Soil acidification and continuous cropping obstacles (CCO) are significant agricultural challenges that threaten crop yield and soil health. Traditional microbial interventions often lack multifunctionality and ecological adaptability, limiting their effectiveness in acidic soil environments. This study aimed to address these challenges by isolating and evaluating multifunctional microorganisms capable of ameliorating soil acidity and suppressing soil-borne diseases. We successfully screened acid-tolerant, alkali-producing bacteria from acidic forest soils and identified strain JL-77 as Paraburkholderia fungorum. This strain demonstrated robust acid tolerance, attributed to its alkali-generating ability which significantly increased soil pH from 5.13 to 5.46 in incubation experiments. Mechanistic studies revealed that JL-77 possesses multiple plant growth-promoting traits, including nitrogen fixation, phosphate solubilization, IAA production, ACC deaminase activity, and the degradation of autotoxins such as benzoic and p-hydroxybenzoic acid. Furthermore, JL-77 successfully colonized the rhizosphere and exhibited strong biocontrol effects against Fusarium oxysporum, F. solani, and Phytophthora cactorum, significantly reducing the disease index in continuous cropping soil. In trials with Atractylodes macrocephala and pak choi, JL-77 application effectively mitigated continuous cropping obstacles and enhanced plant biomass and quality. These findings suggest that JL-77 is a highly effective multifunctional microorganism with potential applications in improving acidic soils, managing soil-borne diseases, and promoting sustainable agricultural practices.

Increasing pressure from xylem-limited pathogens has driven the search for beneficial xylem-inhabiting endophytes that can enhance growth, stress tolerance, and disease resistance in woody plants. This study characterized the culturable xylem microbiota of Salicaceae species (willow and poplar) and evaluated their potential as biological control agents against vascular pathogens. A combination of microbial isolation, metabarcoding, and whole-genome sequencing was used to characterize xylem-associated bacteria. Functional traits were assessed through in vitro assays, while genome mining identified genes linked to plant-beneficial activities. Interactions between endophytes and pathogens were tested using fluorescently labeled strains in tobacco (Nicotiana tabacum) and in vitro-grown willow (Salix caprea). Bacterial genera (Bacillus, Pseudomonas, Erwinia) exhibited plant growth-promoting traits and strong antagonism against bacterial and fungal vascular pathogens, including Xylella fastidiosa, Brenneria salicis, Fusarium spp., and Verticillium dahliae. Genome analyses revealed functions related to nutrient acquisition, biofilm formation, and antimicrobial production. Co-inoculation assays significantly reduced pathogen load and disease symptoms in tobacco and mitigated symptoms in willow. Xylem endophytes act as context-dependent allies in woody plant defence. This study provides a functional and genomic framework supporting microbiome-based strategies to enhance resistance against vascular pathogens in long-lived woody hosts.

Bacterial wilt of capsicum, caused by Ralstonia solanacearum, leads to severe yield losses and remains a major constraint in crop production. To address this challenge, we screened 35 rhizobacterial isolates for antagonistic activity using dual culture assays, biofilm formation, plant growth promoting (PGP) traits, extracellular enzyme production and abiotic stress tolerance. Further, five promising isolates (CR24, CR27, CR32, CR33, CR34) were selected for detailed evaluation. These exhibited nutrient solubilization, IAA, siderophore and HCN production, along with biofilm formation. CR27, CR32 and CR34 showed enhanced PGP traits and enzymatic activities, supporting nutrient mobilization and pathogen suppression. Molecular characterization identified CR27 as Bacillus sp. (PX112639), CR32 as Pseudochrobactrum sp. (PV992584), and CR34 as Lysinibacillus sp. (PV992585). Stress assays revealed high tolerance of Bacillus sp. (CR27) and Pseudochrobactrum sp. (CR32) to pH, salinity, temperature and drought. Greenhouse trials validated their efficacy, with Pseudochrobactrum sp. (CR32) showing lowest disease incidence and highest plant growth. This is the first report of Pseudochrobactrum as an antagonist of R. solanacearum, highlighting its potential as a novel bioinoculant for sustainable capsicum cultivation.

The growing use of nitrile-containing herbicides in agriculture has raised concerns about the environment and human health. In this research, the ability of the bacterial isolate to produce a thermostable enzyme that can degrade nitrile-containing compounds was analysed. The promiscuous nature of the nitrile-degrading enzyme was analysed based on substrate specificity. The enzyme exhibited a notable degradation profile on the nitrile-containing dichlobenil (526.3 µmol/min.mL) and the highest activity towards the native substrate acrylonitrile (555.5 µmol/min.mL). Additionally, divalent metal ions, including Ca2+, Mg2+, and Fe2+, increased the activity of the enzyme but Cu2+, Co2+, Mn2+, Zn2+, and K+ decreased it. The enzymatic breakdown of dichlobenil into its corresponding carboxylic acids was determined by FTIR and GC-MS/MS. The 16S rRNA gene was used to characterise the bacterial isolate, and sequence similarities verified that it was Bacillus subtilis. Subsequently, the sequence was deposited in GenBank with the accession number PX891009. B. subtilis possesses plant growth-promoting traits such as indoleacetic acid and gibberellic acid, ammonia production, phosphate solubilization, and produces hydrolytic enzymes that stimulate defence mechanisms. These results suggest that B. subtilis has the potential to degrade nitrile-containing herbicides to improve soil fertility. This work also contributes to the Sustainable Development Goals (SDGs), especially SDGs 2, 3, 6, 12, and 15, by supporting the biological degradation of herbicides to enhance soil quality.

Plant growth-promoting rhizobacteria (PGPR) enhance plant growth and development through diverse mechanisms, including phytohormone production, nutrient acquisition, and stress mitigation. This study describes the isolation and characterization of two bacterial strains, DT1 and S10, from the rhizospheres of Diplotaxis tenuifolia and Cynodon dactylon, respectively that exhibit multiple plant growth‑promoting traits, including phosphate and zinc solubilization, nitrogen metabolism and the production of indole acetic acid (IAA) and siderophores. Using whole genome sequencing and taxonomic analyses, these two strains were identified as Acinetobacter calcoaceticus (DT1) and Citrobacter braakii (S10). Functional genomic annotation revealed numerous genes associated with key plant growth-promoting traits, including those involved in indole-3-acetic acid (IAA) (trpABCDE, ipdC), cytokinin (miaABE), and riboflavin biosynthesis, which were further supported by targeted metabolomic analyses. In addition, genes associated with nitrogen metabolism, including nitrate/nitrite reduction (nirB, narGHI), as well as phosphate solubilization (gcd, phoARP, pstABCS, pqqEFG) were identified and supported by phenotypic assays. Interestingly, biosynthetic gene clusters for the secondary metabolites enterobactin, bacillibactin, and staphyloferrin B, known to contribute to plant growth promotion, were identified in both genomes. Both strains also harbored genes potentially involved in stress-related metabolic processes. Furthermore, non-targeted metabolomic analysis revealed that DT1 and S10 produced a range of intracellular and extracellular metabolites associated with plant growth promotion and stress resilience, including cadaverine, biotin, arginine, and GABA. Collectively, these findings position DT1 and S10 as promising bioinoculant candidates, offering an integrative genomic and metabolic foundation for their application in next-generation sustainable agricultural strategies.

