Unveiling the bacterial community structure and soil properties in bulk and rhizospheric compartments of Tamarix gallica from an arid Algerian saline ecosystem
Aug 2026· Frontiers in Microbiology· Vol 17· 0 citations· 68 references
Medicine
TL;DR
Bacterial diversity was lower in the rhizosphere, which was characterized by a distinct taxonomic composition, including taxa such as Promicromonospora and Nocardioides potentially involved in nutrient cycling and stress adaptation.
Abstract
Soil salinization is among the most critical threats to agriculture and food security, particularly in arid and semi-arid regions. Despite their ecological and agricultural significance, the microbial processes in saline soils of arid regions remain poorly characterized. This first 16S rRNA amplicon-based study of Algerian saline soils examines bacterial communities and physico-chemical properties in the Naama salt flat, focusing on both bulk and rhizosphere soils associated with Tamarix gallica L. Bacterial diversity and community composition were analyzed through high-throughput 16S rRNA gene sequencing on an Illumina MiSeq platform, and soil parameters, including salinity, nutrients, organic carbon, and water retention were measured. Sequence data were processed with QIIME2, and multivariate analyses were applied to compare soil types and explore correlations between taxa and soil properties. Rhizosphere soils tended towards higher Na+, K+, and Ca2+ levels, whereas bulk soils showed greater phosphorus availability. Bacterial diversity was lower in the rhizosphere, which was characterized by a distinct taxonomic composition, including taxa such as Promicromonospora and Nocardioides potentially involved in nutrient cycling and stress adaptation. Correlation analyses revealed microbial adaptations to salinity and nutrient availability. This study lays the groundwork for developing plant growth-promoting rhizobacteria aiming to combat land degradation and contribute to long-term food security and environmental resilience in arid regions.
Soil multifunctionality (SMF) is a core indicator of plantation soil ecological function, and microbial diversity plays a vital role in sustaining it. However, cross-site rhizosphere and bulk SMF disparities and their microbial driving mechanisms remain unclear in Eucommia ulmoides plantations. Here, we collected rhizosphere and bulk soils from three typical sites (Mengzhou, MZ; Liangyuan, LY; and Yuanyang, YY). Soil chemical properties, extracellular enzymes, microbial alpha diversity, community composition and cross-kingdom network topology were measured. Correlation heatmaps, random forest, Redundancy analysis (RDA) and Partial least path modeling (PLS-PM) were adopted to quantify SMF predictors and regulatory pathways. Rhizosphere soils possessed significantly higher alkaline hydrolyzable nitrogen (AN), available phosphorus (AP) and available potassium (AK) than bulk soils at all sites. LY rhizosphere showed the greatest soil organic carbon (SOC), total potassium (TK), available nutrients and enzyme activities, while YY had higher total nitrogen (TN) and AP, yet the lowest enzyme levels. Rhizosphere bacterial and fungal alpha diversity was consistently higher across locations. SMF varied distinctly by site and compartment: LY had substantially higher SMF than MZ and YY in both rhizosphere and bulk soils, with rhizosphere SMF being consistently greater than bulk values across all sites. The PLS-PM (GOF = 0.70) indicated that soil chemical properties regulated SMF via dual pathways: they directly promoted microbial co-occurrence networks and indirectly modified network structure by altering fungal diversity, while suppressing bacterial diversity. Total effect analysis identified soil chemical properties and microbial co-occurrence networks as the core drivers of SMF variation. This work clarifies that rhizosphere effects and soil chemical properties jointly drive SMF by regulating microbial diversity and co-occurrence networks, offering theoretical guidance for sustainable soil management in E. ulmoides plantations.
Pan-Feng Liu, Huaxiang Wang, Furong Lin et al.· Microorganisms· 0 citations
Soil and root-associated microorganisms are fundamental drivers of plant nutrition and environmental adaptation. However, along aridity gradients, the response patterns and regulatory mechanisms of microbial assemblages across bulk soil, rhizosphere soil, and root endosphere remain largely unclear. In this study, we focused on the leguminous plant Lespedeza davurica. We synchronously collected bulk soil, rhizosphere soil, and root samples from 27 sites along a natural aridity gradient of approximately 1200 km across the Inner Mongolian grasslands. By integrating high-throughput sequencing with structural equation modeling, we examined how aridity affects bacterial and fungal diversity and community composition across different ecological niches. The results indicated that aridity directly and significantly reduced bulk soil and rhizosphere fungal diversity. Aridity indirectly suppressed root endosphere bacterial diversity through changes in soil properties. Total nitrogen, soil organic carbon, and soil water content were identified as significant predictors of root endosphere bacterial diversity, whereas total nitrogen was a significant predictor of fungal diversity in both bulk soil and rhizosphere soil. Aridity altered microbial community composition across different ecological niches. The relative abundance of Proteobacteria increased significantly, whereas Acidobacteria showed a significant decline in the root endosphere. In contrast, the relative abundance of Zygomycota decreased significantly in bulk soil and rhizosphere soil. Under intensifying aridity, plants might selectively recruit specific microorganisms via a “cry-for-help” strategy. This study reveals niche-specific microbial responses to aridity across bulk soil, rhizosphere soil, and root endosphere in the grassland ecosystem, providing new insights into microbial adaptive strategies under aridity conditions.
