Bio-organic fertilizer facilitated phytoremediation of heavy metal(loid)s-contaminated saline soil by mediating the plant-soil-rhizomicrobiota interactions

Alleviation of Plant Abiotic Stress: Mechanistic Insights into Emerging Applications of Phosphate-Solubilizing Microorganisms in Agriculture

Global agricultural productivity and ecosystem sustainability face escalating threats from multiple abiotic stresses, particularly heavy metal contamination, drought, and soil salinization. In this context, developing effective strategies to enhance plant stress tolerance has emerged as a critical research frontier. Phosphate-solubilizing microorganisms (PSMs) have garnered significant scientific attention due to their capacity to convert insoluble soil phosphorus into plant-available forms through metabolite production, and concurrently exhibiting multifaceted plant growth-promoting traits. Notably, PSMs demonstrate remarkable potential in enhancing plant resilience and productivity under multiple stress conditions. This review article systematically examines current applications of PSMs in typical abiotic stress environments, including heavy metal-polluted soils, arid ecosystems, and saline-alkaline lands. We comprehensively analyze the stress-alleviation effects of PSMs and elucidate their underlying mechanisms. Furthermore, we identify key knowledge gaps and propose future research directions in microbial-assisted phytoremediation and stress-mitigation strategies, offering novel insights for developing next-generation bioinoculants and advancing sustainable agricultural practices in challenging environments.

Integrated multi-omics and DNA stable-isotope probing approaches to reveal soil-ryegrass response to ionic rare earth mineral ammonium-lead contamination

The extensive use of ammonium (NH4+) sulfate in ionic rare earth mining has resulted in soil contamination with NH4+ and lead (Pb), posing significant challenges for ecological restoration. Here, multi-omics and DNA stable-isotope probing (DNA-SIP) approaches were utilized to investigate soil nitrogen cycling and the molecular response of ryegrass (Lolium perenne L.) to NH4+ (180-720 mg kg-1)-Pb2+ (207-828 mg kg-1) co-contamination. A synergistic interaction between NH4+ and Pb2+ was observed, significantly inhibited ryegrass growth, and induced oxidative stress and mitochondrial swelling. The EC50 toxicity thresholds were 383 mg kg⁻¹ for NH4+ and 512 mg kg⁻¹ for Pb. The Integrated Biomarker Response (IBRv2) model elucidated the synergistic toxic effects. Transcriptomic and metabolomic analyses indicated that ryegrass roots enhanced carbon metabolism and antioxidant response pathways related to stress tolerance. Galactose metabolism and lysine degradation were identified as key pathways associated with stress response. Co-contamination with NH4+ and Pb2+ reduced ryegrass root 15N-total nitrogen (TN) by 30 % while increasing soil 15N-NH4+ residue by 95 % and decreasing 15N-microbial biomass nitrogen (MBN) by 59 %, compared to NH4+ single contamination. DNA-SIP analysis revealed that ryegrass cultivation under NH4+- Pb2+ co-contamination increased the abundance of plant growth-promoting rhizobacteria (Dyella), acid-tolerant nitrogen (Acidibacter), and sulfur-cycling taxa (Desulfosporosinus). The presence of raffinose and chlorogenic acid in ryegrass root metabolites was associated with shifts in the structure and composition of using NH4+ active microbial taxa. These findings provide valuable insights into plant-soil-microbe interactions under multi-pollutant stress and offer practical strategies for phytoremediation and ecological restoration in areas affected by mining.

Soil resource availability regulates the response of micro-food web multitrophic interactions to heavy metal contamination

