Diversity and structural analysis of rhizosphere soil microbial communities in wild and cultivated Rhizoma Atractylodis Macrocephalae and their effects on the accumulation of active components

Rhizosphere microbial community structure and PICRUSt2 predicted metagenomes function in heavy metal contaminated sites: A case study of the Blesbokspruit wetland

This study investigated the microbial diversity inhabiting the roots (rhizosphere) of macrophytes thriving along the Blesbokspruit wetland, South Africa's least conserved Ramsar site. The wetland suffers from decades of pollution from mining wastewater, agriculture, and sewage. The current study focused on three macrophytes: Phragmites australis (common reed), Typha capensis (bulrush), and Eichhornia crassipes (water hyacinth). The results revealed a greater abundance and diversity of microbes (Bacteria and Fungi) associated with the free-floating E. crassipes compared to P. australis and T. capensis. Furthermore, the correlation between microbial abundance and metals, showed a strong correlation between fungal communities and metals such as nickel (Ni) and arsenic (As), while bacterial communities correlated more with lead (Pb) and chromium (Cr). The functional analysis predicted by PICRUSt2 identified genes related to xenobiotic degradation, suggesting the potential of these microbes to break down pollutants. Moreover, specific bacterial groups - Proteobacteria, Verrucomicrobia, Cyanobacteria, and Bacteroidetes - were linked to this degradation pathway. These findings suggest a promising avenue for microbe-assisted phytoremediation, a technique that utilizes plants and their associated microbes to decontaminate polluted environments.

The influence of rhizosphere microbial diversity on the accumulation of active compounds in farmed Scutellaria baicalensis

Rhizosphere microorganisms are important factors affecting herb quality and secondary metabolite accumulation. In this study, we investigated the diversity of rhizosphere microbial communities (bacteria and fungi) and their correlations with soil physicochemical properties and active compounds of Scutellaria baicalensis (baicalin, oroxindin, baicalein, wogonin, and oroxylin A) from cultivated Scutellaria baicalensis with three different origins via high-throughput sequencing and correlation analysis to further clarify the role of soil factors in the accumulation of the active compounds of Scutellaria baicalensis. The results are summarized as follows. A total of 28 dominant bacterial genera, such as Arthrobacter, Rubrobacter, Microvirga, and Sphingomonas, and 42 dominant fungal genera, such as Alternaria, Spegazzinia, and Minimedusa, were detected. The soil microbial communities associated with cultivated Scutellaria baicalensis were very diverse, but there were some differences in the relative abundances of microbial taxa. Correlation analysis revealed that the bacterial genera Rubrobacter, Ellin6055, Gaiella, norank__f__norank__o___norank__c__bacteriap25, unclassified__f__Micromonosporaceae, norank__f__ Gemmatimonadaceae, Arthrobacter, and Sphingomonas and the fungal genera Tausonia, Minimedusa, Cercospora, Botrytis, Alternaria, Boeremia, Titaea, Solicoccozyma, and Mortierella were positively or negatively correlated with each active component of Scutellaria baicalensis and were important genera affecting the accumulation of the active compounds of Scutellaria baicalensis and correlated with soil physiochemistry to different degrees. These results suggest that rhizosphere microorganisms may play a role in the accumulation of active compounds in medicinal plants and provide a scientific basis for guiding the cultivation of Scutellaria baicalensis, developing biofertilizers, and improving the quality of Scutellaria baicalensis medicinal materials.

Identification of immunostimulatory activities and active compounds from sequentially extracted fractions of rhizosphere fungal fermentation broth of Atractylodes macrocephala Koidz. rhizomes

Introduction

Pharmacological studies have shown that the rhizome of Atractylodes macrocephala Koidz. (Compositae), commonly known as atractylodes macrocephala rhizome (AMR), can modulate immunity. Nevertheless, its resources have been largely depleted, and the pharmacological activity of artificial AMR is relatively modest. We hypothesized that the fermented crude extracts of the rhizosphere fungi of AMR would have similar immunomodulatory effects since the metabolites generated by these fungi are similar to those of the host plant given their long-term synergistic evolution.

Methods

Rhizosphere fungi were isolated from the rhizosphere soil of AMR and cultured to produce the secondary metabolites. These metabolites were then sequentially extracted with four solvents of increasing polarities (petroleum ether, ethyl acetate, n-butanol, and water). The in vitro immunomodulatory activities of the metabolite extracts were evaluated by cell proliferation capacity, cell phagocytosis activity, NO secretion capacity, cell morphology changes, and cytokine (TNF-α, IL-1β and IL-6) secretion capacity in RAW264.7 macrophage cells. The biologically active secondary metabolites produced by the rhizosphere fungi were identified using ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS).

Results

Three rhizosphere fungi, namely Penicillium (MK-1), Penicillium glaucoroseum (MN-1), and Purpureocillium lilalium (MG-1), were isolated from the rhizosphere soil of AMR. The assays for cell proliferation capacity, cell phagocytosis activity, and NO secretion capacity showed that all metabolite extracts exhibited in vitro immunomodulatory activities. The crude extracts of MG-1 exhibited the highest levels of in vitro immunomodulatory activities compared to the other extracts. Furthermore, it was demonstrated that the fermented extracts of MG-1 could facilitate immunological enhancement in vitro by altering the cellular morphology in the resting state and increasing the secretions of TNF-α, IL-1β, and IL-6. Meanwhile, there was no observable endotoxin contamination. The metabolite profiling of MG-1 by UHPLC-Q-TOFMS revealed the presence of several compounds with established immunoreactive activities, including L-arginine, prostaglandin I2, deoxyguanosine, bestatin, and osthole.

