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

研究背景农业产量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，但目前氮肥的效率可能很低，高达50%的氮肥流失到环境中。这些损失大部分是通过微生物的硝化作用和硝酸盐淋洗作用发生的。减少这些过程是提高农业可持续性的关键。土壤硝化作用可以通过化学(合成)和生物(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作用BNI，这种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来抑制氨氧化古生菌和氨氧化细菌硝化菌。植物BNI效率在一些热带牧草中首次被证明。从那时起，它已经在广泛的植物中被发现，包括大量种植的农作物，如水稻。虽然已经鉴定出少量的水稻根部BNI化合物，这些化合物来自有限的几个基因型，虽然在水稻中已经确定了BNI效率的基因变异，但这种变异的遗传基础尚不清楚。这项多学科研究的总体目标是通过了解驯化水稻和野生水稻生物硝化抑制(BNI)效率自然变异的本质，来研究水稻的生物硝化抑制效率。这将通过基因图谱和功能基因组学(以确定提高BNI效率的关键基因)进行，对水稻产生的BNI化合物进行表征，评估BNI变化对土壤微生物群落和过程的影响，并利用模拟来评估提高水稻BNI效率对土壤一氧化二氮排放的影响。研究目的1)描述水稻BNI效率在生长季节中如何变化，以及栽培水管理决策如何影响水稻BNI效率。2)确定影响驯化水稻BNI效率的基因组座位和自然变异基因。3)评估野生稻的BNI效率，以确定BNI效率在野生水稻亲缘关系中是否更高，确定具有BNI特性的材料用于育种，并与普通野生稻物种进行GWA作图。4)确定BNI化合物及其对微生物群落的影响。5)扩大观察影响，模拟BNI效率对N2O排放的影响在国家一级的潜在应用和好处BNI效率高的基因型有可能减缓氨(NH4+)到硝酸盐(NN3-)的硝化作用。由于植物可以同时利用NH4+和NO3-作为氮源，减少硝化作用不会减少植物的氮素利用率。然而，由于NO3-在土壤环境中的流动性比NH4+大得多，因此很容易渗入地下水。此外，好氧硝化作用通过各种过程产生N2O，在适当的条件下，硝化菌还可以通过反硝化过程将N3-转化为N2O，N2O是一种强有力的温室气体。因此，如果能以更高的BNI效率培育植物，就有可能减少N3-淋失，减少土壤中N2O的排放，并减少氮肥的使用量(因为它在土壤中对植物的利用时间更长)。使用系统模型来评估高效BNI基因对温室气体排放的影响，将促进优先培育针对特定气候、土壤和管理情景的BNI高效育种。

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.