Search Results (2,246)

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

Salinization hinders the restoration of vegetation in salt-affected soils by negatively impacting plant growth and development. Halophytes play a key role in the restoration of saline and degraded lands due to unique features explaining their growth aptitude in such extreme ecosystems. Suaeda fruticosa is an euhalophyte well known for its medicinal properties and its potential for saline soil phytoremediation. However, excessive salt accumulation in soil limits the development of this species. Research findings increasingly advocate the use of extremophile rhizosphere bacteria as an effective approach to reclaim salinized soils, in conjunction with their salt-alleviating effect on plants. Here, a pot experiment was conducted to assess the role of a halotolerant plant growth-promoting actinobacterium, Glutamicibacter sp., on the growth, nutritional status, and shoot content of proline, total soluble carbohydrates, and phenolic compounds in the halophyte S. fruticosa grown for 60 d under high salinity (600 mM NaCl). Results showed that inoculation with Glutamicibacter sp. significantly promoted the growth of inoculated plants under stress conditions. More specifically, bacterial inoculation increased the shoot concentration of proline, total polyphenols, potassium (K⁺), nitrogen (N), and K⁺/Na⁺ ratio in shoots, while significantly decreasing Na⁺ concentrations. These mechanisms partly explain S. fruticosa tolerance to high saline concentrations. Our findings provide some mechanistic elements at the ecophysiological level, enabling a better understanding of the crucial role of plant growth-promoting rhizobacteria (PGPRs) in enhancing halophyte growth and highlight their potential for utilization in restoring vegetation in salt-affected soils. Full article

In response to the challenges posed by soil degradation in the arid regions of Xinjiang, China, green and organic management practices have emerged as effective alternatives to conventional agricultural management methods, helping to mitigate soil degradation by promoting natural soil recovery and ecological balance. However, most of the existing studies focus on a single management practice or indicator and lack a systematic assessment of the effects of integrated orchard management in arid zones. This study aims to investigate how different agricultural management practices influence soil physicochemical properties and inter-root microbial communities in apple orchards in Xinjiang and to identify the main physicochemical factors affecting the composition of inter-root microbial communities. Inter-root soil samples were collected from apple orchards under green management (GM), organic management (OM), and conventional management (CM) in major apple-producing regions of Xinjiang. Microbial diversity and community composition of the samples were analyzed using high-throughput amplicon sequencing. The results revealed significant differences (p < 0.05) in soil physicochemical properties across different management practices. Specifically, GM significantly reduced soil pH and C:N compared with OM. Both OM and GM significantly decreased soil available nutrient content compared with CM. Moreover, GM and OM significantly increased bacterial diversity and changed the community composition of bacteria and fungi. Proteobacteria and Ascomycota were identified as the dominant bacteria and fungi, respectively, in all management practices. Linear discriminant analysis (LEfSe) showed that biomarkers were more abundant under OM, suggesting that OM may contribute to ecological functions through specific microbial taxa. Co-occurrence network analysis (building a network of microbial interactions) demonstrated that the topologies of bacteria and fungi varied across different management practices and that OM increased the complexity of microbial co-occurrence networks. Mantel test analysis (analyzing soil factors and microbial community correlations) showed that C:N and available potassium (AK) were significantly and positively correlated with the community composition of bacteria and fungi, and that C:N, soil organic carbon (SOC), and alkaline hydrolyzable nitrogen (AN) were significantly and positively correlated with the diversity of fungi. Redundancy analysis (RDA) further indicated that SOC, C:N, and AK were the primary soil physicochemical factors influencing the composition of microbial communities. This study provides theoretical guidance for the sustainable management of orchards in arid zones. Full article

The unique properties of phthalocyanines (Pcs), such as strong absorption, high photostability, effective singlet oxygen generation, low toxicity and biocompatibility, versatile chemical modifications, broad spectrum of antimicrobial activity, and synergistic effects with other treatment modalities, make them a preferred superior sensitizer in the field of antimicrobial photodynamic therapy. The photodynamic and sonodynamic activity of 3-(3-(diethylamino)phenoxy)propanoxy substituted silicon(IV) Pc were evaluated against bacteria and cancer cells. Stability and singlet oxygen generation upon light irradiation and ultrasound (1 MHz, 3 W) were assessed with 1,3-diphenylisobenzofuran. The phthalocyanine revealed high photostability in DMF and DMSO, although the singlet oxygen yields under light irradiation were low. On the other hand, the phthalocyanine revealed excellent sonostability and caused a high rate of DPBF degradation upon excitation by ultrasounds at 1 MHz. The silicon phthalocyanine presented significant bacterial reduction growth, up to 5 log against MRSA and S. epidermidis upon light excitation, whereas the sonodynamic effect was negligible. The phthalocyanine revealed high activity in both photodynamic and sonodynamic manner toward hypopharyngeal tumor (FaDu, 95% and 42% reduction, respectively) and squamous cell carcinoma (SCC-25, 96% and 62% reduction, respectively). The sensitizer showed ca. 30% aldehyde dehydrogenase inhibition in various concentrations and up to 85% platelet-activating factor acetylhydrolase for 0.25 μM, while protease-activated protein C was stimulated up to 66% for 0.75 μM. Full article

