Rhizobacterial compositions and their relationships with soil properties and medicinal bioactive ingredients in Cinnamomum migao

Profiling and metabolic analysis of microorganisms in bioretention cells vegetated with vetiver and cattail species treating nitrogen and phosphorous

Bioretention cells (BRCs) are increasingly used to treat nutrients in stormwater runoff, with plants known to enhance nitrogen (TN) and phosphorus (TP) uptake. This study investigated the role of rhizosphere microbial communities in TN, TP, and COD removal across three BRCs: an unvegetated control (CP), one vegetated with vetiver (P1), and another with cattail (P2). Detailed microbiome profiling revealed key taxa across phylum, family, and genus levels contributing to nutrient cycling, with P2 showing the highest species richness and diversity based on OTU counts and diversity indices. Proteobacteria, Acidobacteria, and Verrucomicrobiota were the most prominent phyla, aligning with their known roles in nutrient uptake. Key functional taxa included denitrifiers (e.g., Ramlibacter, TRA3-20), Ammonia Oxidizing Bacteria (AOBs) (e.g., MND1, Ellin 6067), and Phosphate Accumulating Organisms (PAOs) (e.g., Comamonadaceae, Vicinamibacteria), supporting TN (>79%) and TP (>84%) removal rates. Distinct microbial compositions between vegetated BRCs confirmed the role of root exudates in microbial selection and enhanced nutrient removal. These findings emphasize the importance of plant-specific rhizosphere effects and microbial selection in optimizing BRC design for stormwater treatment applications.

Bioactive Phenolics of Hyoscyamus muticus L. Subsp. Falezlez: A Molecular and Biochemical Approach to Antioxidant and Urease Inhibitory Activities

This study examines the chemical composition, antioxidant properties, and urease inhibitory effects of Hyoscyamus muticus L. subsp. falezlez (Coss.) Maire. Using LC-ESI-MS/MS, 19 distinct phenolic compounds were identified, with chlorogenic acid being the most abundant. The ethanol extract demonstrated notable antioxidant activity, highlighting its potential for therapeutic use. Urease inhibition assays revealed a remarkable 91.35% inhibition by the H. muticus extract, with an IC50 value of 5.6 ± 1.20 μg/mL, indicating its promising role in addressing conditions linked to urease activity. Molecular docking studies further investigated the interaction between H. muticus phenolic compounds and urease, identifying hyperoside as a leading candidate, with a binding energy of -7.9 kcal/mol. Other compounds, such as rutin, luteolin, apigenin, kaempferol, hesperetin, chlorogenic acid, and rosmarinic acid, also demonstrated significant binding affinities, suggesting their potential to disrupt urease function. These findings highlight the therapeutic potential of H. muticus as a source of natural bioactive compounds, offering promising avenues for the development of novel treatments for urease-related disorders and oxidative stress.

Soil depth and physicochemical properties influence microbial dynamics in the rhizosphere of two Peruvian superfood trees, cherimoya and lucuma, as shown by PacBio-HiFi sequencing

The characterization of soil microbial communities at different depths is essential to understand their impact on nutrient availability, soil fertility, plant growth and stress tolerance. We analyzed the microbial community at three depths (3 cm, 12 cm, and 30 cm) in the native fruit trees Annona cherimola (cherimoya) and Pouteria lucuma (lucuma), which provide fruits in vitamins, minerals, and antioxidants. We used PacBio-HiFi, a long-read high-throughput sequencing to explore the composition, diversity and putative functionality of rhizosphere bacterial communities at different soil depths. Bacterial diversity, encompassing various phyla, families, and genera, changed with depth. Notable differences were observed in the alpha diversity indices, especially the Shannon index. Beta diversity also varied based on plant type and depth. In cherimoya soils, positive correlations with Total Organic Carbon (TOC) and Cation Exchange Capacity (CEC) were observed, but negative ones with certain cations. In lucuma soils, indices like the Shannon index exhibited negative correlations with several metals and specific soil properties. We proposed that differences between the plant rhizosphere environments may explain the variance in their microbial diversity. This study provides insights into the microbial communities present at different soil depths, highlighting the prevalence of decomposer bacteria. Further research is necessary to elucidate their specific metabolic features and overall impact on crop growth and quality.