This study investigates the role of rhizospheric bacteria in enhancing the phytoremediation capacity of Parthenium hysterophorus growing on distillery sludge, aiming at the ecorestoration of polluted environments. Physicochemical analysis revealed notable reductions in pollutants, with salts decreasing to 15.74–53.79 mg/kg and metals reduced by 28.69–80.26 mg/kg. GC–MS profiling of fresh and 50-day-old plant tissues indicated bioconversion and disappearance of several distillery-derived organic pollutants, underscoring the plant’s ability to degrade and transform contaminants. Metal analysis showed bioaccumulation in roots, shoots, and leaves, with bioconcentration factors (BCF > 1) for Fe, Zn, Cu, Ni, Pb, and Cr, and translocation factors (TF > 1) for Fe, Zn, Mn, Ni, and Pb, confirming strong phytoextraction potential. Furthermore, phytostabilization of Cu and Cr was observed. Transmission electron microscopy of roots revealed dense metal deposits in the cytoplasm, along with structural adaptations such as multi-vacuoles, mitochondria, and chloroplasts, indicating high tolerance to metal stress. The rhizospheric bacterial community, dominated by Alcaligenes faecalis, Cytobacillus firmus, Bacillus subtilis, and Niallia circulans, exhibited plant growth-promoting traits that support remediation. Overall, the findings highlight P. hysterophorus as an effective candidate for phytoremediation and bacterial-assisted eco-restoration of industrially contaminated sites.

Apple replant disease (ARD) is a major threat to the sustainable development of China's apple industry. It is primarily caused by the accumulation of phloridzin and the pathogen Fusarium proliferatum f.sp. malus domestica MR5 (Fpmd MR5). MdUGT88F1-mediated phloridzin biosynthesis is known to enhance disease resistance, but its role in shaping the rhizosphere microbiome and conferring resistance against Fpmd MR5 remains unclear. In this study, we used wild-type (WT) and MdUGT88F1 transgenic apple lines to systematically investigate the mechanism by which MdUGT88F1 regulates the rhizosphere microbiome to mitigate ARD. Compared with WT and MdUGT88F1-OE plants, MdUGT88F1-RNAi plants exhibited enhanced tolerance to ARD, as indicated by reduced disease severity, decreased abundance of Fpmd MR5 in the rhizosphere soil, and lower phloridzin content. Further greenhouse experiments demonstrated that the rhizosphere bacterial communities were triggered mainly by changes in community composition. Multi-omics joint analysis revealed that members of the family Bacillaceae with multiple plant growth-promoting traits were enriched in the MdUGT88F1-RNAi plant rhizosphere but only upon Fpmd MR5 invasion. MdUGT88F1-RNAi plants exhibited significantly higher exudation of D-tagatose, D-galactose, sucrose, 3-O-methyl-D-glucose, and maltitol. Interestingly, exogenous application of these compounds promoted the proliferation of Bacillus, enhancing plant resistance to Fpmd MR5. In vitro assays demonstrated that the recruited Bacillus significantly inhibited the hyphal growth and fumonisin B1 production of Fpmd MR5 and alleviated plant disease symptoms. We experimentally validated this observation by inoculating a synthetic microbial community (Bacillus velezensis, Bacillus mojavensis, Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis) into replanted soil, which led to a significant reduction in pathogen Fusarium abundance and promoted plant growth. Overall, these findings highlight that plant disease resistance is a complex trait driven by dynamic interactions among the host genetic background, rhizospheric microbial communities, and pathogens. Targeted modulation of the rhizospheric microbiome represents a potent "prebiotic" strategy. This approach can indirectly enhance plant disease resistance by fostering beneficial microbial activity in the rhizosphere. This study also provides a theoretical basis and practical solutions for the green control of ARD through prebiotics and synthetic microbial communities. Video Abstract.

Endophytic bacteria are usually found within plant tissues. They enhance plant growth, with potential agricultural and environmental applications. They might enhance the plant tolerance to abiotic stresses and inhibit the metal toxicity within metal hyperaccumulator plants. The majority of endophytic bacteria possess plant growth-promoting features. They secrete secondary metabolites that improve plant growth and physiological functions. Twelve endophytic bacteria strains were isolated from the root, stem and leaves of Helianthus annuus plant grown in contaminated soil with the heavy metals lead, zinc and chromium. The isolates were identified and characterized by colony morphology, biochemical tests including gram, spore staining, catalase, starch hydrolysis, hydrogen cyanide and auxin production, phosphate solubilization and nitrogen fixation, along with 16S rRNA gene-based molecular identification of bacteria. Five bacterial isolates showed positive results in all Plant growth-promoting traits. The molecular identification through amplification of bacteria's 16S rRNA using PCR has shown eight Bacillus spp., with two Acinetobacter spp., Providencia vermicola and Enterobacter cloacae. The findings highlight the diversity of endophytic bacteria associated with the COH3 variety of Helianthus annuus plant grown in HM-contaminated soil and evaluate their plant growth-promoting and heavy metal tolerance under in vitro conditions. Further studies are required to evaluate their efficiency under field conditions.