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

Leather biodegradation is a complex microbial process with increasing relevance for sustainable waste management. In this study, we investigated bacterial communities responsible for the degradation of leather treated with different tanning agents (chrome, Zeolite, Biole^®) using high-throughput 16S rRNA gene sequencing and metatranscriptomic analysis. Proteobacteria, Bacteroidetes, and Patescibacteria emerged as the dominant phyla, while genera such as Acinetobacter, Pseudomonas, and Sphingopyxis were identified as key contributors to enzymatic activity and potential metal resistance. A total of 1302 enzymes were expressed across all the conditions, including 46 proteases, with endopeptidase La, endopeptidase Clp, and methionyl aminopeptidase being the most abundant. Collagen samples exhibited the highest functional diversity and total enzyme expression, whereas chrome-treated samples showed elevated protease activity, indicating selective pressure from heavy metals. Differential enzyme expression patterns were linked to both the microbial identity and tanning chemistry, revealing genus- and treatment-specific enzymatic signatures. These findings deepen our understanding of how tanning agents modulate the microbial structure and function and identify proteases with potential applications in the bioremediation and eco-innovation of leather waste processing. Full article

This study elucidates how the quorum-sensing (QS) signal 3OC12-HSL exacerbates enterotoxigenic E. coli (ETEC) pathogenicity and intestinal barrier dysfunction. In vitro, 3OC12-HSL enhanced ETEC C83902 growth (66.7% CFU increase at 8 h) and dysregulated stress/growth genes (e.g., eight-fold rmf upregulation under static conditions). In synthetic gut microbiota, 3OC12-HSL selectively augmented E. coli colonization (37.6% 16S rDNA increase at 12 h). Murine studies revealed 3OC12-HSL reduced jejunal villus height (381.5 μm vs. 543.2 μm in controls), elevated serum LPS, D-lactate, and DAO, and altered microbial composition (Firmicutes/Bacteroidetes imbalance). The lactonase AiiA reversed these effects by degrading 3OC12-HSL. It abrogated bacterial growth stimulation (in vitro CFU restored to baseline), normalized microbiota diversity (Shannon index recovered to control levels), suppressed pro-inflammatory cytokines (IL-6/TNF-α reduction), and restored intestinal integrity (villus length: 472.5 μm, 20.5% increase vs. ETEC-infected mice). Our findings establish AiiA as a potent quorum-quenching agent that counteracts ETEC virulence via targeted signal inactivation, highlighting its translational value. Full article

Cellulose, the most abundant organic polymer in soil, is degraded by the action of microbial communities. Cellulolytic taxa are widespread in soils, enhancing the biodegradation of cellulose by the synergistic action of different cellulase enzymes. β-glucosidases are the last enzymes responsible for the degradation of cellulose by producing glucose from the conversion of the disaccharide cellobiose. Different soils from the states of Delaware, Maryland, New Jersey, and New York were analyzed by direct DNA extraction, PCR analysis, and next generation sequencing of amplicon sequences coding for β-glucosidase genes. To determine the community structure and diversity of microorganisms carrying β-glucosidase genes, amplicon sequence variant analysis was performed. Results showed that the majority of β-glucosidase genes did not match any known phylum or genera with an average of 84% of sequences identified as unclassified. The forest soil sample from New York showed the highest value with 95.62%. When identification was possible, the bacterial phyla Pseudomonadota, Actinomycetota, and Chloroflexota were found to be dominant microorganisms with β-glucosidase genes in soils. The Delaware soil showed the highest diversity with phyla and genera showing the presence of β-glucosidase gene sequences in bacteria, fungi, and plants. However, the Chloroflexota genus Kallotanue was detected in 3 out of the 4 soil locations. When phylogenetic analysis of unclassified β-glucosidase genes was completed, most sequences aligned with the Chloroflexota genus Kallotenue and the Pseudomonadota species Sphingomonas paucimobilis. Since most sequences did not match known phyla, there is tremendous potential to discover new enzymes for possible biotechnological and pharmaceutical applications. Full article

