Exploring the bacterial communities in date palm roots in saline versus non-saline environment

Abstract

Background: Bacterial communities associated with plant roots significantly influence plant growth and adaptation to environmental stresses, particularly in arid agroecosystems. Soil salinity is one critical abiotic stress factor that affects the microbial community structure and functionality. Understanding how soil salinity affects the composition and function of root-associated microbiota in date palms (Phoenix dactylifera L.) could offer valuable insights into enhancing plant resilience and agricultural productivity.

Results: This study investigated the influence of soil salinity on the bacterial communities associated with date palm roots across different cultivars. Root samples were collected from date palms grown under saline (Nashella experimental station) and non-saline conditions (Al Foah experimental station). Using 16S rRNA metabarcoding coupled with culture-dependent isolation methods, significant variations in bacterial community structure and diversity were identified. Physicochemical analysis revealed that saline soils had elevated pH, electrical conductivity, and salinity levels compared with non-saline soils. The bacterial diversity significantly decreased under saline conditions, indicating reduced microbial richness and evenness. In particular, salt-tolerant date palm cultivars exhibited greater variability in bacterial diversity than cultivars grown under non-saline conditions. Non-metric multidimensional scaling (NMDS) analysis demonstrated clear clustering patterns driven by soil salinity and plant genotypes. Differential abundance analysis indicated enrichment of halotolerant and halophilic bacterial taxa in saline soils, whereas non-saline soils favoured bacterial taxa involved in beneficial plant-microbe interactions. Functional analysis using PICRUSt2 revealed that bacterial communities in saline soils had a greater abundance of stress-tolerance mechanisms, whereas those from non-saline soils emphasized metabolic versatility. Additionally, six bacterial isolates from saline and non-saline roots showed notable plant growth-promoting and stress-tolerance capabilities in Arabidopsis thaliana.

Conclusions: Our findings demonstrate the significant influence of soil salinity and date palm genotype on the structure, diversity, and functionality of root-associated bacterial communities. These results suggest potential applications for specific bacterial communities to improve plant tolerance to salinity stress, which is essential for sustainable agriculture in arid environments.

Keywords: Amplicon sequencing; Arid agroecosystems; Bacterial diversity; Date palm; Plant growth promoting bacteria; Saline and non-saline soil.

Fig. 1

Microbial Diversity Across Saline and Non-Saline Sites. Boxplots illustrating microbial diversity using Hill numbers (q-values) between non-saline (Al Foah) and saline (Nashella) sites. Higher q-values assign greater weight to abundant taxa: specifically, q = 0 corresponds to species richness, q = 1 is equivalent to the exponential of Shannon diversity, and q = 2 corresponds to the inverse of Simpson diversity. While species richness (q = 0) shows no significant difference (ns) between sites, significant reductions in diversity were observed at q = 1 (p < 0.01) and q = 2 (p < 0.05) in saline soils, indicating lower evenness and increased dominance of fewer microbial taxa under high salinity. Red boxes indicate non-saline soils, and blue boxes represent saline soils

Fig. 2

Microbial Diversity Across Date Palm Varieties. Boxplots depicting microbial diversity using Hill numbers (q-values) across different date palm varieties. Higher q-values increasingly emphasize abundant taxa: q = 0 represents species richness, q = 1 equals the exponential of Shannon diversity, and q = 2 corresponds to the inverse of Simpson diversity. Salt-tolerant varieties (Bugal White, Mesalli, and Razez) from the saline Nashella site, whereas commonly cultivated varieties (Lulu, Khalas, and Khinaizi) from the non-saline Al Foah site. Khalas and Razez exhibit the highest microbial diversity, whereas Mesalli consistently shows the lowest diversity across all Hill indices

Fig. 3

PERMANOVA analysis showing the relative contribution (R² values) of individual soil environmental parameters to bacterial community variation in date palm roots from saline and non-saline sites. Bars indicate the proportion of community variation explained by each parameter, with significance indicated (p ≤ 0.05). Non-significant parameters are marked as NS

Fig. 4

Non-metric multidimensional scaling (NMDS) plot showing the differences in bacterial communities associated with date palm roots in saline and non-saline environments. Each point represents a sample, colored by date palm variety (Khalas, Khinaizi, Lulu, Bugal White, Razez, and Mesalli) and shaped by site condition (circles for non-saline and triangles for saline). The analysis indicates a significant effect of site (R² = 0.5554, p = 0.001) and variety (R² = 0.8453, p = 0.001) on bacterial community composition

Fig. 5

A Microbial composition of different date palm varieties under saline and non-saline conditions. Stacked bar chart showing the relative abundance of bacterial phyla in saline (Bughal White, Razez, Masselli) and non-saline (Khineizi, Khalas, Lulu) date palm roots. Proteobacteria dominated all samples, especially in saline conditions, whereas Actinobacteria were more abundant in non-saline plants, indicating a beneficial microbial community. Non-saline plants showed higher microbial diversity, whereas saline conditions favoured a less diverse, salt-tolerant microbiome. B The bubble plot displays the top 50 differentially abundant microbial genera in date palm roots under saline vs. non-saline conditions. The x-axis represents the Log2 fold change, where negative values indicate genera more abundant in non-saline roots, while positive values indicate genera enriched in saline roots. Each bubble corresponds to a bacterial genus, with bubble size representing the magnitude of Log2 fold change and color intensity indicating statistical significance (−log10 adjusted p-value). Darker purple colors denote highly significant differences, while yellow indicates lower significance. Genera such as Rhizobium, Pseudoxanthomonas, and Caulobacter are more abundant in non-saline conditions, suggesting a microbial community favoring plant-beneficial interactions. In contrast, saline conditions favor halotolerant and halophilic genera such as Halomonas, Thalassospira, and Muricauda, reflecting microbial adaptation to high salinity

Fig. 6

Heatmap showing the top 30 differentially abundant KEGG Orthologs (KOs) in raw counts across different date palm varieties and saline conditions. The color intensity represents the abundance of each KO, with darker shades indicating higher abundance. Samples are categorized by date palm varieties (Bugal White, Khalas, Khinaizi, Lulu, Mesalli, and Razez) and salinity conditions (Saline and Non-Saline). The clustering of samples suggests variations in functional gene abundance based on both plant variety and environmental conditions

Fig. 7

A Screening assay of A. thaliana inoculated with Arthrobacter sp. (SL 101) and Enterobacter cloacae. (SL 102), and Bacillus aryabhattai, (SL 103), Chrysobacterium (NS201), Providencia rettgeri (NS202) and Pantoe sp. (NS203) in 100mM salt (1/2 MS, 15 days) with and without bacteria (Mock). B Drought stress screening of the bacteria in 20% PEG. The total fresh weight, dry weight and root length of Arabidopsis thaliana plants are presented as the means of three biological replicates and different alphabets indicate the statistical differences