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Background  Plant roots assemble microbial communities both inside the roots and in the rhizosphere, and these root-associated microbiomes play pivotal roles in plant nutrition and productivity. Although it is known that increased synthetic fertilizer input in Chinese farmlands over the past 50 years has resulted in not only increased yields but also environmental problems, we lack a comprehensive understanding of how crops under elevated nutrient input shape root-associated microbial communities, especially through adjusting the quantities and compositions of root metabolites and exudates.    Methods  The compositions of bacterial and fungal communities from the roots and rhizosphere of wheat ( Triticum aestivum L. ) under four levels of long-term inorganic nitrogen (N) fertilization were characterized at the tillering, jointing and ripening stages. The root-released organic carbon (ROC), organic acids in the root exudates and soil organic carbon (SOC) and soil active carbon (SAC) in the rhizosphere were quantified.    Results  ROC levels varied dramatically across wheat growth stages and correlated more with the bacterial community than with the fungal community. Rhizosphere SOC and SAC levels were elevated by long-term N fertilization but varied only slightly across growth stages. Variation in the microbial community structure across plant growth stages showed a decreasing trend with N fertilization level in the rhizosphere. In addition, more bacterial and fungal genera were significantly correlated in the jointing and ripening stages than in the tillering stage in the root samples. A number of bacterial genera that shifted in response to N fertilization, including  Arthrobacter ,  Bacillus  and  Devosia , correlated significantly with acetic acid, oxalic acid, succinic acid and tartaric acid levels.    Conclusions  Our results indicate that both plant growth status and N input drive changes in the microbial community structure in the root zone of wheat. Plant growth stage demostrated a stronger influence on bacterial than on fungal community composition. A number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to N fertilization, and their abundance correlated significantly with the organic acid level, suggesting that the secretion of organic acids may be a strategy developed by plants to recruit beneficial microbes in the root zone to cope with high N input. These results provide novel insight into the associations among increased N input, altered carbon availability, and shifts in microbial communities in the plant roots and rhizosphere of intensive agricultural ecosystems.

Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization