Search Results (434)

Examining the changing patterns and underlying mechanisms of soil biomass carbon stocks constitutes a fundamental aspect of soil biology. Despite the potential influence of the sulfur cycle and the life strategies of organisms on community biomass, these factors have rarely been studied in tandem. Biocrusts are model systems for studying soil ecosystems. In this study, metagenomic analysis of biocrusts related to different life strategies from five batches over four consecutive years demonstrated that, in free-living communities, microbial biomass carbon (MBC) synthesis, via assimilatory sulfate reduction (ASR), is primarily coupled with the 3-hydroxypropionate/4-hydroxybutyrate and Calvin–Benson–Bassham cycles. These pathways are affected by the oxidation-reduction potential (Eh), pH, electrical conductivity, and nutrient levels. The decomposition of organic carbon (OC) via dissimilatory sulfate reduction (DSR) was accompanied by the production of dimethyl sulfide (DMS), which was influenced by the C/S ratio and moisture, whereas the synthesis of MBC by symbiotic communities was found to be affected by Eh and pH, and decomposition was affected by the C/S ratio. The MBC stock was influenced by all strategies, with resource strategies having the greatest impacts during the growing season, and the contribution of chemotrophic energy was most significant in free-living communities. In conclusion, the MBC in biocrusts is associated with both ASR and DSR and is facilitated by the A-, S-, and P-strategies under the regulation of the stoichiometric C/S ratio. The exploration of microbial life strategies and sulfur cycling in biocrusts within arid ecosystems in this study offers a new perspective on the patterns of change in soil biomass carbon stocks. Full article

The natural phenolic compound p-coumaric acid supports honey bee health by enhancing detoxification, immunity and longevity. It also possesses antioxidant, anti-inflammatory and anticancer properties relevant to human health. While commonly detected in honey and pollen, it is absent from nectar and sucrose-based supplements typically used in beekeeping. Concerns have been raised whether supplemental saccharide feeding deprives bees of this essential phytochemical. In this study, we quantified p-coumaric acid in various bee-derived products and in supplementary sucrose syrup before and after feeding to bees, using HPLC-HRMS analysis. Although fresh sucrose syrup contained negligible amounts of p-coumaric acid, syrup stored in capped combs exhibited levels comparable to or higher than those in honey. We identified propolis in combs as the primary source of p-coumaric acid, diffusing into both honey and sucrose syrup during storage. Our findings demonstrate that supplemental feeding with sucrose syrup does not diminish the bees’ access to this key phytochemical and underscore the importance of a propolis-rich environment in bee health management. Full article

The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant–microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed. Full article

Bacterial diseases cause significant economic losses and pose a major challenge to global crop yields. These diseases reduce yields and affect food security, particularly for small-scale farmers in developing regions. Post-harvest losses also contribute to resource waste, soil degradation, and deforestation. Conventional management strategies, such as synthetic fungicides and antimicrobials, raise concerns about environmental sustainability, human health, and pathogen resistance. Bacteriophages—viruses that selectively infect bacterial pathogens—offer a highly specific and eco-friendly alternative for disease management both post-harvest and pre-harvest, reducing the need for chemical pesticides throughout the plant lifecycle. This review examines bacteriophage biology, advantages over traditional treatments, and challenges to their application. Phages effectively target pathogens such as Pectobacterium, Xanthomonas, Xylella, Clavibacter, and Dickeya, while preserving beneficial microorganisms. Key challenges include bacterial resistance, regulatory hurdles, and phage stability under environmental conditions. Advances in phage genomics, bioengineering, and formulation have enhanced viability and efficacy, supporting phages as promising biocontrol agents. Integrating phage therapy with other eco-friendly strategies may improve effectiveness further. Future research should focus on optimizing production, refining regulations, and large-scale field studies to ensure practical feasibility. Addressing these issues will help bacteriophages contribute significantly to sustainable plant disease management and global food security. Full article

