Soil salinization is one of the major land degradation processes that decreases soil fertility and crop production worldwide. In this study, a long-term coastal saline soil remediation experiment was conducted with three salt-tolerant plant species: Lycium chinense Mill. (LCM), Tamarix chinensis Lour. (TCL), and Gossypium hirsutum Linn. (GHL). The three plant species successfully remediated the saline soil but showed different efficacies. The archaeal, bacterial, and fungal communities in barren soil and in four rhizocompartments (distal-rhizosphere soil, proximal-rhizosphere soil, rhizoplane, and endosphere) of the three plant species were assessed. All three plant species significantly decreased the richness of the archaeal communities but increased that of the bacterial and fungal communities in both the rhizosphere and rhizoplane compared with those in the barren soil. The archaeal and bacterial community structures were strongly influenced by the rhizocompartment, while specific fungal communities were recruited by different plant species. The microbial taxa whose abundance either increased or decreased significantly during remediation were identified. Soil electrical conductivity (EC) was identified as the main factor driving the variation in microbial community composition between the remediated and barren soil, and total nitrogen (TN), total carbon (TC), and available potassium (AK) were the main factors driving the differences among plant species. This report provides new insights into the responses of the root zone microbial communities of different salt-tolerant plant species during phytoremediation. IMPORTANCE Despite knowing that phytoremediation by salt-tolerant plants is an effective technology for ameliorating saline soils and that microorganisms contribute significantly to plant stress tolerance and soil fertility, we still lack a comprehensive understanding of how microbes respond to the growth of salt-tolerant plants and the subsequent decline in soil salinity. The results of this study revealed different response patterns among bacterial, archaeal, and fungal communities and indicated that the decline in archaeal abundance might be a sign of successful remediation of coastal saline soils. The recruitment of specific fungal communities by different plant species indicated the importance of fungi in plant species-specific remediation functions. We also identified the taxa that may play key roles during remediation, and these taxa could potentially be used as indicators of phytoremediation. Overall, these findings highlight the importance of microbes in the phytoremediation of saline soil and suggest that the mechanisms involved are plant species specific.

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