Search Results (438)

Soil salinity disrupts rhizosphere interactions, impairing root–microbe symbioses, nutrient uptake, and water relations in onion (Allium cepa L.) and garlic (Allium sativum L.). This study evaluated the efficacy of biofertilizers (Azotobacter chroococcum SARS 10 and Azospirillum lipoferum SP2) and organic amendments (sewage sludge and poultry manure) in salt-affected soils in Kafr El-Sheikh, Egypt. Five treatments were applied: (T1) control (no amendments); (T2) biofertilizer (3 L/ha for onion, 12 L/ha for garlic) + inorganic P (150 kg/ha P₂O₅ for onion, 180 kg/ha for garlic) and K (115 kg/ha K₂SO₄ for onion, 150 kg/ha for garlic); (T3) 50% inorganic N (160 kg/ha for onion, 127.5 kg/ha for garlic) + 50% organic manure (6000 kg/ha for onion, 8438 kg/ha for garlic) + P and K; (T4) biofertilizer + T3; and (T5) conventional inorganic NPK (320 kg/ha N for onion, 255 kg/ha N for garlic + P and K). Soil nutrients (N, P, K), microbial biomass carbon (MBC), dehydrogenase activity, and microbial populations were analyzed using standard protocols. Plant growth (chlorophyll, photosynthetic rate), stress indicators (malondialdehyde, proline), and yield (bulb diameter, fresh yield) were measured. Treatment T4 increased MBC by 30–40%, dehydrogenase activity by 25–35%, available N (39.7 mg/kg for onion, 35.7 mg/kg for garlic), P (17.9 mg/kg for onion), and K (108 mg/kg for garlic). Soil organic matter rose by 8–12%, and cation exchange capacity by 26–36%. Chlorophyll content improved by 25%, malondialdehyde decreased by 20–30%, and fresh yields increased by 20–30% (12.17 tons/ha for garlic). A soybean bioassay confirmed sustained fertility with 20–25% higher dry weight and 30% greater N uptake in T4 plots. These findings highlight biofertilizers and organic amendments as sustainable solutions for Allium productivity in saline rhizospheres. Full article

In the Red List of Threatened Species, released by International Union for Conservation of Nature (IUCN), Paphiopedilum helenae has been classified as an endangered species. It exhibits exceptional decorative value and germplasm resource potential. To elucidate the ecological adaptation of this species and the characteristics of its rhizosphere microbiome, bacterial 16S rRNA and fungal ITS sequences of three wild populations of P. helenae were investigated using Illumina high-throughput sequencing technology and the microbial community structures and diversities were systematically compared. These three populations were spanned across distinct geographical locations in Longzhou County, Guangxi. The results showed that the bacterial community in the rhizosphere soil of P. helenae comprised 31 phyla, primarily including Actinobacteriota, Proteobacteria, Chloroflexi and Acidobacteriota. On the other hand, the fungal community consisted of 10 phyla, dominated by Ascomycota and Basidiomycota. There were significant differences in the diversity of rhizosphere microbes across different populations of P. helenae. The LG population had the highest bacterial richness (Chao index: 2912.71 ± 131.73; p < 0.05) and diversity (Shannon index: 6.40 ± 0.06; p < 0.01), while the MQ population had the lowest diversity (Shannon index: 3.47 ± 0.24; p < 0.01) of fungi. The degree of variation in fungal β-diversity was significantly higher than that of bacteria. Soil organic matter (SOM) and available nitrogen (AN) contents were the core factors shaping the microbial communities in the rhizosphere soil of P. helenae, which jointly explained 49.87% and 16.39% of variations in the bacterial and fungal communities. Furthermore, population-specific enrichment of functionally significant microorganisms was evident. Population MQ was enriched with plant growth-promoting and stress-resistant fungi, such as Geminibasidium, Trichoderma, etc. Population LG was enriched with oligotrophic bacteria (e.g., Patescibacteria), while population SL exhibited an overwhelming dominance of Ascomycota (93.25%) and enrichment of pathogenic fungal genus Nigrospora. This research revealed the variations in the functional adaptation strategy of P. helenae and the microbial communities in the rhizosphere soils across different geographical locations. This suggests that microbial community imbalance in rhizosphere soil may be one of the factors leading to the endangerment of this plant species. The study proposed a differentiated protection strategy for endangered plant species based on microbial resources. The results provide a theoretical basis for development of a “microorganism-assisted protection” strategy for ecological restoration and sustainable utilization of endangered orchid plants. Full article