Discussion

The present study demonstrated that the metabolite extracts of the rhizosphere fungi isolated from the rhizosphere soil of AMR exhibited in vitro immunoreactive activities and that these rhizosphere fungi could produce several bioactive metabolites. The crude extracts of the rhizosphere fungi may hence extend the medicinal utility of AMR and provide a basis for further development of natural plant-based immunomodulators.

Microbial regulation of plant secondary metabolites: Impact, mechanisms and prospects

Plant secondary metabolites possess a wide range of pharmacological activities and play crucial biological roles. They serve as both a defense response during pathogen attack and a valuable drug resource. The role of microorganisms in the regulation of plant secondary metabolism has been widely recognized. The addition of specific microorganisms can increase the synthesis of secondary metabolites, and their beneficial effects depend on environmental factors and plant-related microorganisms. This article summarizes the impact and regulatory mechanisms of different microorganisms on the main secondary metabolic products of plants. We emphasize the mechanisms by which microorganisms regulate hormone levels, nutrient absorption, the supply of precursor substances, and enzyme and gene expression to promote the accumulation of plant secondary metabolites. In addition, the possible negative feedback regulation of microorganisms is discussed. The identification of additional unknown microbes and other driving factors affecting plant secondary metabolism is essential. The prospects for further analysis of medicinal plant genomes and the establishment of a genetic operation system for plant secondary metabolism research are proposed. This study provides new ideas for the use of microbial resources for biological synthesis research and the improvement of crop anti-inverse traits for the use of microbial resources.

Analysis of Salt Stress on Soil Microbial Community Composition and Its Correlation with Active Components in the Rhizosphere of Acanthopanax senticosus

Salt stress can adversely affect plant seed germination, growth and development, and eventually lead to slow growth and even death of plants. The purpose of this study was to investigate the effects of different concentrations of NaCl and Na2SO4 stress on the physicochemical properties, enzyme activities, rhizosphere microbial community and seven active components (L-phenylalanine, Protocatechuic acid, Eleutheroside B, Chlorogenic acid, Caffeic acid, Eleutheroside E, Isofraxidin) of Acanthopanax senticosus rhizosphere soil. Statistical analysis was used to explore the correlation between the rhizosphere ecological factors of Acanthopanax senticosus and its active components. Compared with Acanthopanax senticosus under NaCl stress, Na2SO4 generally had a greater effect on Acanthopanax senticosus, which reduced the richness of fungi in rhizosphere soil and adversely affected the content of multiple active components. Pearson analysis showed that pH, organic matter, ammonium nitrogen, available phosphorus, available potassium, catalase and urease were significantly correlated with active components such as Caffeic acid and Isofraxidin. There were 11 known bacterial genera, 12 unknown bacterial genera, 9 known fungal genera and 1 unknown fungal genus significantly associated with the active ingredient. Salt stress had great changes in the physicochemical properties, enzyme activities and microorganisms of the rhizosphere soil of Acanthopanax senticosus. In conclusion, different types and concentrations of salts had different effects on Acanthopanax senticosus, and the active components of Acanthopanax senticosus were regulated by rhizosphere soil ecological factors.

Enhancing phytoremediation of cadmium and arsenic in alkaline soil by Miscanthus sinensis: A study on the synergistic effect of endophytic fungi and biochar

Endophytic fungi (Trichoderma harzianum (TH) and Paecilomyces lilacinus (PL)) showed potential in phytoremediation for soils contaminated with potentially toxic elements (PTEs (Cd and As)). However, their efficiency is limited, which can be enhanced with the assistance of biochar. This study sought to investigate the effects of TH at two application rates (T1: 4.5 g m-2; T2: 9 g m-2), PL at two application rates (P1: 4.5 g m-2; P2: 9 g m-2), in conjunction with biochar (BC) at 750 g m-2 on the phytoremediation of PTEs by Miscanthus sinensis (M. sinensis). The results showed that the integration of endophytic fungi with biochar notably enhanced the accumulation of Cd and As in M. sinensis by 59.60 %-114.38 % and 49.91 %-134.60 %, respectively. The treatments T2BC and P2BC emerged as the most effective. Specifically, the P2BC treatment significantly enhanced the soil quality index (SQI > 0.55) across all examined soil layers, markedly improving the overall soil condition. It was observed that T2BC treatment could elevate the SQI to 0.56 at the 0-15 cm depth. The combined amendment shifted the primary influences on plant PTEs accumulation from fungal diversity and soil nutrients to bacterial diversity and the availability of soil PTEs. Characteristic microorganisms identified under the combined treatments were RB41 and Pezizaceae, indicating an increase in both bacterial and fungal diversity. This combination altered the soil microbial community, influencing key metabolic pathways. The combined application of PL and biochar was superior to the TH and biochar combination for the phytoremediation of M. sinensis. This approach not only enhanced the phytoremediation potential but also positively impacted soil health and microbial community, suggesting that the synergistic use of endophytic fungi and biochar is an effective strategy for improving the condition of alkaline soils contaminated with PTEs.

Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites

Background

Schisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera?

Methods

In this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed.

Results

The major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new opportunity to further understand the effects of microorganisms on the active secondary metabolites and provided a basis for further research on the sustainable utilization of S. sphenanthera.

The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome

The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted. The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea. The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with "high quality and optimal shape".