Multi-level exploration of biological nitrification inhibition in rice for improved sustainability of crop production

研究背景农业产出目前依赖于合成氮肥的使用。然而，尽管氮肥的使用对实现粮食安全目标至关重要，但目前氮肥的使用效率可能很低，施用的氮有高达50%流失到环境中。这种损失大部分是通过微生物硝化作用和硝酸盐浸出发生的。减少这些过程对于提高农业的可持续性至关重要。土壤硝化可以通过化学（合成）和生物（基于植物）过程来抑制，后者被称为生物硝化抑制（BNI）。一系列作物和草通过分泌特定的根分泌物化合物来进行化感BNI，这些化合物通过阻断氨单加氧酶或羟胺氧化还原酶或通过其他途径抑制氨氧化古菌和氨氧化细菌的硝化物。植物BNI效率首先在一些热带牧草中得到证实。从那时起，它已经在广泛的植物中出现，包括水稻等大量种植的作物。虽然已经鉴定出少量水稻根BNI化合物，但这些化合物来自有限的基因型，虽然已经确定了水稻中BNI效率的基因型变异，但这种变异的遗传基础尚不清楚。此外，育种高BNI高效基因型的潜在影响尚未得到探讨。研究目的：通过了解驯化稻和野生稻生物硝化抑制（BNI）效率自然变异的性质，研究水稻生物硝化抑制（BNI）效率。这将通过遗传作图和功能基因组学（识别与提高BNI效率有关的关键基因）、描述水稻产生的BNI化合物的特征、评估BNI变化对土壤微生物群落和过程的影响，以及使用模型来评估提高水稻BNI效率对土壤氧化亚氮排放的影响。研究目标1)描述水稻生长季节BNI效率的变化特征，以及栽培用水管理决策对水稻BNI效率的影响。2)鉴定驯化水稻（Oryza sativa） BNI效率自然变异的基因组位点和基因。3)评价野生稻品种的BNI效率，确定野生近缘稻品种的BNI效率是否更高，确定具有BNI性状的品种用于育种，并对O. rufipogon进行GWA定位。4)鉴定BNI化合物及其对微生物群落的影响。5)扩大观察到的影响，模拟在国家层面上BNI效率对N2O排放的影响。潜在的应用和效益BNI效率高的基因型有可能减缓铵态氮（NH4+）向硝态氮（NO3-）的硝化作用。由于植物可以同时利用NH4+和NO3-作为氮源，因此减少硝化作用不会降低植物的氮可利用性。然而，NO3-很容易渗入地下水，因为它在土壤环境中比NH4+更具流动性。此外，好氧硝化通过各种过程产生N2O，在适当的条件下，硝化器还可以通过反硝化过程将NO3-转化为N2O，而N2O是一种强效温室气体。因此，如果培育出具有更高BNI效率的植物，就有可能减少NO3-淋失，减少土壤中N2O的排放，并减少氮肥的使用量（因为氮肥在土壤中对植物有效的时间更长）。利用系统建模来评估高BNI效率基因型对温室气体排放的影响，将促进针对特定气候、地理和管理情景的高BNI效率育种的优先次序。

Context of the researchAgricultural output is currently dependent on the use of synthetic nitrogen fertilisers. However, while the use of nitrogen fertilisers is essential to meet food security targets, the current efficiency of nitrogen fertilisers can be low, with up to 50% of applied nitrogen lost to the environment. Most of this loss happens through microbial-based nitrification and nitrate leaching. Reducing these processes is essential to improving agricultural sustainability.Soil nitrification can be inhibited through both chemical (synthetic) and biological (plant-based) processes, and the latter being termed Biological Nitrification Inhibition (BNI). A range of crops and grasses perform allelopathic BNI through secretion of specific root exudate compounds, which inhibit ammonia oxidising archaea and ammonia oxidising bacteria nitrifiers by blocking either the ammonia monooxygenase or hydroxylamine oxidoreductase, or through other pathways. Plant BNI efficiency was first demonstrated in some tropical pasture grasses. Since then, it has been shown in a wide range of plants, including heavily cultivated crops such as rice.While a small number of rice root BNI compounds have been identified, these are from a limited number of genotypes, and while genotypic variation for BNI efficiency has been determined in rice, the genetic basis of this variation is unknown. Additionally, the potential impact of breeding for high BNI efficient genotypes has not been explored.Research aimsThe overall aim of this multi-disciplinary proposal is to investigate biological nitrification inhibition (BNI) efficiency in rice, by understanding the nature of natural variation in BNI efficiency of both domesticated and wild rice. This will be conducted through genetic mapping and functional genomics (to identify key genes involved in increasing BNI efficiency), characterising BNI compounds produced by rice, evaluating the impact of variation in BNI on soil microbial communities and processes and the use of modelling to evaluate the impact of increasing BNI efficiency in rice on nitrous oxide emissions from soil. Research Objectives1) Characterise how BNI efficiency changes during the growing season and how cultivation water management decisions impact rice BNI efficiency. 2) Identify genomic loci and genes for natural variation for BNI efficiency in domesticated rice (Oryza sativa). 3) Evaluate BNI efficiency of wild rice accessions to identify if BNI efficiency is greater in wild rice relatives, identify accessions with BNI traits to be used in breeding, and to conduct GWA mapping with the O. rufipogon species.4) Identify BNI compounds and their influence on microbial communities.5) Scale up the observed impacts to model the impact of BNI efficiency on N2O emissions at the country level Potential applications and benefitsGenotypes with high BNI efficiency have the potential to slow down the nitrification of ammonium (NH4+) to nitrate (NO3-). As plants can utilise both NH4+ and NO3- as a nitrogen source, reducing the nitrification will not reduce nitrogen availability for plants. However, NO3- can easily leach into groundwater as it is much more mobile in the soil environment than NH4+. Additionally aerobic nitrification generates N2O through various processes, and under the right conditions nitrifiers can also convert NO3- into N2O via the denitrification process, with N2O being a potent greenhouse gas. Therefore, if plants could be bred with increased BNI efficiency there is the potential to decrease NO3- leaching, reduce N2O emissions from soil, and reduce the amount of nitrogen fertiliser used (as it will be available in the soils longer for the plants). The use of systems modelling to evaluate the impact of high BNI efficient genotypes on greenhouse gas emissions, will promote for the prioritisation of breeding for high BNI efficiency targeting specific climatic, edaphic and management scenarios.