Abstract:[Background] Gardenia jasminoides Ellis is a perennial evergreen shrub. After years of continuous planting, it will lead to deterioration of the soil micro-ecological environment, aggravation of pests and diseases, and reduced quality. It was found that intercropping was an effective cultivation method in production to improve soil microflora, nutrient and enzyme activity. [Objective] In this study, the dynamic changes of the rhizosphere soil microflora, enzyme activity and nutrients of gardenia under different intercropping patterns were studied, in order to provide a theoretical basis for revealing the soil microecology mechanism of cultivation measures to improve the soil ecological environment and enhance the yield of gardenia.[Methods] To understand the effects of different intercropping patterns on the rhizosphere microecology, three-year-old gardenias were selected for field experiment. Random block design was adopted. Gardenia single cropping and Gardenia/Bletilla striata, Gardenia/Lysimachia christinae, Gardenia/Belamcanda chinensis three intercropping treatment were set, using Gardenia rhizosphere soil as the research material, sampling throughout the growth periods. Illumina high-throughput sequencing technology was used to determine the sequences of bacterial 16S rRNA gene V3—V4 and fungal rDNA ITS1—ITS2, and the physical and chemical properties of the soil in each period were determined, so as to clarify the intercropping of different crops on the gardenia rhizosphere microbial community and soil physical and chemical properties with the growth period.[Results] In the whole growth process of gardenia, the relative abundance of Proteobacteria and Acidobacteria in the rhizosphere bacterial community were 39% and 18%, respectively, which were the dominant bacteria. In the fungal community, the relative abundance of Ascomycota, Basidiomycota and Mortierellomycota accounted for 51%, 22% and 19%, respectively, which were the main fungal groups. In the fruit expansion stage, compared with single cropping, Gardenia/Belamcanda and Gardenia/Bletilla striata can significantly increase the Shannon index of soil bacterial communities by 6.55% and 3.45% (P<0.05), respectively, but there was no significant difference at other stages. In terms of rhizosphere fungi, Gardenia/Belamcanda does not significantly reduce the diversity during the full blooming period, while intercropping with Lysimachia or Bletilla will significantly decrease; In the fruit expansion stage, Gardenia/Belamcanda and Gardenia/Bletilla intercropping can significantly increase the Shannon index of the rhizosphere soil fungal community by 29.19% and 9.12%, respectively. In terms of soil nutrients, The contents of organic matter, total N and available P in rhizosphere soil of gardenia monoculture were higher, while the contents of alkaloid N and available K were lower than the three intercropping treatments. In terms of soil enzymes, except for the acid protease, the activities of the other soil enzymes of the single-cropped gardenia are at a lower level. Correlation analysis between soil physical and chemical properties and rhizosphere microbial diversity showed that the bacterial diversity index Shannon was significantly positive correlated with rhizosphere soil organic matter, available P, and extremely significantly positive correlated with pH (P<0.01); The fungal diversity index Shannon was significantly negative correlated with total K, urease and catalase in rhizosphere soil, and significantly positive correlated with available K, sucrase, acid phosphatase, and acid protease activities. The comprehensive scores of soil fertility in the blooming stage and fruit expansion stage showed that the soil fertility scores of Gardenia/Belamcanda was the highest, and that of Gardenia/Lysimachia was the lowest.[Conclusion] Reasonable intercropping can improve the microbial community structure in the rhizosphere, and improve the comprehensive soil fertility. The soil fertility comprehensive score of Gardenia/Belamcanda is the highest, they may be the desirable intercropping patterns for Gardenia cultivation.

Abstract:Chinese cabbage clubroot is a common soil-borne disease caused by Plasmodiophora brassicae Woron, which mainly damages the roots of Chinese cabbage. Rhizosphere is the most active key micro-domain of plant-soil-microbiome interaction, and the microbial imbalance in rhizosphere is a primary factor leading to soil-borne diseases. Deciphering the interaction mechanism between rhizosphere micro-ecology and soil-borne diseases is beneficial for finding safe and effective ways for the control of soil-borne diseases by rhizosphere microorganisms, disease-inhibiting substances, and functional metabolism. This paper introduced the relationship between rhizosphere micro-ecology and the occurrence of Chinese cabbage clubroot and expounded the mechanism of rhizosphere microorganisms in regulating the occurrence of clubroot disease in Chinese cabbage from the harm of the disease, rhizosphere microecology, and biocontrol strains. This review is expected to provide a theoretical basis for the control of clubroot disease in Chinese cabbage, improve soil health, and maintain the rhizosphere microecosystem stability.