The effects of heavy metal contamination on soil biomes have been of considerable interest. However, the effects of heavy metal pollution on the interactions between soil multi-trophic biota in soil food webs and the regulatory mechanisms still need more research, especially in different soil situations. This study examined the impact of heavy metal contamination on soil micro-food web in two distinct soil resource availability situations. Under low soil resources availability situation, heavy metals mainly affected the community structure of soil bacteria and nematodes, with the number of edges of the bacterial network and network complexity reduced by 60.5% and 187%, respectively. In addition, the presence of heavy metals led to a significant reduction in the energy flow from soil resources to bacterivores in the nematode food web. For micro-food webs, heavy metal contamination increased the network average degree by 18.8% and 11.56% in the low and high resource availability situations, respectively. However, in high soil resource availability, heavy metal contamination decreased micro-food web stability and eased competitive relationships among multitrophic organisms and increased microbial carbon limitation and mitigates nitrogen limitation. In low soil resource availability, it increased network stability and shifted relationships among micro-food web organisms from cooperative to competitive and decreased microbial carbon limitation and aggravated nitrogen limitation. This study offers new research insights into the feedback discrepancy between resource availability and pollution stress from the perspective of multitrophic level interactions and further deepens the understanding of the environmental impacts of heavy metal pollution at the ecosystem level.

An exploration of bacterial consortia in chlorpyrifos degradation, soil remediation, and promotion of plant growth

The eleven combinations of four isolates, S. maltophilia, P. hibiscicola, P. aeruginosa, and P. monteilii, were prepared and screened for chlorpyrifos (CP) degradation. Among these combinations, four highly CP degrading consortia were identified: D: S. maltophilia, P. hibiscicola, P. monteilii, E: P. hibiscicola, P. aeruginosa, P. monteilii, F: S. maltophilia, P. hibiscicola, and G: S. maltophilia, P. aeruginosa. These combinations were found to be mutually compatible, exhibiting no lysis or inhibition zones. Their application significantly decreased in CP content from 37.6 to 68.6% as compared to control. Consortia-treated soil also displayed reduced bio-concentration factor and translocation of CP in W. somnifera. A significant increase in biomass (40-71.2%), protein content (38-66.6%), chlorophyll (24.7-52.3%), and secondary metabolite of W. somnifera was observed after the application of consortia. The activities of soil enzymes (alkaline phosphatase, dehydrogenase, and N-acetyl glucosaminidase), availability of nutrients, and soil microbial biomass carbon were also enhanced by the inoculation of consortia in soil. Overall, the results indicated that the consortium of S. maltophilia and P. aeruginosa exhibited the highest potential for CP degradation and plant growth promotion compared to the others. This consortium could be effectively utilized for the rapid degradation of CP in agricultural soil vis-a-vis improvement in the productivity of the plants.

Enhancing soil health through balanced fertilization: a pathway to sustainable agriculture and food security

Sustainable soil health management is pivotal for advancing agricultural productivity and ensuring global food security. This review comprehensively evaluates the effects of mineral-organic fertilizer ratios on soil microbial communities, enzymatic dynamics, functional gene abundance, and holistic soil health. By integrating bioinformatics, enzyme activity assays, and metagenomic analyses, we demonstrate that balanced fertilization significantly enhances microbial diversity, community stability, and functional resilience against environmental stressors. Specifically, the synergistic application of mineral and organic fertilizers elevates β-glucosidase and urease activities, accelerating organic matter decomposition and nutrient cycling while modulating microbial taxa critical for nutrient transformation and pathogen suppression. Notably, replacing 20-40% of mineral fertilizers with organic alternatives mitigates environmental risks such as greenhouse gas emissions and nutrient leaching while sustaining crop yields. This dual approach improves soil structure, boosts water and nutrient retention capacity, and increases microbial biomass by 20-30%, fostering long-term soil fertility. Field trials reveal yield increases of 25-40% in crops like rice and maize under combined fertilization, alongside enhanced soil organic carbon (110.6%) and nitrogen content (59.2%). The findings underscore the necessity of adopting region-specific, balanced fertilization strategies to optimize ecological sustainability and agricultural productivity. Future research should prioritize refining fertilization frameworks through interdisciplinary approaches, addressing soil-crop-climate interactions, and scaling these practices to diverse agroecosystems. By aligning agricultural policies with ecological principles, stakeholders can safeguard soil health-a cornerstone of environmental sustainability and human wellbeing-while securing resilient food systems for future generations.

Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance

This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.

Ecogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis

BACKGROUND

The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.

RESULTS

Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.

CONCLUSIONS

This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.