Optimizing seeding ratios in mixed cover crop species can maximize their ecological benefits, such as soil properties and weed suppression. A two-year field study assessed seven oat (O) and daikon radish (D) ratios (100:0 to 0:100) for their effects on soil quality, weed pressure, and subsequent spinach yield. Measured parameters included cover crop biomass, C:N ratio, land equivalence ratio (LER), soil organic carbon (SOC), microbial population, soil enzyme activities, bulk density, porosity, moisture, and water infiltration time. The impact of intercrop residues and two weeding strategies (hand weeding and no weeding) on weed pressure and spinach yield was also assessed. Oat monoculture produced the highest biomass (338.7 g m⁻²), while radish monoculture biomass was the lowest (256.1 g m⁻²). Yet the 30:70 (O:D) ratio contributed to the highest SOC (0.96). The C:N ratio of all intercropped combinations was below the critical threshold (25:1) that causes N immobilization, with oat monoculture having the highest value (23:1). The microbial population was highest with the 10:90 (O:D) ratio, with 12.8 × 10⁻⁴ most probable number per g⁻¹ soil. While urease and dehydrogenase enzyme activities were not affected by intercrop ratios, β-glucosidase and alkaline phosphatase activities were up to 30% higher in daikon radish-dominated intercrops. Bulk density decreased by 31.7% in oat monoculture, whereas infiltration time was shortened in daikon radish monoculture by 41.7% (4.6 s). Weed suppression was strongest in oat monoculture and the 90:10 (O:D) intercropping, reducing weed populations by over 30%. Spinach yield was highest in oat monoculture with hand weeding (842.9 g m⁻²), with a 40.2% increase over weeding alone. Overall, daikon radish-dominated intercropping ratios were more effective in enhancing soil properties, whereas oat-dominated intercropping improved spinach yield, mainly due to slower decomposition, thus better suppressing weeds. Full article

Intercropping, especially legume-cereal systems, is a mixed farming approach that can improve agricultural resilience by addressing challenges such as soil degradation, biodiversity loss, and global change, all while promoting the sustainable production of protein-rich and nutritious food. However, its adoption in industrialized countries remains limited due to economic and technical challenges, as well as a fragmented understanding of soil–plant-microbe interactions, which hinders its complete optimization. This article provides an overview of the current situation and future perspectives on the importance of legume–cereal intercropping, with examples such as common bean–maize, soybean–maize, alfalfa–corn–rye, and legumes–pulses–little millet systems. These combinations highlight how intercropping can improve nutrient cycling, increase root growth, forage and grain yield, suppress soil-borne diseases, and promote soil microbial population and enzymatic activity. While it offers environmental benefits, practical challenges such as system design, management complexity, and cost-effectiveness must be addressed to encourage wider adoption. In preparing this review, we synthesized studies published between 2000 and 2025, with a particular emphasis on recent research from China and Southeast Asia. We also considered broader intercropping contexts, including energy crops, agroforestry systems, rice paddy co-cultures, and phytoremediation approaches. The review also highlights legume–cereal as a solution to sustainable soil management, ecosystem health, and the potential for increased nutritional food production in developed countries. Full article

Plant Parasitic Nematodes (PPNs), such as Meloidogyne incognita, cause significant agricultural losses worldwide. Conventional nematicides like methyl bromide are being phased out due to environmental and health concerns, prompting the search for safer alternatives. In previous studies, chalcones 17, 25, and 30, flavonoid compounds, were shown to effectively kill the model nematode Caenorhabditis elegans at concentrations of 10⁻⁴ M. However, the potential of these chalcones to act synergistically at lower concentrations has not been explored. In this study, the nematicidal efficacy of chalcones 17, 25, and 30 was evaluated individually and in combination at concentrations as low as 10⁻⁶ M. The results demonstrate a strong synergistic effect, with combinations achieving 90–100% mortality in C. elegans within 3 days. Additionally, the combination index method revealed significant toxic effects against M. incognita with chalcones 17 and 30 in binary and ternary combinations. To assess the effects of these chalcones on nontarget organisms, chalcones were also tested for antimicrobial activity against soil bacteria; analysis of soil microbiota using 16S rRNA sequencing indicated that chalcones did not significantly disrupt microbial populations. Furthermore, tests on human pluripotent stem cells (hPSCs) reveal no major effects on the viability of these cells at concentrations as high as the concentrations needed to kill nematodes. These findings highlight the potential of chalcones 17, 25, and 30 for effective nematode control without harming soil bacteria or human cells. Full article