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria that directly or indirectly enhance plant growth, crop yields and stress tolerance. In this study, the maize variety ‘Ningdan 33’ was used as the experimental material. Strain PW2, isolated from salinized soil in Yinchuan, Ningxia, was identified as Enterobacter asburiae based on morphological, physiological, and biochemical characteristics as well as 16S rRNA gene sequencing. Pot experiments demonstrated its potential for salt tolerance and growth promotion in maize. The strain can grow in environments with 2.0%–10.0% NaCl and at pH 8.0–11.0, while exhibiting multiple plant growth-promoting traits, such as nitrogen fixation, potassium solubilization, siderophore production, ACC deaminase activity, and IAA synthesis. Under salt stress conditions, inoculation with PW2 significantly promoted maize seed germination, seedling growth, and root system development. Compared to the control group, inoculation with PW2 suspension significantly increased plant height, root length, nitrogen content, and the fresh and dry weights of both shoots and roots. Furthermore, PW2 inoculation significantly enhanced antioxidant enzyme activities in maize leaves and roots. Specifically, the activities of POD, SOD, and CAT in leaves increased by 92.75% (p = 4.0×10-7), 21.79% (p = 0.008), and 17.28% (p = 0.010), respectively, while those in roots increased by 54.32% (p = 2.0×10-6), 19.36% (p = 0.041), and 37.80% (p = 0.002), respectively. Conversely, the MDA content in leaves and roots decreased by 19.53% (p = 0.0058) and 32.91% (p = 0.006), respectively. Additionally, the contents of soluble sugar, soluble protein, and proline in both leaves and roots increased significantly. Collectively, these results indicate that strain PW2 effectively mitigates oxidative damage caused by salt stress through enhanced antioxidant defense and improved osmotic regulation, thereby promoting maize growth.

Unveiling the plant growth-promoting and antifungal potential of Melissa officinalis endophytes: The integrative culture-dependent and metagenomic approaches.

Two yellow-pigmented, Gram-stain-negative, strictly aerobic bacterial strains, designated as XXL09T and CLY1604T, were isolated from healthy citrus leaves collected from a well-known production area located in Deqing County, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains XXL09T and CLY1604T belonged to the genus Sphingomonas and were most closely related to the three validly published species Sphingomonas beigongshangi REN5T, Sphingomonas aquatilis JSS7T and Sphingomonas melonis DAPP-PG 224T. The genome-derived average nucleotide identity values between the two strains and their closely related type strains were below 84.66% and 85.21%, respectively, and the corresponding digital DNA-DNA hybridization values were below 25.70% and 27.70%, respectively. The major fatty acids of two novel strains were identified as summed feature 8 (C18 : 1 ω7c), C14 : 0 2-OH and C16 : 0. The respiratory quinone was determined to be ubiquinone 10 and the polar lipids comprised diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, an unidentified phospholipid, an unidentified glycolipid and five unidentified aminolipids. The genomic DNA G+C contents of strains XXL09T and CLY1604T were 67.1% and 68.3%, respectively. Phenotypic and physiological characterizations further revealed plant growth-promoting traits: both strains produced siderophores and indole-3-acetic acid, suggesting capabilities in iron acquisition and phytohormone synthesis. Notably, only strain XXL09T exhibited inorganic phosphate solubilization activity, highlighting its potential role to enhance nutrient availability to host plants. Integrating comprehensive genomic, phylogenetic, chemotaxonomic and phenotypic evidence, strains XXL09T and CLY1604T are proposed to represent two novel species of the genus Sphingomonas, for which the names Sphingomonas benefaciens sp. nov. and Sphingomonas cellulosilytica sp. nov. are proposed, with XXL09T (=GDMCC 1.5297T=CCM 9448=JCM 37846T) and CLY1604T (=GDMCC 1.5301T=CCM 9452T=JCM 37845T) as the type strains, respectively.

