This study aimed to explore the correlation between rhizosphere soil microorganisms of wild Arnebia euchroma and the content of medicinal components to provide guidance for the selection of the ecological planting base. The total DNA of rhizosphere soil microorganisms of wild A. euchroma was extracted, and the microbial community structure of rhizosphere soil microorganisms was analyzed by IlluminaMiseq high-throughput sequencing technology. The content of total hydroxynaphthoquinone pigment and β,β'-dimethylacrylalkannin in medicinal materials was determined by high-performance liquid chromatography(HPLC). The physicochemical pro-perties of rhizosphere soil of wild A. euchroma in main producing areas were determined, and the correlation of soil microbial abundance with index component content and soil physicochemical properties was analyzed by SPSS software. The results showed that the species composition of rhizosphere fungi and bacteria in A. euchroma from different habitats was similar at the phylum and genus levels, but their relative abundance, richness index(Chao1), and community diversity(Simpson) index were different. Correlation analysis showed that the content of available phosphorus in soil was positively correlated with the content of total hydroxynaphthoquinone pigment and β,β'-dimethylacrylalkannin, and the abundance of five fungal genera such as Solicoccozyma and six bacterial genera such as Pseudo-nocardia and Bradyrhizobium was positively correlated with the content of medicinal components in medicinal materials. The abundance of Bradyrhizobium was significantly positively correlated with the content of β,β'-dimethylacrylalkanin. The abundance of fungi such as Archaeorhizomyces was significantly positively correlated with the content of available phosphorus in rhizosphere soil, and Bradyrhizobium was significantly negatively correlated with soil pH. Therefore, the abundance of fungi and bacteria in the rhizosphere of A. euchroma has a certain correlation with the medicinal components and the physicochemical properties of the rhizosphere soil, which can provide a scientific basis for the selection of ecological planting bases in the later stage.
Rhizosphere ; Soil Microbiology ; Bacteria/genetics* ; Phosphorus ; Soil ; Boraginaceae

In order to determine the changes of bacterial community structure and function in the early, middle and late stage of aerobic composting of chicken manure, high-throughput sequencing and bioinformatics methods were used to determine and analyze the 16S rRNA sequence of samples at different stages of composting. Wayne analysis showed that most of the bacterial OTUs in the three composting stages were the same, and only about 10% of the operational taxonomic units (OTUs) showed stage specificity. The diversity indexes including Ace, Chao1 and Simpson showed a trend of increasing at first, followed by decreasing. However, there was no significant difference among different composting stages (P < 0.05). The dominant bacteria groups in three composting stages were analyzed at the phylum and genus levels. The dominant bacteria phyla at three composting stages were the same, but the abundances were different. LEfSe (line discriminant analysis (LDA) effect size) method was used to analyze the bacterial biological markers with statistical differences among three stages of composting. From the phylum to genus level, there were 49 markers with significant differences among different groups. The markers included 12 species, 13 genera, 12 families, 8 orders, 1 boundary, and 1 phylum. The most biomarkers were detected at early stage while the least biomarkers were detected at late stage. The microbial diversity was analyzed at the functional pathway level. The function diversity was the highest in the early stage of composting. Following the composting, the microbial function was enriched relatively while the diversity decreased. This study provides theoretical support and technical guidance for the regulation of livestock manure aerobic composting process.
Animals ; Manure/microbiology* ; Chickens/genetics* ; Composting ; RNA, Ribosomal, 16S/genetics* ; Soil ; Bacteria/genetics*