Jia Wen, Xiaoqian Gong, Le Ma et al.· Journal of Plant Ecology· 0 citations
Heavy metal pollution (HMP) threatens soil ecosystems and plant health. This study integrated 16S rRNA sequencing, network analysis, environmental mapping, and bacterial isolation to investigate how distinct ecological niches of Casuarina equisetifolia modulate microbial communities under metal stress. Results revealed a spatial pollution gradient, with Pb²⁺, Zn²⁺, and Cd²⁺ decreasing with distance from the mine, while As⁵⁺, Cr³ ⁺, and Ni²⁺ remained near background levels but displayed significant niche-dependent enrichment, especially for Cr³ ⁺, and Ni²⁺ in rhizosphere soil under medium and high pollution. Niche was the primary driver of microbial divergence, with only 0.56% of OTUs shared between the soil and root compartments. Rhizosphere soils harbored more unique OTUs and higher α-diversity than non-rhizosphere soils. Root endosphere and rhizosphere soil communities were consistently dominated by Actinobacteria across all pollution levels, whereas non-rhizosphere soil communities shifted from Proteobacteria (low pollution) to Actinobacteria (medium) and Chloroflexi (high). LEfSe identified niche-specific biomarkers from the phylum to genus levels, with high-pollution roots harboring the most diverse indicators. Heavy metals and soil properties (pH, CEC, and SOM) collectively shaped community assembly, with distinct drivers per niche: CEC and Enterobacter in non-rhizosphere soil, pH and Acidobacteriales in rhizosphere soil, and Zn as the central hub in the root endosphere network. Isolation yielded 63 metal-tolerant strains across eight genera, predominantly Bacillus cereus sensu lato group, whose niche origin shifted from the rhizosphere (low pollution) to the non-rhizosphere (medium) to the roots (high pollution), suggesting pollution-associated enrichment. These findings reveal niche-specific community assembly and pollution-driven enrichment of metal-tolerant Bacillus cereus s.l. in the root endosphere.
Hang Zhang, Jun Shen, Gaolei Bai et al.· Ecotoxicology and Environmen...· 0 citations
Common reed (Phragmites australis) is a native dominant plant in many coastal wetlands. To determine how rhizosphere effects and soil depth shape microbial communities, we sampled the rhizosphere and three bulk-soil layers (0–15, 15–30, and 30–45 cm) in a monodominant common-reed stand in a coastal salt marsh. Soil physicochemical properties and bacterial and fungal α-diversity, community composition, and assembly processes were evaluated using one-way ANOVA, principal coordinates analysis (PCoA), permutational multivariate analysis of variance (PERMANOVA), neutral community models, and phylogenetic null models. Rhizosphere pH was lower than that of 0–15 cm bulk soil (mean 8.434 vs. 8.712) but remained alkaline; soil organic matter, total nitrogen, hydrolyzable nitrogen, and total phosphorus were greatest in the rhizosphere. Neither bacterial nor fungal richness or Shannon diversity differed significantly among compartments (p > 0.05); fungal Shannon means ranged from 2.083 to 3.077, with relatively higher Bacteroidota and lower Acidobacteriota abundance in the rhizosphere. Fungal composition did not differ significantly (pseudo-F = 0.609, R2 = 0.102, p = 0.9112), although Mucoromycota and Rozellomycota were relatively more abundant in the rhizosphere. Phylogenetic null models indicated predominantly deterministic bacterial assembly, with 10% dispersal limitation in the 15–30 cm layer. Fungal assembly was predominantly stochastic in bulk soils, whereas the rhizosphere was an exception: heterogeneous selection accounted for 60% of pairwise comparisons and median βNTI exceeded +2. The Mantel test identified only the association between total phosphorus and bacterial diversity as significant (0.01 < p < 0.05). These results show that rhizosphere filtering strongly structured bacterial composition and imposed deterministic selection on rhizosphere fungi.
Lei Wang, Jun Shi, Liwen Li et al.· Microorganisms· 0 citations
Indigenous bacterial and archaeal communities in agricultural soils were analyzed to provide a basis for biocontrol and bioremediation solutions to be reintroduced in affected areas and showed in vitro the most promising combination of PGP traits, metal tolerance, and antifungal activity against most phytopathogenic fungi.
Suad Alahmed, T. Janakiev, Milica Jović et al.· World Journal of Microbiolog...· 0 citations
It is suggested that selected halotolerant isolates possess multifunctional traits including salt tolerance and potential nutrient-solubilizing capacity, making them promising candidates for biofertilizer development and sustainable agriculture in salt-affected regions.
H. Dixit, Ranjan Singh, Sanjay Arora et al.· Journal of Soil and Water Co...· 0 citations
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