Search Results (213)

The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application. Full article

The scarab species Protaetia brevitarsis, an edible insect, has been used in traditional medicine, as animal feed, and for converting agricultural organic wastes into biofertilizer. The intestinal tract, which contains a diverse array of microbiota, including viruses, plays a critical role in animal health and homeostasis. We previously conducted a comparative analysis of the gut microbiota of third-instar larvae of P. brevitarsis obtained from five different farms and found significant differences in the composition of the gut bacterial microbiota between farms. To better understand the gut microbiota, the composition of DNA viruses in the hindgut contents of P. brevitarsis larvae obtained from five farms was investigated using metagenomic sequencing in this study. The β-diversity was significantly different between metagenomic data obtained from the five farms (PERMANOVA, pseudo-F = 46.95, p = 0.002). Family-based taxonomic analysis indicated that the relative abundance of viruses in the gut overall metagenome varied significantly between farms, with viral reads comprising approximately 41.2%, 15.0%, 4.3%, 4.0%, and 1.6% of metagenomic sequences from the farms Tohamsan gumbengi farm (TO), Secomnalagum gumbengi (IS), Gumbengi brothers (BR), Kyungpook farm (KB), and Jhbio (JH), respectively. More than 98% of the DNA viruses in the hindgut were bacteriophages, mainly belonging to the Siphoviridae family. At the species level, Phage Min1, infecting the genus Microbacterium, was detected in all farms, and it was the most abundant bacteriophage in intestinal microbiota, with a prevalence of 0.9% to 29.09%. The detected eukaryotic DNA viruses accounted for 0.01% to 0.06% of the intestinal microbiota and showed little or no relationship with insect viruses. Therefore, they most likely originated from contaminated feed or soil. These results suggest that the condition of substrates used as feed is more important than genetic factors in shaping the intestinal viral microbiota of P. brevitarsis larvae. These results can be used as reference data for understanding the hindgut microbiota of P. brevitarsis larvae and, more generally, the gut virome of insects. Full article

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

Organic farming is widely recognized as a promising practice for sustainable agriculture, yet its long-term ecological impacts remain insufficiently investigated. In this study, we evaluated these impacts by comparing heavy metal concentrations, soil invertebrate communities, and microbial profiles between long-term organic and conventional farming systems. A comparative analysis was conducted on 24 plot soils from two paired organic and conventional farm systems in Beijing, each managed continuously for over 20 years. Our results revealed that soils under organic management consistently contained 10.8% to 73.7% lower heavy metals, along with reduced geo-accumulation indices (I_geo, a standardized metric for soil contamination assessment), indicating decreased contamination risks. In terms of soil fauna, while conventional soils showed higher Collembola abundance, organic farming significantly enhanced Collembola richness and diversity by 20.6% to 55.0%. Microbial sequencing likewise revealed enhanced richness and diversity of bacteria and fungi in organic soils. These microbial communities also displayed shifts in dominant taxa and more stable co-occurrence networks under organic management. Principal component analysis and Mantel tests identified soil pH and nutrients as key drivers of soil biodiversity, while heavy metals also imposed negative influences. Collectively, these findings demonstrate that long-term organic farming not only mitigates environmental risks associated with soil contaminants but also promotes belowground ecological integrity by supporting biodiversity of soil fauna and microbiota. This study highlights the ecological significance of sustained organic practices and provides critical insights for advancing sustainable agricultural developments. Full article

Assessing microbial community stability and soil quality requires understanding the role of keystone microbial taxa in maintaining diversity and functionality. This study collected soil samples from four major habitats in the urban and peri-urban areas of 20 highly urbanized provinces in China using both the five-point method and the S-shape method and explored their microbiota through high-throughput sequencing techniques. The data was used to investigate changes in the structural diversity and co-occurrence patterns of keystone microbial communities from peri-urban (agricultural land) to urban environments (hospitals, wastewater treatment plants, and zoos) across different regions. Using network analysis, we examined the structure and symbiosis of soil keystone taxa and their association with environmental factors during urbanization. Results revealed that some urban soils exhibited higher microbial diversity, network complexity, and community stability compared to peri-urban soil. Significant differences were observed in the composition, structure, and potential function of keystone microbial taxa between these environments. Correlation analysis showed a significant negative relationship between keystone taxa and mean annual precipitation (p < 0.05), and a strong positive correlation with soil nutrients, microbial diversity, and community stability (p < 0.05). These findings suggest that diverse keystone taxa are vital for sustaining microbial community stability and that urbanization-induced environmental changes modulate their composition. Shifts in keystone taxa composition reflect alterations in soil health and ecosystem functioning, emphasizing their role as indicators of soil quality during urban development. This study highlights the ecological importance of keystone taxa in shaping microbial resilience under urbanization pressure. Full article

Soil contamination with toxic inorganic elements poses a major challenge to rice cultivation, affecting plant physiology, yield, and grain safety. While natural variation in tolerance exists among rice genotypes and related species, recent advances in genomics, breeding, and biotechnology offer new opportunities to enhance adaptation. This review synthesizes the current knowledge on the physiological effects of toxic elements and explores strategies to improve tolerance, from harnessing genetic diversity to genome editing and transgenic approaches. Attention is also paid to the role of microbiota in mitigating toxicity and reducing translocation to seeds, highlighting emerging solutions for sustainable rice production in contaminated environments. Full article

Phyllosphere microbial communities influence the growth and productivity of plants, particularly in epiphytic plants, which are disconnected from nutrients available in the soil. We characterized the phyllosphere of 30 individuals of the epiphytic cycad, Zamia pseudoparasitica, collected from three forest sites during the rainy and dry seasons in the Republic of Panama. We used DNA metabarcoding to describe the total bacteria community with the 16S rRNA gene and the diazotrophic community with nifH gene. Common taxa included members of the Rhizobiales, Frankiales, Pseudonocardiales, Acetobacteriales, and the diazotrophic community was dominated by Cyanobacateria. We observed similar patterns of alpha diversity across sites and seasons, and no community differences were seen within sites between the rainy and dry seasons for either the 16S rRNA or nifH genes. However, pairwise comparisons showed some statistically significant differences in community composition between sites and seasons, but these explained only a small portion of the variation. Beta diversity partitioning indicated that communities were more phylogenetically closely related than expected by chance, indicative of strong environmental or host filtering shaping these phyllosphere communities. These results highlight the influence of host-driven selection and habitat stability in shaping phyllosphere microbiota, offering new insights into microbial assembly in tropical canopy ecosystems. Full article

Soil salinization severely limits global agricultural sustainability, particularly across the saline–alkaline landscapes of the Qinghai–Tibet Plateau. We examined how potassium fulvate (PF) modulates oat (Avena sativa L.) performance, soil chemistry, and rhizospheric microbiota in the saline–alkaline soils of the Qaidam Basin. PF markedly boosted shoot and root biomass, with the greatest response observed at 150 kg hm⁻². At the same time, it enhanced soil fertility by increasing organic matter, nitrate-N, ammonium-N, and available potassium, and improved ionic balance by lowering Na⁺ concentrations and the sodium adsorption ratio (SAR), while increasing Ca²⁺ levels and soil moisture content. Under the high-dose treatment (F2), endogenous fungal contributions declined sharply, exogenous replacements increased, and fungal α-diversity fell; multivariate ordinations confirmed that PF reshaped both bacterial and fungal communities, with fungi exhibiting the stronger response. We integrated three machine learning algorithms—least absolute shrinkage and selection operator (LASSO), Random Forest (RF), and eXtreme Gradient Boosting (XGBoost)—to minimize the bias inherent in any single method. We identified microbial β-diversity, organic matter, and Na⁺ and Ca²⁺ concentrations as the most robust predictors of the Soil Salinization and Alkalization Index (SSAI). Structural equation modeling further showed that PF mitigates salinity chiefly by improving soil physicochemical properties (path coefficient = −0.77; p < 0.001), with microbial assemblages acting as key intermediaries. These findings provide compelling theoretical and empirical support for deploying PF to rehabilitate saline–alkaline soils in alpine environments and offer practical guidance for sustainable land management in the Qaidam Basin. Full article

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article

In the African Sahel, fonio (Digitaria sp.) is a cereal crop that alleviates mid-season hunger before other main crops are harvested. As fonio is valued for its ability to grow under low nutrient and drought conditions, it was hypothesized that it may contain endophytic bacteria that can tolerate such extreme stress. White fonio seeds were obtained from a dry environment (Mali) and a moderate rainfall environment (Guinea). Plants were grown indoors on field soil mixed with sand to mimic Sahelian soils, grown at 30 °C, and exposed to drought, optimal water, and low nitrogen stress conditions. In total, 73 cultured bacteria were classified using full-length 16S rRNA sequencing followed by searching three 16S reference databases. Selected strains were tested in vitro for tolerance to relevant abiotic stresses. Including nine isolates from seeds, the candidate root/shoot endophytes spanned 27 genera and 18–39 top-match species. Several well-known nitrogen-fixing bacteria were cultured, including Ensifer. Leaves were dominated by Bacilli (spore-formers known to withstand dry conditions). There were five root isolates of Variovorax. Leifsonia was isolated from the leaves and showed 100% sequence identity with seed isolates, suggestive of transmission from seed to shoot. In vitro experiments showed that seed isolates, including Leifsonia, survived diverse abiotic stresses relevant to the Sahel. Combined, these results suggest that white fonio hosts stress-tolerant microbiota, and points to Leifsonia as a candidate seed-to-plant transmitted endophyte, pending confirmation by future whole genome sequencing. This microbial collection serves as a starting point for long-term experiments to understand stress tolerance in this under-studied crop. Full article