To explore the changes and the reaction mechanisms between soil microecological environment and the content of secon-dary metabolites of plants under water deficit, this study carried out a pot experiment on the 3-leaf stage seedlings of Rheum officinale to analyze their response mechanism under different drought gradients(normal water supply, mild, moderate, and severe drought). The results indicated that the content of flavonoids, phenols, terpenoids, and alkaloids in the root of R. officinale varied greatly under drought stresses. Under mild drought stress, the content of substances mentioned above was comparatively high, and the content of rutin, emodin, gallic acid, and(+)-catechin hydrate in the root significantly increased. The content of rutin, emodin, and gallic acid under severe drought stress was significantly lower than that under normal water supply. The number of species, Shannon diversity index, richness index, and Simpson index of bacteria in the rhizosphere soil were significantly higher than those in blank soil, and the number of microbial species and richness index decreased significantly with the aggravation of drought stresses. In the context of water deficit, Cyanophyta, Firmicutes, Actinobacteria, Chloroflexi, Gemmatimonadetes, Streptomyces, and Actinomyces were the dominant bacteria in the rhizosphere of R. officinale. The relative content of rutin and emodin in the root of R. officinale was positively correlated with the relative abundance of Cyanophyta and Firmicutes, and the relative content of(+)-catechin hydrate and(-)-epicatechin gallate was positively correlated with the relative abundance of Bacteroidetes and Firmicutes. In conclusion, appropriate drought stress can increase the content of secondary metabolites of R. officinale from physiological induction and the increase in the association with beneficial microbe.
Rhizosphere ; Rheum ; Droughts ; Soil ; Catechin ; Emodin ; Bacteria/metabolism* ; Water/metabolism* ; Firmicutes ; Soil Microbiology

Recently, returning straw to the fields has been proved as a direct and effective method to tackle soil nutrient loss and agricultural pollution. Meanwhile, the slow decomposition of straw may harm the growth of the next crop. This study aimed to determine the effects of rumen microorganisms (RMs) on straw decomposition, bacterial microbial community structure, soil properties, and soil enzyme activity. The results showed that RMs significantly enhanced the degradation rate of straw in the soil, reaching 39.52%, which was 41.37% higher than that of the control on the 30th day after straw return. After 30 d, straw degradation showed a significant slower trend in both the control and the experimental groups. According to the soil physicochemical parameters, the application of rumen fluid expedited soil matter transformation and nutrient buildup, and increased the urease, sucrase, and cellulase activity by 10%‒20%. The qualitative analysis of straw showed that the hydroxyl functional group structure of cellulose in straw was greatly damaged after the application of rumen fluid. The analysis of soil microbial community structure revealed that the addition of rumen fluid led to the proliferation of Actinobacteria with strong cellulose degradation ability, which was the main reason for the accelerated straw decomposition. Our study highlights that returning rice straw to the fields with rumen fluid inoculation can be used as an effective measure to enhance the biological value of recycled rice straw, proposing a viable solution to the problem of sluggish straw decomposition.
Animals ; Rumen/metabolism* ; Agriculture/methods* ; Soil/chemistry* ; Microbiota ; Bacteria/metabolism* ; Oryza/metabolism* ; Soil Microbiology ; Cellulose

The continuous cropping obstacle of Gastrodia elata is outstanding, but its mechanism is still unclear. In this study, microbial changes in soils after G. elata planting were investigated to explore the mechanism correlated with continuous cropping obstacle. The changes of species and abundance of fungi and bacteria in soils planted with G. elata after 1, 2, and 3 years were compared. The pathogenic fungi that might cause continuous cropping diseases of G. elata were isolated. Finally, the prevention and control measures of soil-borne fungal diseases of G. elata were investigated with the rotation planting pattern of "G. elata-Phallus impudicus". The results showed that G. elata planting resulted in the decrease in bacterial and fungal community stability and the increase in harmful fungus species and abundance in soils. This change was most obvious in the second year after G. elata planting, and the soil microbial community structure could not return to the normal level even if it was left idle for another two years. After G. elata planting in soils, the most significant change was observed in Ilyonectria cyclaminicola. The richness of the Ilyonectria fungus in soils was significantly positively correlated with the incidence of G. elata diseases. When I. cyclaminicola was inoculated in the sterile soil, the rot rate of G. elata was also significantly increased. After planting one crop of G. elata and one to three crops of P. impudicus, the fungus community structure in soils gradually recovered, and the abundance of I. cyclaminicola decreased year by year. Furthermore, the disease rate of G. elata decreased. The results showed that the cultivation of G. elata made the Ilyonectria fungi the dominant flora in soils, and I. cyclaminicola served as the main pathogen of continuous cropping diseases of G. elata, which could be reduced by rotation planting with P. impudicus.
Bacteria ; Fungi ; Gastrodia/microbiology* ; Mycobiome ; Soil ; Soil Microbiology