The global antimicrobial resistance crisis demands innovative strategies to combat bacterial infections, including those caused by drug-sensitive pathogens that evade treatment through biofilm formation or metabolic adaptations. Here, we demonstrate that Squama Manitis extract (SME)—a traditional Chinese medicine component—exhibits broad-spectrum bactericidal activity against clinically significant pathogens, including both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) species (MIC = 31.25 mg/mL), achieving significant reduction in bacterial viability within 24 h. Through integrated multi-omics analysis combining scanning electron microscopy and RNA sequencing, we reveal SME’s unprecedented tripartite mechanism of action: (1) direct membrane disruption causing cell envelope collapse, (2) metabolic paralysis through coordinated suppression of TCA cycle and fatty acid degradation pathways, and (3) inhibition of DNA repair systems (SOS response and recombination downregulation). Despite its potent activity, SME shows low cytotoxicity toward mammalian cells (>90% viability) and can penetrate Gram-negative outer membranes. These features highlight SME’s potential to address drug-resistant infections through synthetic lethality across stress response, energy metabolism, and DNA integrity pathways. While advocating for synthetic alternatives to endangered animal products, this study establishes SME as a polypharmacological template for resistance-resilient antimicrobial design, demonstrating how traditional knowledge and modern systems biology can converge to guide sustainable anti-infective development. Full article

This study aims to evaluate the effect of adding a chitosan/perlite (Ch/P) carrier to anaerobic digestion (AD) on the efficiency and kinetics of the process, as well as the directional changes in the bacterial microbiome. A carrier with this composition was applied in the AD process for the first time. A laboratory experiment using wafer waste (WF) and cheese (CE) waste was conducted under mesophilic conditions. The analysis of physico-chemical properties confirmed the suitability of the tested carrier material for anaerobic digestion. Both components influenced the microstructural characteristics of the carrier: perlite contributed to the development of specific surface area, while chitosan determined the porosity of the system. Using next-generation sequencing (NGS), the study examined how the additive affected the genetic diversity of bacterial communities. Fourier-transform infrared spectroscopy (FTIR) revealed that the degradation rate depended on both the carrier and the substrate type. Consequently, the presence of the carrier led to an increase in the volume of biogas and methane produced. The volume of methane for the wafer waste (WF–control) increased from 351.72 m³ Mg⁻¹ (VS) to 410.74 m³ Mg⁻¹ (VS), while for the cosubstrate sample (wafer and cheese, WFC–control), it increased from 476.84 m³ Mg⁻¹ (VS) to 588.55 m³ Mg⁻¹ (VS). Full article

Untreated sewage sludge (SS) and misused stabilization technologies have contributed to great contamination and the accumulation of various pollutants in agricultural soils. Regarding micro-pollutants’ degradation, scalable and effective technologies are still scarce. Although many attempts at composting adaptations have been discussed, only a few have been tested individually under outdoor conditions. To investigate different composting methods (bioaugmentation and semipermeable cover) for the removal of micro-pollutants frequently found in SS, we performed a set of on-site experiments. Windrows of SS and olive pruning were used as the compostable material and were subjected to (i) bioaugmentation with the fungus Penicillium oxalicum, (ii) covered composting, (iii) covered and bioaugmented composting, and (iv) a conventional composting pile, which was included as a control. The entire experiment lasted 99 days. Bioaugmentation without cover increased the phosphorus content, favored a reduction in heavy metal content, and was the only treatment that reduced carbamazepine at the end of the process. Moreover, the inoculation of P. oxalicum under semipermeable cover increased the richness, diversity, and dominance of specific microbial taxa and total bacterial abundance. The four mature composts obtained met the standards required to be classified in the B fertilizer category, showing that we reduced most of the micro-pollutants, and passed the germination test. Full article

A novel cellulose-degrading bacterial strain, D3-1, capable of degrading cellulose under medium- to high-temperature conditions, was isolated from soil samples and identified as Staphylococcus caprae through 16SrRNA gene sequencing. The strain’s cellulase production was optimized by controlling different factors, such as pH, temperature, incubation period, substrate concentration, nitrogen and carbon sources, and response surface methods. The results indicated that the optimal conditions for maximum cellulase activity were an incubation time of 91.7 h, a temperature of 41.8 °C, and a pH of 4.9, which resulted in a maximum cellulase activity of 16.67 U/mL, representing a 165% increase compared to pre-optimization levels. The above experiment showed that, when maize straw flour was utilized as a natural carbon source, strain D3-1 exhibited relatively high cellulase production. Furthermore, gas chromatography–mass spectrometry (GC-MS) analysis of products in the degradation liquid revealed the presence of primary sugars. The results indicated that, in the denitrification of simulated sewage, supplying maize straw flour degradation liquid (MSFDL) as the carbon source resulted in a carbon/nitrogen (C/N) ratio of 6:1 after a 24 h reaction with the denitrifying strain WH-01. The total nitrogen (TN) reduction was approximately 70 mg/L, which is equivalent to the removal efficiency observed in the glucose-fed denitrification process. Meanwhile, during a 4 h denitrification reaction in urban sewage without any denitrifying bacteria, but with MSFDL supplied as the carbon source, the TN removal efficiency reached 11 mg/L, which is approximately 70% of the efficiency of the glucose-fed denitrification process. Furthermore, experimental results revealed that strain D3-1 exhibits some capacity for nitrogen removal; when the cellulose-degrading strain D3-1 is combined with the denitrifying strain WH-01, the resulting TN removal rate surpasses that of a single denitrifying bacterium. In conclusion, as a carbon source in municipal sewage treatment, the degraded maize straw flour produced by strain D3-1 holds potential as a substitute for the glucose carbon source, and strain D3-1 has a synergistic effect with the denitrifying strain WH-01 on TN elimination. Thus, this research offers new insights and directions for advancement in environmental sewage treatment. Full article