Effects of Water and Nitrogen on Growth, Rhizosphere Environment, and Microbial Community of Sophora alopecuroides: Their Interrelationship

The effective management of water and nitrogen is crucial in the artificial cultivation of medicinal plants. Sophora alopecuroides, a perennial herbaceous plant in the Fabaceae family, is extensively used in medicine, with alkaloids as its primary bioactive constituents. Nevertheless, there remains a significant knowledge gap regarding how rhizospheric microbial communities respond to varying water and nitrogen conditions and their intricate relationships with soil environments and the growth of S. alopecuroides. In this study, two-year-old S. alopecuroides were used in a two-factor, three-level water-nitrogen interaction experiment. The irrigation levels included W1 (30-35% of maximum water holding capacity), W2 (50-55%), and W3 (70-75%), while nitrogen levels comprised N1 (32 mg/kg), N2 (64 mg/kg), and N3 (128 mg/kg). The study assessed plant growth indicators, total alkaloid content, and rhizospheric soil physicochemical parameters of S. alopecuroides. High-throughput sequencing (16S rRNA and ITS) was employed to analyze variations in rhizospheric microbial community composition and structure. The results showed that Proteobacteria and Ascomycota are the predominant bacterial and fungal phyla in the rhizosphere microbial community of S. alopecuroides. The highest biomass and alkaloid accumulation of S. alopecuroides were observed under the N1W3 treatment (50% nitrogen application and 70-75% of maximum water holding capacity). Specifically, six bacterial genus-level biomarkers (TRA3_20, MND1, env_OPS_17, SBR1031, Haliangium, S0134_terrestrial_group) and six fungal genus-level biomarkers (Pseudeurotium, Rhizophagus, Patinella, Pseudeurotium, Patinella, Rhizophagus) were identified under the N1W3 treatment condition. In the partial least squares path modeling (PLS-PM), water and nitrogen treatments demonstrated markedly positive direct effects on soil physicochemical parameters (p < 0.01), while showing significant negative direct impacts on alkaloid accumulation and plant growth indicators (p < 0.05). Soil physicochemical parameters, in turn, significantly negatively affected the rhizosphere fungal community (p < 0.05). Additionally, the rhizosphere fungal community exhibited highly significant negative direct effects on both the plant growth indicators and total alkaloid content of S. alopecuroides (p < 0.01). This study provides new insights into the interactions among rhizosphere soil environment, rhizosphere microbiota, plant growth, and alkaloid accumulation under water and nitrogen regulation, offering a scientific basis for the water and nitrogen management in the cultivation of S. alopecuroides.

Quality analysis and function prediction of soil microbial communities of Polygonatum cyrtonema in two indigenous-origins

Polygonatum cyrtonema Hua (PCH), as an important economic crop, is used as raw industrial materials and traditional Chinese medicine. There are significant variations in the quality of PCH from different geographical origins. It can be due to the change of the endophytic fungi and soil microbial communities of PCH. Therefore, the aim of this study is to investigate the composition and functional prediction of the main microbial communities in the rhizomes and soil of PCH and explore their impact on medicinal quality. High-throughput sequencing techniques targeting ITS and 16S rDNA were employed to compare the structure and biodiversity differences of endophytic fungi in the rhizomes and soil microbial communities of PCH from 12 different locations in Sichuan and Guangxi province. Heatmap analysis was used for comprehensive statistics and visualization of the richness of rhizome and soil microbial communities from all locations. Venn analysis was conducted to determine the total number of shared fungi between rhizomes and soil, and GraphPad Prism analysis was employed to predict and compare the microbial communities related to phenotypes at the genus level in Sichuan and Guangxi. Tax4Fun and Fungild were used for metabolic function prediction of microbial communities in the rhizomes and soil of PCH. The results revealed the identification of 19,387 bacterial amplicon sequence variants (ASVs) in the rhizomes and 37,990 bacterial ASVs in the soil, with 6,889 shared bacterial ASVs. In addition, 2,948 fungal ASVs were identified in the rhizomes and 8,868 in the soil, with 1,893 shared fungal ASVs. Microbial sequencing results indicated that the fungal communities between soil and rhizomes were mainly composed of Ascomycota and Basidiomycota, while bacterial communities included Proteobacteria, Acidobacteria, Bacteroidota, Gammatimonadota, and Firmicutes. Dominant bacterial groups such as Nitrospira, Acidibacter, and fungal groups including Mortierella, Ceratobasidium, and Fusarium were identified as potential contributors to the observed traits. In the top 15 microbial genera, both Sichuan and Guangxi contain 15 bacterial genera, but there are differences in their abundance. Guangxi has three unique fungal genera, including the genera Scleroderma, Russula, and Gliocladiopsis. On the other hand, Sichuan has the unique fungal genus Chamaeota. The correlation analysis between the microbiota and the chemical content from 12 different collecting spots was performed by GraphPad Prism. Burkholderia-Caballeronia-Paraburkholderia, Acidibacter, and Amycolatopsis show an inverse proportionality to total polysaccharides and saponins, while Enterobacter shows a direct proportionality to total polysaccharides and inverse proportionality to saponins. The metabolism pathways show a significant positive correlation with PCH polysaccharides and saponins. This study provide new insights into the mechanisms underlying the quality differences between the two major indigenous areas.