Aims: Intercropping system in oil palm plantation is recognized as one of a nature-based solution as well as a promising sustainable practice. This study aimed to observe the advantages of existing intercropping system in one of North Sumatra’s oil palm plantation. It is achieved by analyzing the population of soil bacteria and fungi in oil palm intercropping fields with sorghum and cassava, compared with the non-intercropping field that using Mucuna bracteata (MB) as a common legume cover crop in oil palm plantations. Methodology and results: Soil samples were collected from the weeded circle and windrow area (the area between palms within the row). The results showed that the highest and the lowest soil bacteria populations were in sorghum (1.7 ± 1.4 × 108 CFU/g) and MB (1.7 ± 0.4 × 107 CFU/g), while the highest and the lowest soil fungi populations were in sorghum (4.3 ± 2.9 × 106 CFU/g) and cassava (2.1 ± 0.8 × 106 CFU/g). Conclusion, significance and impact of study The intercropping system in this study showed a significant difference in the bacteria population, while the fungi population had no difference compared to the non-intercropping system. The bacterial and fungi population results also indicate that the intercropping system potentially enhances the soil's biological activity as an indicator of improved soil health. It is also followed by a slightly higher soil organic carbon value in intercropping system. This research suggests that further studies should be done to identify specific soil functional microbes (nutrients fixers and solubilizers). The future research will be used as a reference for promising biofertilizer agents in supporting sustainable crop production.
Palm Oil ; Soil Microbiology

Aims: This study was aimed to screen and isolate soil and endophytic fungi with the ability to biosynthesize stable silver nanoparticles (SNPs) with antimicrobial and antiproliferative activities. Methodology and results: A total of 60 fungal isolates isolated from soil and plant samples were screened for their ability to biosynthesize SNPs. Among which, 21 isolates have supported the biosynthesis of SNPs. Furthermore, the endophytic isolate PRR2.1 synthesized highly thermostable SNPs with long shelf life. The PRR2.1 isolate was identified as Albifimbria verrucaria by morphological and molecular means. The synthesis of SNPs was initially monitored by UV-Vis spectroscopy. Further characterization by transmission electron microscopy, X-ray diffraction and dynamic light scattering revealed well-dispersed spherical crystalline in nature SNPs with a mean size of 14 nm and zeta potential of –24.47 mV. Fourier transform infrared spectroscopy showed the presence of biomolecules adsorbed on the surface of biosynthesized SNPs responsible for their synthesis and stability. The mycosynthesized SNPs exhibited stronger antifungal activity against pathogenic strains of Aspergillus niger, A. flavus, A. fumigatus and Candida albicans with respect to its antibacterial activity against Escherichia coli, Staphylococcus aureus, Bacillus cereus and Klebsiella pneumoniae compared to standard antifungal itraconazole and antibiotic cefadroxil with mostly consistent minimum inhibitory concentration of 5.31 μg/mL. The biosynthesized SNPs demonstrated dose-dependent in vitro antiproliferative activity against cancerous HeLa cell line with IC50 value of 2.52 μg/mL and less cytotoxic activity against WI-38 (normal human lung fibroblasts) cell line with CC50 value of 10.2 μg/mL. Conclusion, significance and impact of study These results show the potential of endophytic fungi biosynthesized SNPs as possible biofriendly, safe and efficient antimicrobial agents with promising antiproliferative activity and low cytotoxicity, which can be furtherly implemented in various biomedical and biotechnological applications.
Silver ; Nanoparticles ; Soil Microbiology ; Endophytes ; Anti-Infective Agents ;

Aims: Meloidogyne incognita adversely affects numerous crop plants worldwide. Therefore, the modern world has been moving towards biocontrol methods to prevent nematode attacks. This study was aimed to (i) investigate the potential use of Trichoderma harzianum NFCF160 and T. virens Isf-77 in managing M. incognita in soil and (ii) identify trapping mechanisms employed by both Trichoderma strains to suppress M. incognita. Methodology and results: Three weeks old, Basella alba L. plants were subjected to five different treatments. The above and below ground growth parameters and the galling indices of these plants were measured every four weeks for three sampling times. Trapping mechanisms employed by Trichoderma strains were examined following plate assays. Plants treated with T. harzianum NFCF160 and T. virens Isf-77 had significantly higher values for the total number of leaves (34 ± 2.84) and (27 ± 2.61), fresh weight of the shoot (81 ± 9.51 g) and (91 ± 9.70 g), dry weight of the shoot (71 ± 5.24 g) and (62 ± 5.81 g), respectively eight weeks after inoculation of M. incognita. Significantly low galling indices (2 and 2) were recorded in B. alba treated with Trichoderma strains. Both Trichoderma strains exhibited various nematode-trapping mechanisms, such as non-constricting rings and adhesive spores. Conclusion, significance and impact of study This investigation highlighted the potential of both Trichoderma strains as biocontrol agents to control M. incognita effect in sustainable agriculture.
Tylenchoidea ; Trichoderma ; Soil Microbiology

