Effects of Facility Cultivation Shaping Soil Microbial Community Structure in Jujube Orchard

Abstract

Facility cultivation systems provide protection for jujube (Ziziphus jujuba) against rain-induced fruit cracking during the maturation and regulate the fruit ripening process. Prolonged cultivation within these controlled environments may alter the soil microbial community structure, potentially detrimentally affecting plant growth and fruit quality. There is a lack of information regarding the arbuscular mycorrhizal fungi (AMF) and bacterial communities in orchards under facility conditions. This study compared the soil bacterial and AMF communities in jujube orchards under greenhouse and rain shelter conditions. Greenhouse cultivation significantly increased soil organic carbon (SOC), total nitrogen (TN), and electrical conductivity, while it decreased soil pH compared to rain shelters. These changes were associated with reduced α-diversity indices in both bacterial and AMF communities. Non-metric multidimensional scaling analysis demonstrated distinct differences between bacteria and AMF communities under the two cultivation types. The phyla Actinobacteria, Gemmatimonadetes, and Rokubacteria were identified as key contributors to the observed alterations in the bacterial community, while variations in the genus Glomus and Paraglomus were responsible for changes in the AMF communities between the two cultivation types. Redundancy analysis revealed that pH was the primary factor shaping microbial community structure across the two cultivation types. Using a Zi-Pi plot, we identified several keystone ASVs, which showed a positive correlation with pH, SOC, and TN. The findings highlight the significant impact of cultivation type on soil microbial community structure and function, which has important implications for optimizing cultivation practices and ensuring sustainable jujube production.

Keywords: Arbuscular mycorrhizal fungi; Environmental factors; Facility cultivation; Jujube; Microbial communities.

Fig. 1

Soil physical and chemical properties under greenhouse and rain shelter. A, pH; B, electrical conductivity (EC); C, total nitrogen (TN); D, nitrate-nitrogen (NO₃^–-N); E, NH₄⁺-N, ammonium-nitrogen (NH₄⁺-N); F, active contents of phosphorus (AP); G, active contents of potassium (AK); H, total contents of carbon (TC); I, soil organic carbon (SOC); J, urease (Ure); K, alkaline phosphatase (Alp); L, sucrase (Suc). The number of orchards sampled was 19 for greenhouses (n = 19) and 13 for rain shelters (n = 13). An asterisk indicates significant differences among soil samples as calculated by t-test. *, p < 0.05; **, p < 0.01; ***, p < 0.001; ns, no significant differences

Fig. 2

Spore density, root mycorrhizal colonization, GRSP content under greenhouse, and rain shelter. A, root mycorrhizal colonization (RMC); B, spore density (SD); C, easily extractable glomalin related soil protein (EE-GRSP); D, Total GRSP. An asterisk indicates significant differences among soil samples as calculated by t-test. *, p < 0.05; **, p < 0.01; ***, p < 0.001; ns, no significant differences. The number of orchards sampled was 19 for greenhouses (n = 19) and 13 for rain shelters (n = 13)

Fig. 3

Alpha diversity of arbuscular mycorrhizal fungi (AMF) (A, B) and bacteria (C, D). E Pearson correlation between soil chemical properties and microbial alpha diversity, with the horizontal and vertical axes representing the soil chemical properties and alpha diversity indices, respectively. TN, total nitrogen; SOC, soil organic carbon. An asterisk indicates significant differences among soil samples as calculated by t-test. *, p < 0.05; **, p < 0.01; ***, p < 0.001; ns, no significant differences. *, p < 0.05; **, p < 0.01

Fig. 4

Bacterial and AMF community compositions and linear discriminant analysis effect size (LEfSe) analyses. A, B The relative abundances of AMF/bacteria at genus/phylum levels, respectively. C, D Linear discriminant analysis effect size (LEfSe) analyses for bacterial (C) and AMF (D) taxa with the non-parametric factorial Kruskal–Wallis (KW) sum-rank test. The taxonomic branching diagram illustrates the hierarchical structure of major taxa within the sample community, with phyla represented in the inner circle and genera in the outer circle. The size of each node corresponds to the average relative abundance of the taxon. Colored nodes and letters indicate taxa that exhibit significant differences between groups. E, F Histogram of the LDA scores for differentially abundant bacterial (E) and AMF (F) taxa

Fig. 5

Redundancy analyses (RDA) of AMF (A) and bacteria (B) community and environmental factors. Different colored or shaped dots in the graph indicate groups of samples in different environments, and arrows indicate environmental factors

Fig. 6

Co-occurrence networks and Zi-Pi analysis of bacterial and AMF community. Co-occurrence networks of the bacterial (A, B) communities and the AMF communities (C, D) under greenhouse and the rain shelter soil, respectively. The top 3000 ASVs/OTUs were selected. Only ASVs/OTUs with strong significant correlations are shown in the figure (p < 0.01 and Spearman’ s correlation coefficients > 0.6). The size of nodes indicates the size of ASVs/OTUs abundance. Different colors indicate different phyla in bacteria and genus in AMF. Red lines and blue lines indicate positive correlation and negative correlation, respectively. The classification of nodes to identify keystone species within the bacterial (E, F) and AMF (G, H) community networks under greenhouse and the rain shelter soil, respectively

Fig. 7

Correlation between environmental factors and the relative abundance of key bacterial ASVs taxa. A Greenhouse. B Rain shelter. Red panel indicates positive correlation, and blue panel indicates negative correlation. An asterisk indicates significant relevance, *, p < 0.05; **, p < 0.01; ***, p < 0.001