Aerobic soils serve as significant sinks for atmospheric methane, with their effectiveness influenced by the diversity and activity of soil methanotrophs. Land-use changes, particularly the conversion of natural ecosystems to agriculture, can substantially alter these microbial communities. A promising strategy to restore methane oxidation capacity is the introduction of active, ambient methane-oxidizing bacteria. The stable methane-oxidizing microbial consortium T1, dominated by Methylocystis (74%), was isolated from the soil of the unique Chernevaya Taiga forest ecosystem. The effects of inoculating this consortium were evaluated in a four week laboratory incubation experiment, using microcosms of soddy-podzolic agro-soil. Methane oxidation potential was assessed to measure methanotroph activity; methanotrophs were quantified using qPCR targeting pmoA genes; and the diversity of soil microbial communities was examined through 16S rRNA gene profiling. Inoculated soils exhibited significantly higher methane oxidation potentials compared to non-inoculated soils. Furthermore, pmoA gene copy numbers in the inoculated soils were significantly elevated (10⁶ copies pmoA g⁻¹), indicating stable persisted methanotrophic populations throughout the incubation period. These findings suggest that enriched methanotrophic consortium inoculation into agro-soils may be a promising strategy for restoring methane-oxidizing activity. Full article

The ecological interface between grasslands and farmlands forms a critical landscape component, significantly contributing to the stability and functioning of ecosystems within the agro-pastoral transition zone of northern China. Nevertheless, the variation patterns and interactions between soil physicochemical attributes and microbial community diversity at this interface remain poorly understood. In this study, we investigated nine sites located within 50 m of the grassland–farmland boundary in the Songnen Plain, northeastern China. We assessed the soil’s physicochemical properties and the composition of bacterial and fungal communities across these sites. Results indicated a declining gradient in soil physicochemical characteristics from grassland to farmland, except for pH and total phosphorus (TP). The composition of bacterial and fungal communities differed notably in response to contrasting land-use types across the ecological interface. Soil environmental variables were closely aligned with shifts observed in bacterial and fungal assemblages. Concentrations of total nitrogen (TN), available phosphorus (AP), alkali-hydrolyzable nitrogen (AN), and available potassium (AK) exhibited inverse correlations with both bacterial and fungal populations. Alterations in microbial community composition were significantly linked to TN, TP, total potassium (TK), AN, AP, AK, and soil pH levels. Variability in soil properties, as well as microbial biomass and diversity, was evident across the grassland–cropland boundary. Long-term utilization and conversion of grassland into cultivated land altered the soil’s physicochemical environment, thereby indirectly shaping the structure of microbial communities, including both bacteria and fungi. These findings provide a valuable basis for understanding the ecological implications of land-use transitions and inform microbial-based indicators for assessing soil health in agro-pastoral ecotones. Full article

Feeding a growing global population requires sustainable, innovative, and cost-effective solutions, especially in light of the environmental damage and nutrient imbalances caused by excessive chemical fertilizer use. Microalgae have gained prominence due to their phylogenetic diversity, physiological adaptability, eco-compatible characteristics, and potential to support regenerative agriculture and mitigate climate change. Functioning as biofertilizers, biostimulants, and bioremediators, microalgae accelerate nutrient cycling, improve soil aggregation through extracellular polymeric substances (EPSs), and stimulate rhizospheric microbial diversity. Empirical studies demonstrate their ability to increase crop yields by 5–25%, reduce chemical nitrogen inputs by up to 50%, and boost both organic carbon content and enzymatic activity in soils. Their application in saline and degraded lands further promotes resilience and ecological regeneration. Microalgal cultivation platforms offer scalable in situ carbon sequestration, converting atmospheric carbon dioxide (CO₂) into biomass with potential downstream vaporization into biofuels, bioplastics, and biochar, aligning with circular economy principles. While the commercial viability of microalgae is challenged by high production costs, technical complexities, and regulatory gaps, recent breakthroughs in cultivation systems, biorefinery integration, and strain optimization highlight promising pathways forward. This review highlights the strategic importance of microalgae in enhancing climate resilience, promoting agricultural sustainability, restoring soil health, and driving global bioeconomic transformation. Full article