Understanding the distribution patterns of soil bacterial community structure and diversity across different forest types is essential for elucidating the mechanisms underlying microbial community assembly and its ecological drivers, particularly under the pressures of climate change. In this study, we examined six forest types—including four monocultures and two mixed-species stands—to systematically evaluate the structural composition, diversity metrics, and functional potential of soil bacterial communities. Significant differences in microbial structure and functional composition were observed among forest types. Mixed forests exhibited higher soil nutrient levels, more complex structures, and greater water retention capacity, resulting in significantly higher bacterial and functional diversity compared to monoculture forests. Bacterial diversity was greater in subsurface layers than in surface layers. Surface communities in monoculture forests showed relatively high structural heterogeneity, whereas deeper communities in mixed forests displayed more pronounced differentiation. The dominant bacterial phyla were mainly related to carbon and nitrogen metabolism, compound degradation, and anaerobic photosynthesis. Surface bacterial communities were primarily influenced by catalase activity, alkali-hydrolysable nitrogen, bulk density, and pH, whereas subsurface communities were largely controlled by pH, with supplementary regulation by nitrogen and potassium availability. Therefore, forest type and soil depth jointly influence the diversity, composition, and functional attributes of soil microbial communities by modulating soil physicochemical conditions. Full article

Aromatic compounds are vital in both natural and synthetic chemistry, and they are traditionally sourced from non-renewable petrochemicals. However, plant biomass, particularly lignin, offers a renewable alternative source of aromatic compounds. Lignin, a complex polymer found in plant cell walls, is the largest renewable source of aromatic compounds, though its degradation remains challenging. Lignin can be chemically degraded through oxidation, acid hydrolysis or solvolysis. As an alternative, microorganisms, including fungi, could offer a sustainable alternative for breaking down lignin. The aromatic compounds released from lignin, by either microbial, chemical or enzymatic degradation, can be used by microorganisms to produce valuable compounds. Fungi possess unique enzymes capable of converting aromatic compounds derived from lignin or other sources into chemical building blocks that can be used in several industries. However, their aromatic metabolic pathways are poorly studied compared to bacterial systems. In the past, only a handful of genes and enzymes involved in the aromatic metabolic pathways had been identified. Recent advances in genomics, proteomics, and metabolic engineering are helping to reveal these metabolic pathways and identify the involved genes. This review highlights recent progress in understanding fungal aromatic metabolism, focusing on how Aspergillus niger converts plant-derived aromatic compounds into potentially useful products and the versatility of aromatic metabolism within the Aspergillus genus. Addressing the current knowledge gaps in terms of fungal pathways could unlock their potential for use in sustainable technologies, promoting eco-friendly production of chemical building blocks from renewable resources or bioremediation. Full article

Quorum quenching (QQ) is of interest for potential application as a sustainable strategy for bacterial disease control via communication interruption. The QQ enzyme can be used as a good alternative antagonist to combat antibiotic abuse and bacterial resistance. Here, genomic DNA sequencing was performed on N-acyl homoserine lactonase from the deep-sea strain Bacillus velezensis DH82 with Cluster of Orthologous Groups of proteins (COGs) annotation. The homologous sequences with β-lactamase domain-containing protein were predicted to be potential QQ enzymes and were cloned and expressed to study their quorum quenching properties by comparing them with the reported enzyme AiiA_3DHB. The experimental results of enzyme activity analysis and steady-state kinetics, as well as enzyme structure and substrate docking simulations and predictions, all consistently demonstrated that YtnP_DH82 presented superior enzyme structural stability and higher degradation efficiency of N-acyl homoserine lactones than AiiA_DH82 under the effects of pH, and temperature, and performed better on short -chain and 3-O-substituted AHSLs. The findings revealed the structural and biochemical characterization of YtnP_DH82 from the deep sea, which provide the capacity for further application in sustainable aquaculture as an alternative to antibiotics. Full article