The natural forest and artificial shed are the main cropping modes of Coptis chinensis. This study is aimed to reveal the rhizosphere soil bacterial community structure difference between under tow C. chinensis cropping modes-natural forest and artificial shed, and to assist us to completely understand soil quality condition,and provide theoretical guidance for soil improvement and C. chinensis planting. The rhizosphere soil samples of 1-5-year-old C. chinensis under tow cropping modes-natural forest and artificial shed were collected. Illumina high-throughput sequencing technology was used to analyze the alpha diversity, community composition, community structure of soil bacteria under the tow cropping modes,and the effects of soil nutriment indices on soil bacterial community structure. Through the analysis of species number, Shannon, Chao1 index and ACE index of bacterial community, it was found that the bacterial diversity of 1-year-old C. chinensis soil under natural forest cropping mode was significantly lower than that under artificial shed cropping mode, and the diversity of bacterial communities in soil of 2-5-years old C. chinensis were not significant different between two cropping modes. A total of 53 phyla,60 classes,140 orders and 266 families were detected in the rhizosphere soil of C. chinensis under the cropping modes of natural forest, respectively. The rhizosphere soil of C. chinensis under the cropping modes of artificial shed included 54 phyla,65 classes,140 orders and 264 families, respectively. Under the two cropping modes, the top 10 dominant species of bacterial community abundance are the same, they are Proteobacteria, Acidobacteria, Actinobacteria,Bacteroidetes, Planctomycetes, Chloroflexi, Verrucomicrobia, Gemmatimonadetes, Firmicutes and Cyanobacteria, but there are differences in the abundance sequence. The top 10 dominant species of bacterial community abundance accounted for 74.36% to 74.30% of the total bacteria, and 3.15% to 3.92% of the bacteria are unclassified. The results of Metastat analysis showed that the abundance of Gemmatimonadetes in the rhizosphere soil of C. chinensis under the cropping modes the artificial shed was significantly higher than that under the natural forest cropping mode(P<0.05). MRPP analysis of community structure differences showed that under tow cropping modes, there were significant differences in the bacterial community structure of 1-4-year-old soil bacteria, among which the difference between 1-year-old soil samples was the largest. With the increase of cropping years, the difference gradually decreases, and there is no significant difference in the bacterial community structure between 5-year-old soil samples. RDA analysis and correlation analysis of bacterial community structure and soil physical and chemical properties showed that the order of environmental factors on the rhizosphere soil bacteria of Coptis chinensis was: pH>available P> total P> total K>bulk density>total N>available N>organic matter. The results are helpful to understand the soil health of C. chinensis and provide scientific basis and theoretical guidance for soil improvement and C. chinensis planting.
Child, Preschool ; Coptis ; Forests ; Humans ; Infant ; Rhizosphere ; Soil ; Soil Microbiology

Petroleum hydrocarbon pollutants are difficult to be degraded, and bioremediation has received increasing attention for remediating the hydrocarbon polluted area. This review started by introducing the interphase adaptation and transport process of hydrocarbon by microbes. Subsequently, the advances made in the identification of hydrocarbon-degrading strains and genes as well as elucidation of metabolic pathways and underpinning mechanisms in the biodegradation of typical petroleum hydrocarbon pollutants were summarized. The capability of wild-type hydrocarbon degrading bacteria can be enhanced through genetic engineering and metabolic engineering. With the rapid development of synthetic biology, the bioremediation of hydrocarbon polluted area can be further improved by engineering the metabolic pathways of hydrocarbon-degrading microbes, or through design and construction of synthetic microbial consortia.
Bacteria/genetics* ; Biodegradation, Environmental ; Hydrocarbons ; Petroleum ; Petroleum Pollution/analysis* ; Soil Microbiology ; Soil Pollutants