Despite their effectiveness in eliminating weeds, herbicides can indirectly and directly affect organisms, leading to a decline in species abundance as well as disruptions to the structure and functioning of ecosystems. Boxer 800 EC, whose active ingredient is prosulfocarb, is an active herbicide commonly used for weed control, but its potential ecological risks are not well understood. With this in mind, a study was conducted to evaluate the effectiveness of sodium alginate and sodium polyacrylate in restoring homeostasis to soil exposed to Boxer 800 EC herbicide. This involved a two-factor pot experiment: factor I—herbicide dose (0.0, 0.8, 4.8, and 48.0 mg kg⁻¹ d.m.); factor II—polymer type (soil with the polymer additives sodium alginate, and sodium polyacrylate). The experiment was carried out on Eutric Cambisols with four replicates and lasted for 50 days. The test plant was Triticum aestivum L., cultivar “KWS Dorium C1”. The contaminant herbicide doses inhibited the proliferation of organotrophic bacteria and actinobacteria and reduced the colony development index (CD) and ecophysiological diversity index (EP) values for these microorganisms. The addition of sodium alginate to the soil increased the proliferation of these microorganisms, whereas sodium polyacrylate inhibited their development. Sodium alginate also increased the colony development index value of organotrophic bacteria and actinobacteria. Across all the analyzed factors, bacteria from the phylum Proteobacteriota dominated. However, the presence of herbicides and polymers changed the abundance of these bacteria. Bacteria of the genus Sphingomonas were the most prevalent genus in the samples. The herbicide Boxer 800 EC exerted a toxic effect on the growth and development of spring wheat, which was reflected in the plant biomass yield (shoot and ear) and the SPAD index. The recommended herbicide dose (0.80 mg kg⁻¹) did not cause significant changes in the growth and development of spring wheat. The hydrogel control additives deepened the negative effect of the herbicide on plant development. While the herbicide significantly reduced the levels of available carbon and total nitrogen in the soil, the polymers increased these parameters. Full article

Phytoremediation using Avena sativa offers a sustainable strategy for mitigating sulfentrazone contamination while integrating bioenergy production. This study proposes an analysis of the bioenergy potential and the microbial metagenomic profile associated with Avena sativa in the presence and absence of sulfentrazone, aiming at the synergistic bioprospecting of microbial communities capable of biodegradation and remediation of contaminated environments. Using a randomized block design, we evaluated the bioenergy potential and rhizospheric microbial dynamics of A. sativa in soils with and without sulfentrazone (600 g ha⁻¹). Herbicide residues were quantified via UHPLC-MS/MS, and metagenomic profiles were obtained through 16S rRNA gene and ITS region sequencing to assess shifts in rhizospheric microbiota. Microbial diversity was analyzed using the Shannon and Gini–Simpson Indices, complemented by Principal Component Analysis (PCA). Bioenergy yields (biogas and ethanol) were estimated based on plant biomass. Over 80 days, the cultivation of A. sativa promoted a 19.7% dissipation of sulfentrazone, associated with rhizospheric enrichment of plant growth-promoting taxa (Bradyrhizobium, Rhodococcus, and Trichoderma), which increased by 68% compared to uncontaminated soils. Contaminated soils exhibited reduced microbial diversity (Gini–Simpson Index = 0.7), with a predominance of Actinobacteria and Ascomycota, suggesting adaptive specialization. Despite herbicide-induced stress (39.3% reduction in plant height and 60% reduction in grain yield), the biomass demonstrated considerable bioenergy potential: 340.6 m³ ha⁻¹ of biogas and 284.4 L ha⁻¹ of ethanol. The findings highlight the dual role of A. sativa in soil rehabilitation and renewable energy systems, supported by plant–microbe synergies. Scalability challenges and regulatory gaps in ecotoxicological assessments were identified, reinforcing the need to optimize microbial consortia and implement region-specific management strategies. These results support the integration of phytoremediation into circular bioeconomy models, balancing ecological recovery with agricultural productivity. Future research should focus on microbial genetic pathways, field-scale validation, and the development of regulatory frameworks to advance this green technology in global soil remediation efforts. Full article