Seed-related traits such as seed size, germination, vigour, dormancy, biochemical composition, and stress resistance are critical to ensuring agricultural productivity and global food security, particularly in current scenarios of climate change and environmental unpredictability. This review examines the transformative potential of omics technologies, encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics, in enhancing our understanding of seed biology and its applications in crop improvement. Genomics and transcriptomics are key technologies in future plant breeding and gene editing to optimise seed yield and quality. We reviewed the role of metabolomic approaches in uncovering the molecular mechanisms behind seed germination, vigour, dormancy, and the proteomic advances to elucidate markers of seed quality, combining these omic technologies to decipher DOG1 as a marker of dormancy. Both biotic and abiotic stress resistance in seeds were reviewed from a multi-omics perspective to determine the best avenues for improving the resilience of seeds against drought, salinity and pathogens. Moreover, omics approaches have been reviewed to optimise plant–microbe interactions, particularly in enhancing symbiotic relationships within the soil microbiome. Full article

The alarming increase in the use of chemically driven pesticides for enhanced crop productivity has severely affected soil fertility, ecosystem balance, and consumer health. Inadequate handling protocols and ineffective remediation strategies have led to elevated pesticide concentrations, contributing to human respiratory and metabolic disorders in humans. In the current context, where agricultural activities and pesticide applications are intertwined, strong and sustainable remediation strategies are essential for environmental protection without sacrificing crop productivity. Various bio-inspired methods have been reported, such as phytoremediation, bioremediation, and in situ remediation; however, limited success has been observed with either single or combined approaches. Consequently, biopolymer biomanufacturing, nanoparticle-based bioengineering, and computational biology for improved understanding of mechanisms have been revisited to incorporate updated methodologies that detail the fate and action of harmful chemical pesticides in agriculture. An in silico mechanistic approach has been emphasized to understand the molecular mechanisms involved in agricultural pesticides’ degradation using nanomaterials. A roadmap has been created by integrating cutting-edge machine learning techniques to develop nature-inspired sustainable agricultural practices and contaminant disposal methods. This review represents a pioneering effort to explore the roles of wet-lab chemistry and in silico methods in mitigating the effects of agricultural pesticides, providing a comprehensive strategy for balancing environmental sustainability and agricultural practices. Full article

Biological control with beneficial bacteria offers a sustainable alternative to synthetic agrochemicals for managing plant pathogens and enhancing plant health. However, bacterial biocontrol agents (BCAs) remain underexploited due to regulatory hurdles (such as complex registration timelines and extensive dossier requirements) and limited strain characterization. Recent advances in omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have strengthened the bioprospecting pipeline by uncovering key microbial traits involved in biocontrol. Genomics enables the identification of biosynthetic gene clusters, antimicrobial pathways, and accurate taxonomy, while comparative genomics reveals genes relevant to plant–microbe interactions. Metagenomics uncovers unculturable microbes and their functional roles, especially in the rhizosphere and extreme environments. Transcriptomics (e.g., RNA-Seq) sheds light on gene regulation during plant-pathogen-bacteria interactions, revealing stress-related and biocontrol pathways. Metabolomics, using tools like Liquid Chromatography–Mass Spectrometry (LC-MS) and Nuclear Magnetic Resonance spectroscopy (NMR), identifies bioactive compounds such as lipopeptides, Volatile Organic Compounds (VOCs), and polyketides. Co-culture experiments and synthetic microbial communities (SynComs) have shown enhanced biocontrol through metabolic synergy. This review highlights how integrating omics tools accelerates the discovery and functional validation of new BCAs. Such strategies support the development of effective microbial products, promoting sustainable agriculture by improving crop resilience, reducing chemical inputs, and enhancing soil health. Looking ahead, the successful application of omics-driven bioprospection of BCAs will require addressing challenges of large-scale production, regulatory harmonization, and their integration into real-world agricultural systems to ensure reliable, sustainable solutions. Full article

