically grown plants in a glasshouse during March–May of 2007 and 2008 (adapted from Subbarao et al., 2009a).

Fig. 12.

(A) Split-root system of B. humidicola. (B) Influence of nitrogen form (NH₄⁺ vs. NO₃⁻) in the exudate collection solutions on the release of BNI activity. (C) Release of brachialactone from the roots of B. humidicola in a split-root system (adapted from Subbarao et al., 2009a).

Fig. 13.

BNI activity released from roots of two cultivars of cultivated wheat and its wild relative L. racemosus. Plants were grown with either NH₄⁺ or NO₃⁻ as their N source. Root exudate was collected from intact roots in aerated distilled water with 200 µm Ca over a 24 h period. The vertical bar represents Fisher's l.s.d. (P < 0·001) for the interaction term (N source × species; adapted from Subbarao et al., 2007c).

Fig. 14.

Karyotype analysis of DALr#n, a chromosome addition line derived from L. racemosus × T. aestivum. (A) DAPI (4′,6-diamidino-2-phenylindole) staining revealed 44 chromosomes. (B) The probe of L. racemosus genomic DNA (green) and TaiI and Afa family repetitive sequences showed the presence of two Lr#n chromosomes. The arrows indicate Lr#n chromosomes (adapted from Subbarao et al., 2007c).