Morel mushrooms (Morchella spp.) are prized for their nutritional and medicinal value. Despite extensive research on their cultivation, the species’ impacts on the soil microbiota and minerals remain unclear. This study systematically evaluated six Morchella species, analyzing their effects on soil physicochemical properties, microbial communities, and mineral nutrients levels. The results showed that yield varied significantly among the species, with an order of M. sextelata > M. exuberans > M. eximia > M. importuna > Mel-13 > Mel-21. Cultivation led to a consistent reduction in soil NO₃⁻-N levels, particularly in M. eximia and Mel-13 (40–50% decrease), while NH₄⁺-N levels did not change significantly, indicating mycelial nitrate preference. Mineral nutrient alterations exhibited distinct species-dependent patterns, with M. eximia showing the greatest increase in exchangeable Ca, while M. importuna and M. sextelata caused the most obvious decreases in available B. Morchella species exerted more pronounced impacts on fungal than bacterial communities, evidenced by significant reductions in alpha diversity—particularly in high-yield M. sextelata—suggesting species-specific fungal inhibition. At the phylum level, consistent depletion of Ascomycota but enrichment of Mortierellomycota were noted. Moreover, correlation analyses identified significant positive associations between morel yield and both fungal community diversity and exchangeable Ca content. This implies that Morchella species restructures soil fungal communities through nutrient competition and mineral-mediated regulation, with calcium acting as a key modulator. Overall, by elucidating the interconnected ‘Morchella species–microbe–mineral’ relationships, this study highlights Morchella species’ distinct regulation of soil microecology, providing valuable insights for the selection of optimized species like M. eximia and targeted soil management in morel cultivation. Full article

Pleurotus tuoliensis is a valuable edible mushroom native to Xinjiang in northwest China. It colonizes the roots and stems of Ferula plants. Field inoculation in its natural habitat has been shown to significantly enhance the colonization rate of P. tuoliensis hyphae in Ferula plants. However, the effects of field inoculation on P. tuoliensis hyphal colonization, soil properties, and microbial communities remain underexplored. In this study, we examined the characteristics of rhizosphere soil and microbial communities under four conditions: natural environments with and without hyphal colonization, and field inoculation with and without colonization. High-throughput sequencing results revealed that field inoculation markedly increased the relative abundance of Pleurotus species (57.98%) compared to natural colonization (14.11%). However, field inoculation also resulted in a reduction in microbial community diversity compared to hyphal colonization. Concurrently, the relative abundance of Pseudomonadota, Bacteroidota, and Bacillota significantly increased following field inoculation. LEfSe analysis suggested that the identified potential biomarkers were most likely associated with the Bacillus genus within Bacillota. Furthermore, mushroom growth-promoting bacteria were successfully isolated and identified as members of the Bacillus cereus group (L5) and Bacillus safensis (S16). This finding suggests that field inoculation with P. tuoliensis in its natural habitat promotes microbial communities that enhance its growth. This study offers new insights into conserving wild edible fungi and their interactions with soil microbiota. Full article

This study evaluated the effects of Trichoderma harzianum strain T-22 on wheat (Triticum turgidum L. var. Durum, cv. Vitron) growth and soil microbial dynamics. Three inoculation levels (I0, I1, and I2) were applied to different soil substrates: Villacañas soil (V), Quero soil (Q), and composted sewage sludge (C) from Alcázar de San Juan. Over six months, soil physicochemical properties, fungal diversity, and plant development were analyzed. The results showed that Trichoderma significantly increased fungal diversity, particularly in compost-amended substrates. In treatments with composted sludge and Trichoderma (CVI2 and CQI2), Trichoderma colonization reached up to 112,000 propagules/g, enhancing microbial activity. Higher shoot biomass and spike weight were observed when combining compost with Trichoderma since it improved nutrient availability and plant growth. Additionally, Trichoderma inoculation reduced the presence of pathogenic fungi such as Helminthosporium and Fusarium, reinforcing its biocontrol potential. However, high salinity of the soil limited microbial proliferation and plant performance. In conclusion, composted sludge and Trichoderma improved soil microbiota, enhanced wheat growth, and increased resistance against pathogens. The results highlight the potential of Trichoderma as a sustainable alternative to chemical treatments in crop production. Further studies should further investigate field-scale applications to validate these findings under real agricultural conditions. Full article