Although significant progress has been made in the conservation of Père David’s deer (Elaphurus davidianus) populations, rapid population growth in coastal wetlands has caused severe habitat degradation. This highlights the urgent challenge of balancing ungulate population dynamics with wetland restoration efforts, particularly considering the limited data available on post-disturbance ecosystem recovery in these environments. In this study, we evaluated soil quality and bacterial community dynamics at an abandoned feeding site and a nearby control site within the Dafeng Milu National Nature Reserve during 2020–2021. The goal was to provide a theoretical basis for the ecological restoration of Père David’s deer habitat in coastal wetlands. The main findings are as follows: among the measured indicators, bulk density (BD), soil water content (SWC), sodium (Na⁺), total carbon (TC), total nitrogen (TN), total phosphorus (TP), available potassium (AK), microbial biomass nitrogen (MBN), and the Chao index were selected to form the minimum data set (MDS) for calculating the soil quality index (SQI), effectively reflecting the actual condition of soil quality. Overall, the SQI at the feeding site was lower than that of the control site. Based on the composition of bacterial communities and the functional prediction analysis of bacterial communities in the FAPROTAX database, it is shown that feeding sites are experiencing sustained soil carbon loss, which is clearly caused by the gathering of Père David’s deer. Co-occurring network analyses demonstrated the structure of the bacterial community at the feeding site was decomplexed, and with a lower intensity than the control. In RDA, Na⁺ is the main soil property that affects bacterial communities. These findings suggest that the control of soil salinity is a primary consideration in the development of Père David’s deer habitat restoration programmes, followed by addressing nitrogen supplementation and carbon sequestration. Full article

This study evaluated the effects of different doses of the herbicide fluroxypyr on soil microbial communities under controlled laboratory conditions. Specific enzymatic activities ((dehydrogenase (DA), urease (UA), catalase (CA), phosphatase (PA)) and quantitative variations in bacterial and fungal populations were measured regarding key physico-chemical soil parameters (temperature, pH, electrical conductivity, moisture, organic matter, ammonium, nitrate nitrogen, and available phosphate content). The effects of the herbicide on the targeted parameters were dose- and time-dependent. Fluroxypyr induced a clear decrease in DA, CA, and PA during the first 14 days after administration, while UA showed a decrease in the first 7 days, followed by a slight increase starting on day 14, closely related to the applied dose. Microbial populations decreased in direct relation to the fluroxypyr dose. Organic matter content exhibited a positive correlation with DA, UA, CA, as well as with microbial populations. In addition, three natural compounds structurally similar to fluroxypyr were identified via 3D virtual screening, demonstrating potential herbicidal activity. Fluroxypyr can alter soil metabolic activity and disrupt microbial communities, thereby affecting soil fertility. Used as a reference in 3D screening, fluroxypyr helped identify three natural compounds with potential herbicidal activity as safer alternatives to synthetic herbicides. Full article

