Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations

The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13%, PS: 0.39%, MF: 0.14%, MS: 0.21%)—which plays a key role in soil phosphorus cycle—was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon ( rbcL and ppc ) and phosphorus cycle ( phoP and ppk2 ). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism. • Mixed cropping benefited the supplement of eucalyptus rhizosphere microorganisms. • Continuous cropping reduces the complexity of the microbial co-occurrence network. • Continuous cropping enhances the potential function of phosphorus mineralization. • The pure first-generation plantation contained the most unique metabolites (68). • Echinocystic acid has the potential to promote nutrient circulation.