This study investigated the potential of native rhizobacteria from the Lut Desert, one of the hottest and most arid regions on Earth, to enhance drought tolerance in Maize (Zea mays L.). Bacterial isolates were screened for abiotic stress tolerance and plant growth-promoting traits. The selected strain, THU2, which demonstrated minimal growth inhibition under drought, heat, and salinity stress, was used in comprehensive greenhouse and field experiments under both optimal and water-deficit conditions. Results revealed that THU2 inoculation significantly improved maize growth and physiological performance, increasing shoot fresh weight by approximately 40-50% under optimal conditions and by over 100% under water-deficit conditions compared to mock. Key mechanisms identified included: (1) root and xylem modifications that improved water uptake and transport; (2) stomatal regulation leading to enhanced water-use efficiency and photosynthetic rate; and (3) biochemical protection through elevated proline content (up to 53% increase) and reduced oxidative damage (up to 35% reduction in MDA). Field trials confirmed the greenhouse findings, with THU2-inoculated plants showing superior growth, higher photosynthetic efficiency, and increased yield under drought stress. This research demonstrates that the extreme-adapted bacterium THU2 is a highly effective bio-inoculant, offering a sustainable strategy to improve crop resilience in water-limited environments.

Pseudomonas corni sp. nov., Pseudomonas oplopanacis sp. nov., Pseudomonas salicis sp. nov., Pseudomonas rosaeacicularis sp. nov., Pseudomonas artemisiae sp. nov., Pseudomonas imperatae sp. nov. and Zestomonas ipomoeae sp. nov., isolated from rhizospheres showing plant growth promoting potential.

Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica, and T. mirabilis from geographically distinct locations in Thailand. Despite geographic separation, Thismia spp. consistently harbored bacterial compositions taxonomically and functionally distinct from surrounding soil microbiomes. Root endospheres were significantly enriched in Pseudomonadota and Bacteroidota, particularly Puia, while showing reduced compositional dynamics of Acidobacteriota and Planctomycetota. Bacterial communities in Thismia roots were markedly distinct from surrounding soil, while root endosphere communities from geographically distinct habitats clustered together regardless of spatial separation. Mantel and partial Mantel tests confirmed that host species identity, not geographical location, was the primary predictor of root bacterial community structure. Functional prediction analyses suggested root-associated communities were enriched for nitrogen cycling pathways, particularly nitrogen fixation and nitrate reduction. The selective enrichment of Bacteroidota, known for nitrogen fixation and phosphate mobilization, suggests these bacteria provide critical nutritional support in nutrient-poor forest floor environments. Isolated root strains belonged exclusively to Bacillota, including Neobacillus with plant growth-promoting traits. Our findings highlight the importance of tripartite plant–fungal–bacterial interactions in Thismia nutritional ecology.

The study aimed to identify beneficial indigenous microorganisms to control root-knot nematodes on vegetables. This research isolated, selected, and identified three promising indigenous Bacillus strains (Bacillus velezensis BHMT 4.1, B. amyloliquefaciens CCCX 2.2, and B. subtilis CCCX 2.1) for controlling root-knot nematodes (Meloidogyne spp.) and promoting vegetable plant growth. The study qualitatively assessed several plant growth-promoting traits of Bacillus strains. All of them were capable of producing IAA (indole-3-acetic acid), solubilizing phosphate (with solubilization halos ranging from 1.57 to 2.0 mm), and producing siderophores (with siderophore production indices from 3.33 to 6.33 mm). Furthermore, three Bacillus strains exhibited nematicidal activity against the second juvenile stage (J2) and inhibited egg hatching of Meloidogyne spp. B. velezensis BHMT 4.1 strain demonstrated the highest mortality rate of 66.67% against J2 after 48 h and achieved a 44% inhibition rate of egg hatching after 7 days. These findings suggest that indigenous Bacillus strains have strong potential for application in the biological control of root-knot nematodes (Meloidogyne spp.) on vegetables.

