The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng

Effect of different fertilization strategies on the yield, quality of Euryales Semen and soil microbial community

Introduction

Euryales Semen, a medicinal herb widely utilized in Asia, faces a critical constraint in its production, primarily attributed to fertilizer utilization. Understanding the impact of different fertilization schemes on Euryales Semen (ES) planting and exploring the supporting mechanism are crucial for achieving high yield and sustainable development of the ES planting industry.

Methods

In this study, a field plot experiment was conducted to evaluate the effects of four different fertilization treatments on the yield and quality of ES using morphological characteristics and metabolomic changes. These treatments included a control group and three groups with different organic fertilizer to chemical fertilizer ratios (3:7, 5:5, and 7:3). The results of this study revealed the mechanisms underlying the effect of the different treatments on the yield and quality of Euryales Semen. These insights were achieved through analyses of soil physicochemical properties, soil enzyme activity, and soil microbial structure.

Results

We found that the quality and yield of ES were the best at a ratio of organic fertilizer to chemical fertilizer of 7:3. The optimality of this treatment was reflected in the yield, soil available nitrogen, soil available phosphorus, and soil enzyme activity of ES. This ratio also increased soil microbial diversity, resulting in an increase and decrease in Proteobacteria and Firmicutes abundances, respectively. In addition, linear discriminant analysis showed that Chloroflexi, Gammaproteobacteria, and Hypocreales-incertae-sedis were significantly enriched in the ratio of organic fertilizer to chemical fertilizer of 7:3. Variance partitioning analysis showed that the soil properties, enzyme activities, and their interactions cumulatively can explain 90.80% of the differences in Euryales Semen yield and metabolome. In general, blending organic and chemical fertilizers at a 7:3 ratio can enhance soil fertility, boost Euryales Semen yield and quality, and bring forth conditions that are agriculturally beneficial to microbial (bacteria and fungi) dynamics.

Discussion

This study initially revealed the scientific connotation of the effects of different fertilization patterns on the planting of Euryales Semen and laid a theoretical foundation for the study of green planting patterns of Euryales Semen with high quality and yield.

Synergistic effects of earthworms and cow manure under reduced chemical fertilization modified microbial community structure to mitigate continuous cropping effects on Chinese flowering cabbage

The substitution of chemical fertilizers with organic fertilizers is a viable strategy to enhance crop yield and soil quality. In this study, the aim was to investigate the changes in soil microorganisms, soil chemical properties, and growth of Chinese flowering cabbage under different fertilization treatments involving earthworms and cow manure. Compared with the control (100% chemical fertilizer), CE (30% reduction in chemical fertilizer + earthworms) and CFE (30% reduction in chemical fertilizer + cow dung + earthworms) treatments at soil pH 8.14 and 8.07, respectively, and CFC (30% reduction in chemical fertilizer + cow manure) and CFE treatments increased soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), and available potassium (AK) contents. Earthworms and cow manure promoted the abundance of Bacillus and reduced that of the pathogens Plectosphaerella and Gibberella. The mantle test revealed that pH was not correlated with the microbial community. Random forest analysis verified that AN, SOM, and TN were important factors that jointly influenced bacterial and fungal diversity. Overall, the synergistic effect of earthworms and cow manure increased soil fertility and microbial diversity, thereby promoting the growth and development of Chinese flowering cabbage. This study enhanced the understanding of how bioregulation affects the growth and soil quality of Chinese flowering cabbage, and thus provided a guidance for the optimization of fertilization strategies to maximize the yield and quality of Chinese flowering cabbage while reducing environmental risks.

Waterlogging stress alters the structure of sugar beet rhizosphere microbial community structure and recruiting potentially beneficial bacterial

Waterlogging has been shown to have a significant inhibitory effect on plant growth. However, the response mechanisms of the soil environment of sugar beet seedlings under waterlogging conditions still need to be fully understood. This study aimed to investigate the effects of waterlogging treatments on the content of effective nutrients and the microbial communities in the rhizosphere and non-rhizosphere using high-throughput sequencing. We set up waterlogging and non-waterlogging treatments, sampled sugar beet seedlings after 10 days of waterlogging, determined the effective soil nutrients in the rhizosphere and non-rhizosphere of the plants, and analyzed the differences in microbial diversity at ten days of waterlogging. The results showed that waterlogging significantly affected available potassium (AK) content. The Ak content of waterlogged soil was significantly higher than that of non-waterlogged soil. Waterlogging caused no significant difference in available nitrogen (AN) content and pH. Moreover, the plant growth-promoting bacteria Pseudomonas was significantly enriched in sugar beet waterlogged rhizospheres compared with the non-waterlogged ones. Similarly, the harmful fungi Gibellulopsis and Alternaria were enriched in sugar beet non-waterlogged rhizosphere. The network analysis revealed that waterlogging built a less complex root-microbial network than non-waterlogging. These findings implied that sugar beets subjected to waterlogging stress were enriched with beneficial microorganisms in the rhizosphere, potentially alleviating the stress.