Antibiotic resistance remains one of the most formidable challenges to modern medicine, threatening to outpace therapeutic innovation and undermine decades of clinical progress. While resistance was once viewed narrowly as a clinical phenomenon, it is now understood as the outcome of complex ecological and molecular interactions that span soil, water, agriculture, animals, and humans. Environmental reservoirs act as silent incubators of resistance genes, with horizontal gene transfer and stress-induced mutagenesis fueling their evolution and dissemination. At the molecular level, advances in genomics, structural biology, and systems microbiology have revealed intricate networks involving plasmid-mediated resistance, efflux pump regulation, integron dynamics, and CRISPR-Cas interactions, providing new insights into the adaptability of pathogens. Simultaneously, the environmental dimensions of resistance, from wastewater treatment plants and aquaculture to airborne dissemination, highlight the urgency of adopting a One Health framework. Yet, alongside this growing threat, novel therapeutic avenues are emerging. Innovative β-lactamase inhibitors, bacteriophage-based therapies, engineered lysins, antimicrobial peptides, and CRISPR-driven antimicrobials are redefining what constitutes an “antibiotic” in the twenty-first century. Furthermore, artificial intelligence and machine learning now accelerate drug discovery and resistance prediction, raising the possibility of precision-guided antimicrobial stewardship. This review synthesizes molecular insights, environmental drivers, and therapeutic innovations to present a comprehensive landscape of antibiotic resistance. By bridging ecological microbiology, molecular biology, and translational medicine, it outlines a roadmap for surveillance, prevention, and drug development while emphasizing the need for integrative policies to safeguard global health. Full article

Amidst the rapid development of renewable energy, wind power, as a major renewable energy source, has raised ecological concerns regarding its impacts on ecosystems and biodiversity. Insects, as direct displays and feedback of the environment, have become a hot topic in ecology and conservation biology research due to the impact of environmental changes on them. So this study investigates the effects of wind power density on insect diversity and their mechanisms in the Ningxia desert steppe wind farms. The results indicated that minimal disturbance marginally increased insect aggregation at low wind power densities (2 turbines/km²). However, higher wind power densities caused pronounced insect population declines toward turbines (6, 11 turbines/km²), and with the increase in wind power density, the number of insects decreased significantly. Increased wind power disturbance led to decreases in soil total nitrogen (TN), total carbon (TC), nitrate nitrogen (NO₃⁻-N), and soil moisture content (SM) and a significant decrease in total phosphorus (TP). While direct impacts on vegetation were relatively minor and irregular, vegetation height exhibited strong positive correlations with soil nutrient depletion, suggesting that wind-induced soil degradation indirectly constrains plant growth. Consequently, the effect of wind power on insects is mediated through coupled vegetation–soil interactions. These findings underscore the necessity of integrating ecological thresholds into wind farm management protocols. Full article

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in Galicia (NW Spain) and their relationship with Boletus edulis and Boletus reticulatus mycelium prevalence and concentration. Soil microbiota richness, diversity, and composition, as well as seasonal variation in Boletus mycelium, were assessed using DNA metabarcoding and qPCR, respectively. Sampling was conducted in autumn at two 30–40-year-old Q. robur stands. Bacterial communities were dominated by Acidobacteria (34%) and Proteobacteria (33%), with Acidobacterium (12%), Paludibaculum (9%), and Edaphobacter (7%) identified as most abundant. Fungal communities were primarily Basidiomycota (93%), led by Russula (46%). For both bacteria and fungi, the highest OTU richness was observed in September, followed by a significant decrease in October and a partial recovery in November. Boletus species were found to exhibit positive correlations with specific bacteria (e.g., Massilia, Rhizobium) and fungi (e.g., Amanita, Clavaria, Inocybe, Scleroderma, Suillus and Mortierella), suggesting a potential influence of these microbes on mycelium development. This study provides novel insights into the seasonal dynamics of soil microbiota and their potential role in Boletus ecology, thereby advancing understanding of host–microbe interactions in temperate forests. Full article