The impact of long-term organic (ECO) versus conventional (CON) agricultural management on subsurface soil microbiota diversity and soil physicochemical properties remains unclear in Mediterranean vineyards. This study evaluated long-term ECO and CON effects in the Alt Penedès terroir (Spain), focusing on subsurface soil microbial diversity and soil characteristics. ECO increased the fungal-to-bacterial ratio and ammonium-oxidizing bacteria but reduced total subsurface soil bacterial populations and soil organic carbon. While ECO did not enhance annual yield production in the vineyard, fungal abundance, and ammonium-oxidizing archaea, it slightly increased the overall alpha diversity (Shannon and Inverse Simpson indexes) and significantly altered taxa composition in subsurface soil with a more robust and modular community. Crop management, soil texture, training system, and rootstock, but not vine variety, significantly influenced beta diversity in subsurface soil. The Mantel test revealed subsurface soil texture, Ca²⁺/Mg²⁺ ratio, and salinity as the main key soil drivers shifting the microbial community (beta diversity), while C/N and topsoil organic matter significantly correlated with bacterial abundance; NH₄⁺ correlated with fungal abundance; and N-Kjeldahl, pH, and Mg²⁺/K⁺ correlated with alpha diversity. Integrating soil microbiota and physicochemical monitoring allowed us to confirm the positive effect of long-term agroecological practices on subsurface soil health and to identify the critical factors shaping their microbial communities in Mediterranean vineyards. Full article

Climate change has intensified extreme weather events and accelerated soil salinization, posing serious threats to crop yield and quality. Salinity stress, now affecting about 20% of irrigated lands, is expected to worsen due to rising temperatures and sea levels. At the same time, the global population is projected to exceed 9 billion by 2050, demanding a 70% increase in food production (UN, 2019; FAO). Agriculture, responsible for 34% of global greenhouse gas emissions, urgently needs sustainable solutions. Microbial inoculants, known as “plant probiotics,” offer a promising eco-friendly alternative by enhancing crop resilience and reducing environmental impact. In this study, we evaluated the plant growth-promoting (PGP) traits and melatonin-producing capacity of Bacillus aerius EH2-5. To assess its efficacy under salt stress, soybean seedlings at the VC stage were inoculated with EH2-5 and subsequently subjected to salinity stress using 150 mM and 100 mM NaCl treatments. Plant growth parameters, the expression levels of salinity-related genes, and the activities of antioxidant enzymes were measured to determine the microbe’s role in promoting plant growth and mitigating salt-induced oxidative stress. Here, our study shows that the melatonin-synthesizing Bacillus aerius EH2-5 (7.48 ng/mL at 24 h after inoculation in Trp spiked LB media) significantly improved host plant (Glycine max L.) growth, biomass, and photosynthesis and reduced oxidative stress during salinity stress conditions than the non-inculcated control. Whole genome sequencing of Bacillus aerius EH2-5 identified key plant growth-promoting and salinity stress-related genes, including znuA, znuB, znuC, and zur (zinc uptake); ptsN, aspA, and nrgB (nitrogen metabolism); and phoH and pstS (phosphate transport). Genes involved in tryptophan biosynthesis and transport, such as trpA, trpB, trpP, and tspO, along with siderophore-related genes yusV, yfhA, and yfiY, were also detected. The presence of multiple stress-responsive genes, including dnaK, dps, treA, cspB, srkA, and copZ, suggests EH2-5′s genomic potential to enhance plant tolerance to salinity and other abiotic stresses. Inoculation with Bacillus aerius EH2-5 significantly enhanced soybean growth and reduced salt-induced damage, as evidenced by increased shoot biomass (29%, 41%), leaf numbers (12% and 13%), and chlorophyll content (40%, 21%) under 100 mM and 150 mM NaCl compared to non-inoculated plants. These results indicate EH2-5′s strong potential as a plant growth-promoting and salinity stress-alleviating rhizobacterium. The EH2-5 symbiosis significantly enhanced a key ABA biosynthesis enzyme-related gene NCED3, dehydration responsive transcription factors DREB2A and NAC29 salinity stresses (100 mM and 150 mM). Moreover, the reduced expression of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) by 16%, 29%, and 24%, respectively, and decreased levels of malondialdehyde (MDA) and hydroxy peroxidase (H₂O₂) by 12% and 23% were observed under 100 mM NaCl compared to non-inoculated plants. This study demonstrated that Bacillus aerius EH2-5, a melatonin-producing strain, not only functions effectively as a biofertilizer but also alleviates plant stress in a manner comparable to the application of exogenous melatonin. These findings highlight the potential of utilizing melatonin-producing microbes as a viable alternative to chemical treatments. Therefore, further research should focus on enhancing the melatonin biosynthetic capacity of EH2-5, improving its colonization efficiency in plants, and developing synergistic microbial consortia (SynComs) with melatonin-producing capabilities. Such efforts will contribute to the development and field application of EH2-5 as a promising plant biostimulant for sustainable agriculture. Full article