Albizia lebbeck (L.) Benth. is a leguminous tree with significant potential in agroforestry. Root nodules are known to harbour rhizobia as well as non‑rhizobial endophytes with plant growth‑promoting (PGP) traits. The present study was undertaken to isolate and characterize endophytic bacteria from root nodules of A. lebbeck. A total 48 bacterial isolates were isolated and purified from root nodules of A. lebbeck and were screened qualitatively for four PGP traits; IAA production, ammonia production, phosphate solubilization and chitinase activity. Identification of the effective PGP bacterial strains were done by sequencing of 16S rRNA gene. Results revealed that 52.08% of bacterial isolates exhibited IAA production, 50% of bacterial isolates exhibited ammonia production, while 31.25% isolates showed phosphate solubilization. Chitinase activity was present in only one bacterial isolate (Al-DOB7). Pseudomonas sp. Al-DOB7 were identified as multifunctional PGP bacteria and showed all four PGP activity screened. Three bacterial isolates; Rhizobium sp. Al-Am1, Rhizobium sp Al-Kh2 and Ensifer sp. Al-Rs5 exhibited IAA production, ammonia production and phosphate solubilization. Further quantitative screening and greenhouse validation of these nodule-associated bacteria are essential for their sustainable application in agricultural and agroforestry systems.

The soil beneath agricultural fields harbours an extraordinary diversity of microbial life that constitutes a largely invisible yet profoundly influential workforce governing agroecosystem functioning. Bacteria, archaea, fungi, and their complex mycorrhizal networks collectively mediate nutrient cycling, organic matter decomposition, plant hormone production, pathogen suppression, and stress alleviation—processes that underpin crop productivity and long-term ecological sustainability. Despite decades of investigation, our understanding of how these communities are assembled, how they interact, and how agricultural management practices modulate their composition and function remains incomplete. This review synthesises current knowledge on the structural and functional dimensions of the soil microbiome and mycorrhizal networks in agricultural contexts, with particular emphasis on mechanisms by which these biological agents enhance crop resilience to biotic and abiotic stresses, mediate critical nutrient transformations, and contribute to the sustainability of agroecosystems. Key findings highlight that mycorrhizal fungi—especially arbuscular mycorrhizal fungi—extend plant root architecture, facilitate phosphorus and micronutrient acquisition, and strengthen plant defences through systemic signalling pathways. Rhizobacteria possessing plant growth-promoting traits, including nitrogen fixation, phosphate solubilisation, phytohormone production, and ACC deaminase activity, substantially improve crop performance under stress conditions. The emerging consensus indicates that agricultural intensification, agrochemical dependency, and tillage disruption critically impair microbial diversity and network complexity, with cascading consequences for ecosystem services. Conversely, organic farming, reduced tillage, and targeted bioinoculant applications demonstrably restore and enhance microbial community richness and functionality. The integration of microbiome science into precision agriculture and sustainable crop management strategies thus represents a compelling frontier for twenty-first-century food systems. Future research must address the challenges of translating microbiome knowledge into reliable field-scale interventions whilst accounting for edaphic variability and climate change pressures.