Earthworms and enchytraeids are two very important groups of soil organisms that influence soil biology and ecology, as well as physicochemical processes occurring in the soil. The interactions within and between these major groups of soil fauna are currently among the most pressing topics in soil ecology and are still insufficiently understood. In a field mesocosm experiment, we examined the effects of the density of the following five key earthworm species in Central Europe: Dendrobaena octaedra, Lumbricus rubellus, L. terrestris, Aporrectodea caliginosa, and Allobophora chlorotica. These species were selected to represent the following three major ecological groups of lumbricids: epigeic, endogeic, and anecic. The mesocosm experiment examined the effect of these species across density gradients and at two soil profile horizons—litter and mineral soil—and at the entire soil profile within the mesocosm. This comprehensive and unique approach was used to compare the effects of earthworm density gradient on enchytraeid abundance under identical conditions in the forest soil. The results indicate that all studied species of earthworm negatively affected enchytraeid density. The strength of this effect depended on the earthworm species, earthworm density, and the level of the analyzed soil profile. Epigeic L. rubellus, endogeic Aporrectodea caliginosa, and anecic L. terrestris appeared to be the most effective. Higher earthworm density had a greater effect on the density of enchytraeids. The most significant results concerned the litter layer, where the density of enchytraeids was highest due to their natural occurrence. Our results provide new insights into the ecological relationships among key groups of soil fauna and can be a starting point for predicting changes caused by earthworms in newly occupied ecosystems. Full article

Soil saline–alkali stress is a major problem faced by global agriculture, and there is an urgent need to develop efficient amelioration strategies. While both probiotics and plant stress-resistant molecules play critical roles in the alleviation of crop stress, their efficient retention in crop rhizosphere regions remains a great challenge. In this study, the nanocarrier ZIF-8@SPBP@betaine (ZSBet) was constructed by introduction of the synthesized polysaccharide-binding protein (SPBP) and the stress-resistant molecule betaine to the metal–organic framework ZIF-8. During co-incubation, the probiotic Novosphingobium capsulatum and ZSBet efficiently bound together to form ZSBet + Novo co-assemblies, i.e., the integrated protein-ZIF-8-probiotic complexes mediated by polysaccharide-receptor recognition, which exhibited strong root-binding abilities. Microbiome analysis revealed that ZSBet + Novo reduced the α-diversity of rhizosphere bacteria and increased the absolute abundance of biofilm formation-related bacteria, e.g., Novosphingobium, Sphingobium, and Lactococcus. During wheat cultivation in saline–alkali soil, ZSBet + Novo reduced soil pH by 0.63 units, decreased soil salt content by 0.11 g/kg, and increased soil nutrient levels. Furthermore, the co-assembly enhanced the wheat grain number by 145.05% and reduced root malondialdehyde and proline contents by 42.00% and 39.13%, respectively. This study provides a new strategy for improving crop resistance under saline–alkali stress in combination with nanotechnology and synthetic biology. Full article

Soil organic carbon (SOC) represents a crucial factor in agricultural production, and its accumulation is influenced by soil microbial community and microbial metabolism. Straw returning combined with decomposing agents is recognized practice to enhance SOC. On the other hand, the impacts of controlled-release nitrogen fertilizer (CR) on the function of the decomposing agent in degrading straw are underexplored. In this study, an incubation experiment with ¹³C labeled straw in three nitrogen fertilizer treatments (CK, no nitrogen applied; UR, urea applied; CR, controlled-release fertilizer applied) was carried out to elucidate how CR regulates the straw decomposition agent and bacterial community to influence the SOC sequestration, based on field experiments. And we examined the changes in soil organic carbon and the stability of the bacterial networks by combining co-occurrence networks and a structural equation model. In the incubation experiment, the results demonstrated that CR increased the relative abundance of straw decomposition agent and straw-derived SOC (SO¹³C). Additionally, CR enhanced the stability of soil bacterial networks, compared with UR, by strengthening the interactions within the soil bacterial community. Pearson correlations confirmed that straw decomposition agent was positively associated with SO¹³C. Moreover, the straw decomposition agent was positively correlated with the activities of the nitrogen-cycling enzyme (urease, N-acetyl-β-glucosaminidase) and carbon-degrading enzyme (β-1,4-glucosidase, cellulase). Furthermore, structural equation modeling indicated that soil inorganic nitrogen played the most direct role in changes in the straw decomposition agent and then indirectly stimulated the activity of cellulase, ultimately increasing straw-derived carbon in the soil. This study elaborates the mechanism of straw returning combined with straw decomposition agent and controlled-release fertilizers to enhance the SOC of coastal saline–alkali soil from the perspective of underground biology. Collectively, the results of this research might improve the management of straw returning and sustainable utilization of fertility in saline–alkali soil. It provides a new perspective on fertilization for increasing soil carbon sequestration in future farmland ecosystems. Full article