Drought is a global issue that affects agricultural productivity and sustainable development. The application of Bacillus subtilis has significant potential in alleviating drought stress and increasing yield. However, it is not yet clear how Bacillus subtilis affects microbial populations, crop yield, and the biochemical characteristics of rhizosphere soil, as well as the interactions among these factors. In this study, cotton was used as the experimental crop, and different application rates of Bacillus subtilis (0 kg·ha⁻¹ and 45 kg·ha⁻¹ (B)) and drought stress levels (H represents conventional irrigation, 350 mm; L represents 80% of conventional irrigation, 280 mm) were set as three replicates per group. The changes in rhizosphere-soil-related variables, microbial community diversity, enzyme activity, and cotton yield were studied. Compared to the control, the available nitrogen content increased by 19.76–62.40%, and soil moisture increased by 2.48–7.72%. The activities of urease, sucrase, and alkaline phosphatase increased, malondialdehyde content decreased, the Soil Plant Analysis Development (SPAD) value increased, and cotton yield increased by 8.94–9.28%. According to the structural equation model, Bacillus subtilis can increase microbial community diversity and network complexity, improve soil nutrients and enzyme activity, and increase cotton yield. This study’s findings may offer a theoretical foundation for enhancing soil quality and raising agricultural yields in arid regions. Full article

The widespread use of pesticides in modern agriculture has significantly enhanced food production by managing pests and diseases; however, their degradation in soil can lead to unintended consequences for soil fertility and nutrient cycling. This review explores the mechanisms of pesticide degradation, both abiotic and biotic, and the soil factors influencing these processes. It critically examines how degradation products impact soil microbial communities, organic matter decomposition, and key nutrient cycles, including nitrogen, phosphorus, potassium, and micronutrients. This review highlights emerging evidence linking pesticide residues with altered enzymatic activity, disrupted microbial populations, and reduced nutrient bioavailability, potentially compromising soil structure, water retention, and long-term productivity. Additionally, it discusses the broader environmental and agricultural implications, including decreased crop yields, biodiversity loss, and groundwater contamination. Sustainable management strategies such as bioremediation, the use of biochar, eco-friendly pesticides, and integrated pest management (IPM) are evaluated for mitigating these adverse effects. Finally, this review outlines future research directions emphasizing long-term studies, biotechnology innovations, and predictive modeling to support resilient agroecosystems. Understanding the intricate relationship between pesticide degradation and soil health is crucial to ensuring sustainable agriculture and food security. Full article

Due to human activities and the invasion of Spartina alterniflora, the population of Scirpus mariqueter (S. mariqueter) in the Yangtze River Estuary has gradually declined. To address this issue, numerous restoration efforts have been undertaken. To investigate the changes and influencing factors of soil bacterial communities during the restoration of S. mariqueter wetlands, we selected S. mariqueter populations as the research focus and divided the samples into two years, S1 and S2. High-throughput sequencing technology was employed for observation and analysis. The results revealed that from S1 to S2, soil bacterial diversity in the S. mariqueter wetland increased significantly and displayed clear seasonal patterns. The dominant bacterial phyla included Proteobacteria, Bacteroidota, Firmicutes, and Acidobacteriota. Among these, Proteobacteria had the highest relative abundance, while Acidobacteriota showed the most pronounced increase, surpassing Bacteroidota and Firmicutes to become the second most abundant group. Redundancy analysis (RDA) indicated that soil organic matter and electrical conductivity were the key factors influencing the composition and diversity of the soil bacterial community, with Acidobacteriota playing a dominant role during wetland restoration. In conclusion, during the ecological restoration of the S. mariqueter wetlands, attention should be given to environmental factors such as soil organic matter and electrical conductivity, while the regulatory role of Acidobacteriota in wetland soils should not be overlooked. This study provides a microscopic perspective on the interactions between microbial diversity and ecosystem functions in coastal wetlands, offering valuable guidance for the ecological restoration of degraded wetlands. Full article