Soil salinization due to anthropogenic activity and climate change is a bottleneck to the global agricultural yield and food security. Conventional approaches for mitigating salt stress, including utilization of chemical fertilizers, have shown limited success, and the use of genetically engineered microbes as bioinoculants or salt-tolerant crop varieties against abiotic salinity stress often faces regulatory challenges with extended timelines. Contrary to the existing approaches, employment of halophilic bacteria and archaea offers a promising platform for eco-friendly and sustainable crop cultivation under salt-affected soils. These unique salt-loving microbes can thrive in hypersaline ecosystems and exhibit physiological features for tolerating salt stress along with plant growth-promoting traits. They have distinctive adaptations in homeostasis, biosynthesis, and accumulation of compatible solutes like glycine betaines and amino acids, production of Volatile Organic Compounds (VOCs) as osmo-protectants, and exopolysaccharide (EPS) formation. Apart from salt tolerance, plant growth-promoting bacteria and Halobacteria (PGP-HB) exhibit direct and indirect mechanisms. Direct mechanisms involve 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, phytohormone production, siderophore production, nutrient solubilization, and biological nitrogen fixation, whereas indirect mechanisms involve the production of lytic enzymes, hydrogen cyanide (HCN), and antimicrobial production, as well as induced systemic resistance. Biochar and Nano-encapsulated halophilic plant growth-promoting rhizobacteria (HT-PGPR) together are an effective strategy for plant growth promotion. This review highlights the importance of halobacteria and halotolerant PGPR with an integrated omics approach to potentiate molecular mechanisms underlying adaptations and plant growth promotion in salt-affected soils. The focal point of this review is to explore the possibilities of exploiting halophilic bacteria and archaea in mitigating the negative impact of salt stress on crop production. It emphasizes solutions to current challenges, limitations, prospects of exploiting halophiles, and provides a translational route of eco-friendly bioformualtion production for sustainable agriculture with food security and is aligned with Sustainable Development Goal 2 (SDG 2).

This study investigated Serratia bockelmanii sp. 201 (strain C2), a bacterium isolated from the rhizosphere ofOpuntia ficus-indica. This strain demonstrates relevant plant growth-promoting (PGP) traits and enhances salt stress tolerance in crops. While its phenotypic characteristics have been documented, the genomic basis of these traits remains unexplored. Whole genome sequencing of the strain C2 revealed a 5.24 Mbp circular chromosome with 59.18% GC content, encoding 4,841 protein-coding genes. Pan-genome analysis demonstrated a 99.06% average nucleotide identity (ANI) with Serratia bockelmanii. Functional genomic annotation identified key plant growth-promoting (PGP) genes, including those involved in phosphate solubilization, siderophore biosynthesis, indole-3-acetic acid (IAA) production, and volatile organic compound (VOC) synthesis. Notably, the genome lacked high-risk antimicrobial resistance (AMR) genes while possessing genes associated with stress tolerance. Furthermore, WGS illuminated the pathways and regulatory networks employed by strain C2 to synthesize various growth regulators, enhance nutrient availability, and consequently promote plant health and stress tolerance, with tomato seedling assays specifically confirming VOC-mediated salt stress alleviation by this strain. This study provides the first genomic evidence for the multifunctional PGP traits and salt stress mitigation mechanisms of Serratia bockelmanii sp. 201. The absence of pathogenic markers supports its potential as a safe biofertilizer for saline agriculture. Moreover, in vitro tomato growth assays demonstrate the beneficial effects of VOCs emitted by Serratia bockelmanii sp. 201. Further studies are needed to profile these VOCs and to validate the performance of this PGPR strain under stress conditions in greenhouse and field trials.

This study demonstrates that desert-derived bacterial isolates can be rationally assembled into a stable and functionally complementary EcoBiome with plant growth-promoting traits. By integrating phenotypic screening with community dynamics across environmental conditions, we demonstrate that simplified bacterial consortia derived from synthetic communities (SynCom) can retain key ecological traits, such as persistence, biofilm formation, and water deficit tolerance. These findings expand our knowledge of how bacterial molecular resources adapted to desert environments can be harnessed as biostimulants and provide a framework for the development of EcoBiomes aimed at improving plant resilience to abiotic stress.