Abstract:[Background] Kalidium foliatum are typical salt-tolerant plants widely distributed in saline-alkali desert areas. Salt accumulation constructed a salt island in the rhizosphere. There was rare investigation about how the microorganism succeed and adapted in the salt accumulation process. However, it was important to reveal the salt tolerance of Kalidium foliatum and formation of the salt island. [Objective] We analyzed the distribution characteristics of microorganism in soils of the rhizosphere, the root zone and the environment, and determined the effect of different salt concentration treatments on metabolic diversity of rhizosphere bacteria using Biolog Eco microplate. [Methods] Soils of the rhizosphere, the root zone and the environmental were sampled from Heshuo County, Xinjiang. The Biolog Eco microplate technique was used to analyze the utilization of microbial carbon sources. The rhizosphere soil samples were diluted by different NaCl concentrations, and then the dilution was taken to add into Biolog Eco microplates. The effect of the salt concentration on rhizosphere microbial activity and diversity was analyzed. [Results] Microbial metabolic activity of the samples showed a trend of the rhizosphere > the root zone > the environment. With the increase of distance from the root, the proportion of microorganisms using amino acids and amines as carbon sources decreased significantly, while the proportion of microorganisms using polymeric compound carbon sources increased significantly such as Tween, Glycogen and so on. Analysis of diversity showed that the Shannon index (H) decreased with significant difference. The significant effect of dilution solutions in different NaCl concentrations was observed on the metabolic activity and distribution of microbial community. And microbial activity of the rhizosphere was the highest at 5% NaCl solution as dilution solution. [Conclusion] The composition and distribution of microorganisms around the roots of Kalidium foliatum showed obvious evolution regularity. And it is necessary to optimize the cultivation condition using Biolog Eco microplate.

Abstract:[Background] Rhizosphere microorganisms directly or indirectly affect the growth, development, and quality of medicinal plants. They improve the physical and chemical properties of soil to increase the diversity of probiotics, promote the biocontrol of plant diseases and insect pests, and improve the plant yield and quality. [Objective] To explore the effects of soil supplementation with hot pepper stalks on the growth quality and rhizosphere bacterial community structure of Polygonatum kingianum. [Methods] The rhizosphere soil samples of P. kingianum were collected from the control field (CK, without any treatment), the field fertilized with decomposed hot pepper stalks (X treatment), and the field fertilized with commercial compound fertilizer (Y treatment). The growth quality of P. kingianum was evaluated, and the bacterial community structure in rhizosphere soil was studied by high-throughput sequencing. [Results] The growth quality of P. kingianum in X treatment was significantly better than that in CK and had no significant difference from that in Y treatment. The polysaccharide content and root activity in X treatment were 24.48% and 56.98%, respectively, higher than those in Y treatment. In addition, the organic matter and soil porosity were also higher in X treatment than in Y treatment. In the rhizosphere bacterial community, Proteobacteria had the highest relative abundance, which was 34.8% in CK, 34.6% in X treatment, and 41.3% in Y treatment, and its relative abundance in Y treatment was significantly higher than that in other treatments. Chloroflexi had the second highest relative abundance, being higher in X treatment (10.2%) than in CK (8.7%) and Y treatment (5.8%). X treatment had significantly higher relative abundance of Cyanobacteria than CK and significantly higher relative abundance of Gemmatimonadetes and Desulfobacteria than Y treatment. The ternary phase diagram (at the genus level) indicated that the genera with the highest relative abundance were Verrucomicrobium and Lysobacter in CK, JG30-KF-AS9 in X treatment, and Pseudomonas and Mitochondria in Y treatment. The α diversity indexes showed no significant difference among treatments. The redundancy analysis showed that organic matter and total porosity were the main factors affecting the changes of bacterial community in X treatment. The cluster of orthologous group (COG) annotation showed that X treatment significantly increased the COGs, with the number of specific COGs (81) significantly higher than that of CK (3) and Y treatment (7). [Conclusion] X treatment improved the growth quality of P. kingianum, changed the structure of rhizosphere bacterial community, and enriched beneficial microorganisms. This study is conducive to the exploration of new functional groups of microorganisms and the research on microorganism-mediated plant response to the environment and microbial synergy under specific environmental conditions. Meanwhile, it gives new insights into the cultivation of P. kingianum.

Abstract:The total amount of colony forming units (CFU) of bacteria, fungi and actinomycetes in the rhizosphere and surrounding soils were investigated at four different growing stages of tomato plants using traditional plate-counting method. The amount of bacteria reached its peak value at the blossoming stage and the fruiting stage. From seedling stage to late period, actinomycete number decreased gradually with time, but fungi increased. For bacteria, the rhizosphere effect of tomato plant (R/S) was the highest at the early blossoming stage and the early fruiting stage. The variation and diversity of microbial populations in the rhizosphere soil of tomato plants were also studied using cultivation-independent analysis. DGGE profile indicated high diversity of microbial populations in the rhizosphere soil at different growth stages. The bacterial species kept stable but the population of particular species changed in different patterns. Manifest change in rhizosphere bacterial species and populations occurred at the early blossoming stage, and the most abundant bacterial species was observed at the early fruiting stage. This investigation successfully revealed the community features of the culturable and unculturable microbes in the rhizosphere soil of tomato plants, and indicated that the most abundant bacterial species occurred at the fruiting stage, suggesting this stage a suitable period for screening antagonistic bacteria.