Preliminary Investigation of Astragalus arpilobus subsp. hauarensis: LC-MS/MS Chemical Profiling, In Vitro Evaluation of Antioxidant, Anti-Inflammatory Properties, Cytotoxicity, and In Silico Analysis against COX-2

The search results offer comprehensive insights into the phenolic compounds, antioxidant, anti-inflammatory, cytotoxic effects, LC-MS/MS analysis, molecular docking, and MD simulation of the identified phenolic compounds in the Astragalus arpilobus subsp. hauarensis extract (AAH). The analysis revealed substantial levels of total phenolic content (TPC), with a measured value of 191 ± 0.03 mg GAE/g DM. This high TPC was primarily attributed to two key phenolic compounds: total flavonoid content (TFC) and total tannin content (TTC), quantified at 80.82 ± 0.02 mg QE/g DM and 51.91 ± 0.01 mg CE/g DM, respectively. LC-MS/MS analysis identified 28 phenolic compounds, with gallic acid, protocatechuic acid, catechin, and others. In the DPPH scavenging assay, the IC50 value for the extract was determined to be 19.44 ± 0.04 μg/mL, comparable to standard antioxidants like BHA, BHT, ascorbic acid, and α-tocopherol. Regarding anti-inflammatory activity, the extract demonstrated a notably lower IC50 value compared to both diclofenac and ketoprofen, with values of 35.73 µg/mL, 63.78 µg/mL, and 164.79 µg/mL, respectively. Cytotoxicity analysis revealed significant cytotoxicity of the A. arpilobus extract, with an LC50 value of 28.84 µg/mL, which exceeded that of potassium dichromate (15.73 µg/mL), indicating its potential as a safer alternative for various applications. Molecular docking studies have highlighted chrysin as a promising COX-2 inhibitor, with favorable binding energies and interactions. Molecular dynamic simulations further support chrysin's potential, showing stable interactions with COX-2, comparable to the reference ligand S58. Overall, the study underscores the pharmacological potential of A. arpilobus extract, particularly chrysin, as a source of bioactive compounds with antioxidant and anti-inflammatory properties. Further research is warranted to elucidate the therapeutic mechanisms and clinical implications of these natural compounds.

Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand

Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.

The effect of white grub (Maladera Verticalis) larvae feeding on rhizosphere microbial characterization of aerobic rice (Oryza sativa L.) in Puer City, Yunnan Province, China

BACKGROUND

Rhizosphere microorganisms are vital in plants' growth and development and these beneficial microbes are recruited to the root-zone soil when experiencing various environmental stresses. However, the effect of white grub (Maladera verticalis) larvae feeding on the structure and function of rhizosphere microbial communities of aerobic rice (Oryza sativa L.) is unclear.