Heavy metals represent long-lasting contaminants that pose significant risks to both human health and ecosystem integrity. Originating from both natural and anthropogenic activities, they bioaccumulate in organisms through the food web, leading to widespread and long-lasting contamination. Industrialization, agriculture, and urbanization have exacerbated soil and water contamination through activities such as mining, industrial production, and wastewater use. In response to this challenge, biochar produced from waste materials such as sewage sludge has emerged as a promising remediation strategy, offering a cost-effective and sustainable means to immobilize heavy metals and reduce their bioavailability in contaminated environments. Here we explore the potential of phosphate-enriched biochar, derived from sewage sludge, to adsorb and stabilize heavy metals in polluted soils. Sewage sludge was pyrolyzed at various temperatures to produce biochar. A soil incubation experiment was conducted by adding phosphate-amended biochar to contaminated soil and maintaining it for one month. Heavy metals were extracted using a CaCl₂ extraction method and analyzed using atomic absorption spectrophotometry. Results demonstrated that phosphate amendment significantly enhanced the biochar’s capacity to immobilize heavy metals. Amending soils with 2.5 wt% phosphate-enriched sewage sludge biochar led to reductions in bioavailable Cd (by 65–82%), Zn (40–75%), and Pb (52–88%) across varying pyrolysis temperatures. Specifically, phosphate-amended biochar reduced the mobility of Cd and Zn more effectively than unamended biochar, with a significant decrease in their concentrations in soil extracts. For Cu and Pb, the effectiveness varied with pyrolysis temperature and phosphate amendment, highlighting the importance of optimization for specific metal contaminants. Biochar generated from elevated pyrolysis temperatures (500 °C) showed an increase in ash content and pH, which improved their ability to retain heavy metals and limit their mobility. These findings suggest that phosphate-amended biochar reduces heavy metal bioavailability, minimizing their entry into the food chain. This supports a sustainable approach for managing hazardous waste and remediating contaminated soils, safeguarding ecosystem health, and mitigating public health risks. Full article

The structure of a scientific article is crucial for clearly conveying research findings. Modern scientific publications combine text with various elements—such as tables, graphs, images, diagrams, and maps—that support the narrative and aid data interpretation. Understanding how these components influence a publication’s reception and scientific impact is essential. This study analyzes differences among 15 soil science journals (indexed in the Web of Science) in terms of visual elements, tables, number of authors, and article length. The journals had a 5-year Impact Factor (2023) ranging from 0.9 (Soil and Environment) to 10.4 (Soil Biology and Biochemistry). The Kruskal–Wallis test and Bonferroni-adjusted Dunn’s post hoc tests revealed statistically significant differences across all variables (p < 0.05). The relationships were further assessed using Pearson’s correlation, based on the median number of authors and article length, as well as the percentage of articles that include at least one element of a given type (e.g., table, graph, image, diagram, or map). Key findings show that journals with a higher impact factor tend to publish articles with more authors (r = 0.62, p = 0.014), use diagrams more frequently (r = 0.69, p = 0.004), and include fewer tables (r = –0.85, p < 0.001). These results suggest that journals with a higher 5-year IF tend to include articles with a greater number of authors and a higher frequency of diagram use, while relying less on tables. Full article