Exogenous and Endophytic Fungal Communities of Dendrobium nobile Lindl. across Different Habitats and Their Enhancement of Host Plants' Dendrobine Content and Biomass Accumulation

Both the biosynthesis and array of bioactive and medicinal compounds in plants can be influenced by interactions with endophytic and exogenous fungi. However, the composition of endophytic and exogenous fungal communities associated with many medicinal plants is unknown, and the mechanism by which these fungi stimulate the secondary metabolism of host plants is unclear. In this study, we conducted a correlative analysis between endophytic and exogenous fungi and dendrobine and biomass accumulation in Dendrobium nobile across five Chinese habitats: wild Danxia rock, greenhouse-associated large Danxia stone, broken Danxia stone, broken coarse sandstone, and wood spile. Across habitats, fungal communities exhibited significant differences. The abundances of Phyllosticta, Trichoderma, and Hydropus were higher in wild habitats than in greenhouse habitats. Wild habitats were host to a higher diversity and richness of exogenous fungi than were greenhouse habitats. However, there was no significant difference in endophytic fungal diversity between habitats. The differences between the fungal communities' effects on the dendrobine content and biomass of D. nobile were attributable to the composition of endophytic and exogenous fungi. Exogenous fungi had a greater impact than endophytic fungi on the accumulation of fresh weight (FW) and dendrobine in D. nobile. Furthermore, D. nobile samples with higher exogenous fungal richness and diversity exhibited higher dendrobine content and FW. Phyllosticta was the only genus to be significantly positively correlated with both FW and dendrobine content. A total of 86 strains of endophytic fungi were isolated from the roots, stems, and leaves of D. nobile, of which 8 strains were found to be symbiotic with D. nobile tissue-cultured seedlings. The strain DN14 (Phyllosticta fallopiae) was found to promote not only biomass accumulation (11.44%) but also dendrobine content (33.80%) in D. nobile tissue-cultured seedlings. The results of this study will aid in the development of strategies to increase the production of dendrobine in D. nobile. This work could also facilitate the screening of beneficial endophytic and exogenous fungal probiotics for use as biofertilizers in D. nobile.

Differences in Soil Microbial Communities between Healthy and Diseased Lycium barbarum cv. Ningqi-5 Plants with Root Rot

For a long time, the development of the Lycium barbarum industry has been seriously restricted by root rot disease. In general, the occurrence of plant root rot is considered to be closely related to the composition and diversity of the soil microbial community. It is critical to understand the relationship between the occurrence of root rot in L. barbarum and the soil microbial composition. In this study, samples of the rhizosphere, rhizoplane, and root zone were collected from diseased and healthy plants. The V3–V4 region of bacterial 16S rDNA and the fungal ITS1 fragment of the collected samples were sequenced using Illumina MiSeq high-throughput sequencing technology. The sequencing results were first quality controlled and then aligned with the relevant databases for annotation and analysis. The richness of fungal communities in the rhizoplane and root zone of the healthy plants was significantly higher than that of the diseased plants (p < 0.05), and the community evenness and diversity of all the rhizoplane samples were significantly different from those of the rhizosphere and root zone. The richness of the bacterial communities in the rhizosphere and root zone of healthy plants was significantly greater than those of diseased plants (p < 0.05). The community composition of the rhizoplane was quite different from the other parts. The abundance of Fusarium in the rhizoplane and rhizosphere soil of diseased plants was higher than that in the corresponding parts of healthy plants. The abundances of Mortierella and Ilyonectria in the three parts of the healthy plants were correspondingly higher than those in the three parts of the diseased plants, and Plectosphaerella was the most abundant in the rhizoplane of diseased plants. There was little difference in the composition of the dominant bacteria at the phylum and genus levels between healthy plants and diseased plants, but the abundances of these dominant bacteria were different between healthy and diseased plants. Functional prediction showed that the bacterial community had the largest proportion of functional abundance belonging to metabolism. The functional abundances of the diseased plants, such as metabolism and genetic information processing, were lower than those of the healthy plants. The fungal community function prediction showed that the Animal Pathogen-Endophyte-Lichen Parasite-Plant Pathogen-Soil Saprotroph-Wood Saprotroph group had the largest functional abundance, and the corresponding fungi were Fusarium. In this study, we mainly discussed the differences in the soil microbial communities and their functions between the healthy and diseased L. barbarum cv. Ningqi-5, and predicted the functional composition of the microbial community, which is of great significance to understanding the root rot of L. barbarum.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

INTRODUCTION

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

METHODS

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

RESULTS

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

DISCUSSION

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.

Effects of mulching film on soil microbial diversity and community of cotton

Different types of mulching film could variously influence soil properties and plant growth. Yet, surprisingly few studies have investigated the effects of mulching film upon soil microbial diversity and community structure. In this research, two kinds of mulching film, a traditional PE (polyethylene) mulching film and a degradable PBAT ((Poly [butyleneadipate-co-terephthalate])) mulching film, were applied to cotton (Gossypium spp.) plants grown in Xinjiang Province, China. The respective influence of the two mulching films on the cotton’s soil microbial (bacteria and fungi) diversity and community were investigated. The results showed that applying the PBAT mulching film could significantly alter the diversity of non-rhizosphere soil fungi when compared to using the PE mulching film. However, neither the PE nor PBAT mulching film had any significant influence on the diversity of soil bacteria and rhizosphere soil fungi. Nevertheless, soil microbial community composition differed under the PBAT mulching film treatment vis-à-vis the PE mulching film treatment. The abundance of Gibellulopsis was higher under the PBAT than PE mulching film treatment. Our study’s findings provided an empirical basis for the further application of degradable PBAT mulching film for the sustainable development of cotton crops.

Degradable mulching film alter the diversity of cotton non-rhizosphere soil fungi.

Degradable mulching film alter the soil microbial composition of cotton.

Degradable mulching film dose not alter the diversity of cotton rhizosphere fungi.

Degradable mulching film dose not alter the diversity of cotton soil bacteria.