RESULTS

In this study, we compared physicochemical properties, enzyme activities, and microbial communities using 18 samples under healthy and M. verticalis larvae-feeding aerobic rice rhizosphere soils at the Yunnan of China. 16 S rRNA and ITS amplicons were sequenced using Illumina high throughput sequencing. M. verticalis larvae feeding on aerobic rice can influence rhizosphere soil physicochemical properties and enzyme activities, which also change rhizosphere microbial communities. The healthy and M. verticalis larvae-feeding aerobic rice rhizosphere soil microorganisms had distinct genus signatures, such as possible_genus_04 and Knoellia genera in healthy aerobic rice rhizosphere soils and norank_f__SC - I-84 and norank_f__Roseiflexaceae genera in M. verticalis larvae-feeding aerobic rice rhizosphere soils. The pathway of the metabolism of terpenoids and polyketides and carbohydrate metabolism in rhizosphere bacteria were significantly decreased after M. verticalis larvae feeding. Fungal parasite-wood saprotroph and fungal parasites were significantly decreased after M. verticalis larvae feeding, and plant pathogen-wood saprotroph and animal pathogen-undefined saprotroph were increased after larvae feeding. Additionally, the relative abundance of Bradyrhizobium and Talaromyces genera gradually increased with the elevation of the larvae density. Bacterial and fungal communities significantly correlated with soil physicochemical properties and enzyme activities, respectively.

CONCLUSIONS

Based on the results we provide new insight for understanding the adaptation of aerobic rice to M. verticalis larvae feeding via regulating the rhizosphere environment, which would allow us to facilitate translation to more effective measures.

Microplastics induced the differential responses of microbial-driven soil carbon and nitrogen cycles under warming

The input of microplastics (MPs) and warming interfere with soil carbon (C) or nitrogen (N) cycles. Although the effects of warming and/or MPs on the cycles have been well studied, the biological coupling of microbial-driven cycles was neglected. Here, the synergistic changes of the cycles were investigated using batch incubation experiments. As results, the influences of MPs were not significant at 15, 20, and 25 °C, and yet, high temperature (i.e., 30 °C) reduced the respiration of high-concentration MPs-amended soil by 9.80%, and increased dissolved organic carbon (DOC) by 14.74%. In contrast, high temperature did not change the effect of MPs on N. The decrease of microbial biomass carbon (MBC) and the constant of microbial biomass nitrogen (MBN) indicated that microbial N utilization was enhanced, which might be attributed to the enrichments of adapted populations, such as Conexibacter, Acidothermus, and Acidibacter. These observations revealed that high temperature and MPs drove the differential response of soil C and N cycles. Additionally, the transcriptomic provided genomic evidence of the response. In summary, the high temperature was a prerequisite for the MPs-driven response, which underscored new ecological risks of MPs under global warming and emphasized the need for carbon emission reduction and better plastic product regulation.

Morchella esculenta cultivation in fallow paddy fields and drylands affects the diversity of soil bacteria and soil chemical properties

The properties of paddy field (DT) and dry land (HD) soil and food production can be enhanced by the cultivation of Morchella esculenta (ME) during the fallow period. However, whether ME cultivation affects the soil health and microbial diversity of paddy fields and drylands during the cultivation period remains unclear, and this has greatly limited the wider use of this cultivation model. Here, we analyzed the soil chemical properties and bacterial diversity (via metabarcoding sequencing) of DT and HD soils following ME cultivation. Our findings indicated that ME cultivation could enhance soil health. The content of soil phosphorus and potassium (K) was increased in DT soil under ME cultivation, and the K content was significantly higher in HD soil than in DT soil under ME cultivation. ME cultivation had a weak effect on alpha diversity, and ME cultivation affected the abundance of some genera of soil bacteria. The cultivation of ME might reduce the methane production capacity of DT soil and enhance the nitrogen cycling process of HD soil based on the results of functional annotation analysis. Network analysis and correlation analysis showed that Gemmatimonas, Bryobacter, and Anaeromyxobacter were the key bacterial genera regulating soil chemical properties in DT soil under ME cultivation, and Bryobacter, Bacillus, Streptomyces, and Paenarthrobacter were the key taxa associated with the accumulation of K in HD soil. The results of our study will aid future efforts to further improve this cultivation model.