European Journal of Sustainable Agroecosystems

Background: Rainfed agriculture is common across the globe as it contributes extensively to agriculture on smallholdings. However, the development of rainfed agriculture is restricted due to various factors including the low levels of nitrogen and phosphorus utilization combined with the unpredictable water availability. Additionally, farmers operating in these conditions do not have sufficient materials/resources to apply fertilizers in order to resolve their nutritional problems. Nonetheless, the application of plant growth-promoting rhizobacteria (PGPR) could modify the rhizosphere showing the necessity of making the changes to microbial activities that are guided by the nutrient needs of the crops. Nevertheless, the existing relationship between specific genes and their influence on profitability of nitrogen fertilizer application in rainfed farming is still under research.
Objectives: To analyze the relevant scientific literature published during the period of 2015-2026 in order to explore the relationship between the genes of PGPR belonging to nifH, phoD/phoC/pqqC, acdS, as well as ipdC/iaaM that are responsible for nutrient acquisition, root development, and preventive systems in the effort of understanding the agronomic efficiency of nitrogen using in rainfed farming.
Literature sources: A comprehensive literature search via PubMed, Scopus, ScienceDirect, SpringerLink, Web of Science, and FAO/FAOSTAT databases returned 168 results out of which 34 publications were eligible for further thematic analyses by means of PRISMA method.
Conclusions: Being reviewed in the literature, the usage of diazotrophs along with phosphate-solubilizing and ACC-deaminase producing bacteria indicated higher N and P efficiency than in the control plots where those bacteria were not used and where fertilizer application was performed. Additionally, the authors of the study reported that functional gene abundance, namely the number of copies of nifH and phoD genes, is more strongly associated with nutrient use efficiency than taxonomic diversity reported by means of 16S rRNA indicating the importance of using functional gene approaches in rhizosphere management practices.
Research gaps: The lack of designated field methods causes an inability to link together quantitative measurements of functional genes with NUE parameters. The information is typically obtained from short-term trials with limited replication of the genotype × environment × microbiome combination. Reliable metagenomic or metatranscriptomic proof of inoculant survival in dry soils is infrequent.
Conclusions: Using PGPR consortia based on functional genetic traits is a promising solution to solve the nutrients use efficiency issue in dryland agriculture but the successful implementation of such findings in farm practices demands validation in multi-omics studies, multi-site trials, and assistance from government organizations in practice of locally appropriate bioinoculants application.