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Our findings suggest that SOC served as a deep trait due to it negative correlation with deeper branches of phylogenetic clustering, while nitrate functioned as a shallow trait due to its positive correlation with phylogenetic clustering at finer branches. Soil salinity acted as a complex trait effected on both finer and deeper branches. Further potential functional gene co-occurrence network analysis revealed that land reclamation induced shifts of metabolic function by altering the functional gene connectivity. We found that the photo