In this review, we present the recent developments and future prospects of improving nitrogen use efficiency (NUE) in crops using various complementary approaches. These include conventional breeding and molecular genetics, in addition to alternative farming techniques based on no-till continuous cover cropping cultures and/or organic nitrogen (N) nutrition. Whatever the mode of N fertilization, an increased knowledge of the mechanisms controlling plant N economy is essential for improving NUE and for reducing excessive input of fertilizers, while maintaining an acceptable yield and sufficient profit margin for the farmers. Using plants grown under agronomic conditions, with different tillage conditions, in pure or associated cultures, at low and high N mineral fertilizer input, or using organic fertilization, it is now possible to develop further whole plant agronomic and physiological studies. These can be combined with gene, protein and metabolite profiling to build up a comprehensive picture depicting the different steps of N uptake, assimilation and recycling to produce either biomass in vegetative organs or proteins in storage organs. We provide a critical overview as to how our understanding of the agro-ecophysiological, physiological and molecular controls of N assimilation in crops, under varying environmental conditions, has been improved. We have used combined approaches, based on agronomic studies, whole plant physiology, quantitative genetics, forward and reverse genetics and the emerging systems biology. Long-term sustainability may require a gradual transition from synthetic N inputs to legume-based crop rotation, including continuous cover cropping systems, where these may be possible in certain areas of the world, depending on climatic conditions. Current knowledge and prospects for future agronomic development and application for breeding crops adapted to lower mineral fertilizer input and to alternative farming techniques are explored, whilst taking into account the constraints of both the current world economic situation and the environment.

The role of NADH-dependent glutamate dehydrogenase (GDH) was investigated by studying the physiological impact of a complete lack of enzyme activity in an Arabidopsis thaliana plant deficient in three genes encoding the enzyme. This study was conducted following the discovery that a third GDH gene is expressed in the mitochondria of the root companion cells, where all three active GDH enzyme proteins were shown to be present. A gdh1-2-3 triple mutant was constructed and exhibited major differences from the wild type in gene transcription and metabolite concentrations, and these differences appeared to originate in the roots. By placing the gdh triple mutant under continuous darkness for several days and comparing it to the wild type, the evidence strongly suggested that the main physiological function of NADH-GDH is to provide 2-oxoglutarate for the tricarboxylic acid cycle. The differences in key metabolites of the tricarboxylic acid cycle in the triple mutant versus the wild type indicated that, through metabolic processes operating mainly in roots, there was a strong impact on amino acid accumulation, in particular alanine, γ-aminobutyrate, and aspartate in both roots and leaves. These results are discussed in relation to the possible signaling and physiological functions of the enzyme at the interface of carbon and nitrogen metabolism.

Current agricultural practices rely heavily on synthetic fertilizers, which not only consume a lot of energy but also disrupt the ecological balance. The overuse of synthetic fertilizers has led to soil degradation. In a more sustainable approach, alternative methods based on biological interactions, such as plant growth-promoting bacteria (PGPRs), are being explored. PGPRs, which include both symbiotic and free-living bacteria, form mutualistic relationships with plants by enhancing nutrient availability, producing growth regulators, and regulating stress responses. This study investigated the potential of Sphingomonas sediminicola Dae20, an α-Proteobacteria species commonly found in the rhizosphere, as a beneficial PGPR. We observed that S. sediminicola Dae20 stimulated the root system and growth of three different plant species in the Brassicaceae family, including Arabidopsis thaliana, mustard, and rapeseed. The bacterium produced auxin, nitric oxide, siderophores and showed ACC deaminase activity. In addition to activating an auxin response in the plant, S. sediminicola Dae20 exhibited the ability to modulate other plant hormones, such as abscisic acid, jasmonic acid and salicylic acid, which are critical for plant development and defense responses. This study highlights the multifunctional properties of S. sediminicola Dae20 as a promising PGPR and underscores the importance of identifying effective and versatile beneficial bacteria to improve plant nutrition and promote sustainable agricultural practices.

The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.

The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR Paenibacillus sp. strain B2 (PB2), PB2 in co-inoculation with Arthrobacter agilis 4042 (Mix 2), or with Arthrobacter sp. SSM-004 and Microbacterium sp. SSM-001 (Mix 3). Inoculation of PB2, Mix 2, and Mix 3 into non-sterile field soil had a positive effect on root and aboveground dry biomass, depending on the wheat cultivar. The efficiency of the PGPR was further confirmed by the protection they provided against Mycosphaerella graminicola, the causal agent of Septoria leaf blotch disease. PB2 exhibited protection of ≥37.8%, while Mix 2 showed ≥47.9% protection in the four cultivars tested. These results suggest that the interactions between PGPR and native soil microbial communities are crucial for promoting wheat growth and protection. Additionally, high-throughput sequencing of microbial communities conducted 7 days after PGPR inoculations revealed no negative effects of PB2, Mix 2, and Mix 3 on the soil microbial community structure. Interestingly, the presence of Arthrobacter spp. appeared to mitigate the potential negative effect of PB2 on bacterial community and foster root colonization by other beneficial bacterial strains.

A field study was conducted in northern France over two consecutive years to evaluate the combined effect of conventional tillage (CT) vs no till (NT) with or without cover crops (cc) and nitrogen (N) fertilization on various agronomic traits related to N use efficiency in winter wheat. Five years after conversion of CT to NT, significant increases in N use efficiency, N utilization efficiency, N agronomic efficiency, N partial factor productivity, N apparent recovery fraction and N remobilization were observed under three N fertilization regimes (0, 161, 215 kg ha⁻¹). It was also observed that grain yield and grain N content were similar under CT and NT. The N nutrition index was higher under NT at the three rates of N fertilization. Moreover, N use efficiency related traits were increased in the presence of cc both under NT and CT. Thus, agronomic practices based on continuous NT in the presence of cc, appear to be promising strategies to increase N use efficiency in wheat, while reducing both the use and the loss of N-based fertilizers.