Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers

Abstract

The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4+-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4+, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.

Uncovering the Research Gaps to Alleviate the Negative Impacts of Climate Change on Food Security: A Review

“…For example, alternate wetting and drying system for irrigation and eco-efficient fertilizer managements (green manuring, organic manures) can be adopted as agronomic adaptations to reduce water and nutrient losses, thereby increasing resource use-efficiency with increased yield. Aerobic rice can be an eco-efficient transformation to traditional rice system ( Farooq et al, 2022 ) to sustain the rice production with increased input use-efficiencies under future projected climate change and scarcity of resources ( Fukai and Mitchell, 2022 ).…”

Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system

“…Multiple chemical and biochemical pathways along with environmental variables impact the complex trait of NUE ( Farooq et al, 2022a ). Different agricultural major research wings define NUE differently, such as plant physiologists take into account various steps during N management, that is, N uptake, N assimilation, N allocation, and N remobilization, more obviously during leaf senescence ( Sandhu et al, 2021 ).…”

“… Understanding the N dynamics and overviewing the pathways of the N cycle under the aerobic rice system ( Farooq et al, 2022a ). …”

“…Ammonification is the process of N mineralization where the reduced form of organic N (NH 2 ) is converted into gaseous NH 3 or reduced inorganic form (NH 4 + ) as the end product, as discussed in the previous sections ( Farooq et al, 2022a ). Many species of ammonia oxidizers are involved in this biochemical reaction, such as bacteria (AOB) and archaea (AOA), to obtain the required energy for their metabolism via oxidation of organic N to NH 4 + .…”

“…Inefficient, excessive, and uncontrolled incorporation of N fertilizers subsequently produces enhanced crop yield, however, by compromising the economic and atmospheric concerns. To make the future inflating population more food secure, it is necessary to make the food production systems more sustainable with no harm to atmospheric sustainability ( Farooq et al, 2022b ), which can only be possible through an urgent upgradation to increase NUE in the agriculture sector ( Farooq et al, 2022a ). Poor plant population, traditional incorporation methods, and uncontrolled excessive application usually increase the N losses, ultimately posing environmental threats ( Mahmud et al, 2021 ).…”