Emerging crops and plant growth-promoting bacteria (PGPB): a synergistic approach to climate-resilient agriculture

(2025) 13:228 Pérez‑Montaño et al. Microbiome https://doi.org/10.1186/s40168-025-02225-4 Microbiome Open Access REVIEW Emerging crops and plant growth‑promoting bacteria (PGPB): a synergistic approach to climate‑resilient agriculture Francisco Pérez‑Montaño1*†, Nieves Aparicio2†, Francisco Arenas3†, Jose M. Arjona2†, María Camacho4†, Nieves Fernández‑García5†, Paula García‑Fraile6†, Nieves Goicoechea7†, Sandra Macías‑Naranjo2,8,9†, Javier Matías10†, María del Carmen Montero‑Calasanz4†, Asunción Morte3†, Enrique Olmos5†, José J. Pueyo11†, Miguel A. Quiñones11†, Luis Rey12,13† and María Reguera14*† Abstract This review highlights the benefits of mutualistic plant–microbe interactions in enhancing the resilience of emergent crops and underlies the potential of these crops as valuable resources for exploring novel plant growth-promoting bacteria (PGPB). Emergent crops such as quinoa, amaranth, millet, lupins, hemp and desert truffles exhibit physiological and ecological traits that make them suitable for stress-prone environments. PGPB offer sustainable solutions to mitigate abiotic stress by improving nutrient availability, modulating phytohormone levels, enhancing root development and inducing systemic resistance. While their benefits have been extensively documented in model crops under controlled conditions, their application in emergent crops remains underexplored. This review examines current knowledge on the individual and combined roles of these crops and microbes, highlighting specific examples where PGPB have improved plant performance, yield and stress tolerance. Microbial inoculants show potential not only to boost productivity but also to reduce agrochemical inputs, contributing to sustainability. The review also discusses the need for tailored microbial formulations and effective field application strategies to bridge the gap between experimental research and real-world agricultural practices. Identifying key knowledge gaps, it emphasizes the importance of further research on strain specificity, crop-microbe interactions and multi-strain consortia for scalable and climate-smart agriculture. Ultimately, harnessing the synergisms between PGPB with emergent crops could convert marginal lands into productive, climate-smart farms, increasing food security in the face of environmental challenges posed by global climate change. † Francisco Pérez-Montaño, Nieves Aparicio, Francisco Arenas, Jose M. Arjona, María Camacho, Nieves Fernández-García, Paula García-Fraile, Nieves Goicoechea, Sandra Macías-Naranjo, Javier Matías, María del Carmen Montero-Calasanz, Asunción Morte, Enrique Olmos, José J. Pueyo, Miguel A. Quiñones, Luis Rey and María Reguera contributed equally to this work on behalf of the NutriCrop and RedPlantMicro Spanish Consortia/Groups. *Correspondence: Francisco Pérez‑Montaño María Reguera Full list of author information is available at the end of the article © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. Pérez‑Montaño et al. Microbiome (2025) 13:228 Introduction Climate change poses an unprecedented challenge to global agriculture, impacting crop productivity and food security through increasing temperatures, erratic precipitation and extreme weather events [1]. These environmental stressors intensify soil degradation, exacerbate water scarcity and threaten conventional crop systems, demanding innovative approaches to sustain agricultural yields. In response, emergent crops and plant growthpromoting bacteria (PGPB) have gained attention as sustainable strategies to enhance crop resilience under changing climatic conditions [2, 3]. Emergent crops such as quinoa (Chenopodium quinoa), amaranth (Amaranthus spp.), lupins (Lupinus spp.), hemp (Cannabis sativa) and desert truffles (Terfezia and Tirmania spp.) are increasingly recognised for their resilience to abiotic stresses, including drought and poor soils, as well as for their rich nutritional profiles. These traits, including drought tolerance, efficient nutrient uptake and adaptability to marginal environments, make them promising alternatives for sustainable agriculture in climate-vulnerable regions such as the Mediterranean and arid zones, where water scarcity and soil degradation are critical challenges [3]. Their cultivation not only diversifies agricultural systems but also promotes food security and economic resilience [4]. Additionally, these crops exhibit outstanding nutritional properties. Quinoa and amaranth are rich in high-quality proteins with well-balanced essential amino acid profiles, particularly lysine, which is often deficient in cereals. Lupins are excellent sources of plant-based protein and dietary fibre, with low levels of antinutritional factors in modern varieties. Hemp seeds provide a balanced ratio of omega-3 and omega-6 fatty acids, along with bioactive compounds with potential health benefits. They are also an excellent source of highquality protein due to their favourable amino acid profile and substantial protein content. Desert truffles, known for their high antioxidant content, polysaccharides and bioactive metabolites, have been traditionally consumed in arid regions for their nutritional and medicinal properties [3]. On the other hand, PGPB offer multiple benefits to plants by enhancing nutrient availability, improving water-use efficiency, modulating phytohormone production and inducing systemic resistance against pathogens [5, 6]. Well-documented examples include Azospirillum, Rhizobium, Bacillus and Pseudomonas species, which facilitate nitrogen fixation, phosphate and potassium solubilization, iron acquisition and the production and regulation of phytohormones, thereby improving plant growth under stress conditions [7–9]. Despite extensive research on PGPB in staple crops, their interaction with emerging crops remains largely unexplored. This gap Page 2 of 27 presents a significant opportunity for developing sustainable, climate-resilient agriculture. This review examine (...truncated)