Abstract:[Background] Ophiopogon japonicus-maize intercropping is the main planting mode in Ophiopogonis Radix producing areas. Revealing the microbiome structure and functional changes in the rhizosphere soil of this mode is crucial for ecological intercropping. [Objective] To investigate the diversity and functions of rhizosphere microbiome in the O. japonicus-maize intercropping system. [Methods] We employed Illumina-NovaSeq high-throughput sequencing of the 16S rRNA gene of bacteria and the ITS rDNA of fungi to study the microbiome structure and functions in the rhizosphere soil samples of the O. japonicus-maize intercropping system and monoculture systems. [Results] Intercropping significantly increased the plant height and yield of O. japonicus but had little effect on maize. The bacterial diversity in rhizosphere soil of both plants had no significant difference between intercropping and monoculture patterns. However, compared with monoculture, intercropping increased the fungal diversity in the rhizosphere soil of O. japonicus and decreased the fungal diversity in the rhizosphere soil of maize. Compared with monoculture, intercropping reduced the relative abundance of Actinobacteriota, Mortierellomycota, Xenomyrothecium, and Gibberella but enriched Ascomycota, Mucoromycota, Pyrenochaetopsis, Rhizopus, Fusarium, Alternaria, Lysobacter, and Rhodanobacter in the rhizosphere of O. japonicus. In the rhizosphere of maize, intercropping increased the relative abundance of Ascomycota, Desulfobacterota, Myxococcota, Coprinellus, and Fusarium, while decreasing the relative abundance of ten families including Cladosporiaceae and two genera of Xenomyrothecium and Gibberella. No significant differences were observed in the relative abundance of KEGG pathways of rhizosphere microbiome between monoculture and intercropping modes. Intercropping significantly increased the relative abundance of plant pathogens, soil saprotrophs, and wood saprotrophs in the rhizosphere of both O. japonicus and maize. However, it decreased the relative abundance of fungal parasites in the rhizosphere of maize while increasing that in the rhizosphere of O. japonicus. Furthermore, intercropping reduced the relative abundance of plant pathogens in the rhizosphere of maize but significantly increased that in the rhizosphere of O. japonicus. [Conclusion] The intercropping of O. japonicus and maize promotes the growth and increases the yield of O. japonicus. It has mild effects on the structure and functions of rhizosphere bacterial community of O. japonicus and maize, and most bacterial genera displayed no significant difference between the two cropping modes. However, the structure and functions of fungal community were greatly influenced by intercropping, and most fungal genera showed significant convergence or divergence.

Abstract:[Background] Potato late blight is a devastating disease caused by Phytophthora infestans(Mont.) de Bary.When environmental conditions are suitable,the P. infestans remaining in the soil will infect potato plants and cause late blight.[Objective] To clarify the bacterial community structure and diversity of the rhizosphere soil of healthy and diseased potato plants.[Methods] The rhizosphere soil samples of healthy (M2J) and diseased (M2G) potato plants in a potato field with late blight occurrence were collected.The metagenomic high-throughput sequencing was performed on the Illumina MiSeq platform to analyze the bacterial communities in the soil samples.[Results] The soil samples of diseased plants had 1 747 fewer high-quality sequences and 1 466 fewer OTUs than those of healthy plants.At the phylum level,the microorganisms in the rhizosphere soil had similar community composition while different abundance between healthy plants and diseased plants.After the occurrence of late blight,the relative abundance of Proteobacteria and Chloroflexi in the rhizosphere soil increased by 17.70% and 1.58%,respectively,while that of Acidobacteria,Actinobacteria,Gemmatimonadetes,and Verrucomicrobia decreased by 6.13%,4.28%,1.41%,and 3.11%,respectively.At the genus level,the relative abundance of Rhodanobacter and Sphingomonas in the rhizosphere of diseased plants increased by 8.63% and 3.51% compared with healthy plants;while the Vicinamibacteraceae,norank_f__norank_o__Vicinamibacterales,norank_f__Gemmatimonadaceae,Chujaibacter and Flavobacterium have lower species abundance than healthy plants.[Conclusion] The community structure and diversity of bacteria in the rhizosphere soil of plants infected with P. infestans were significantly lower than those of healthy plants,and the proportions of some dominant bacterial phyla and genera changed after disease occurrence.

Abstract:[Background] Carriers influences the effects and costs of microbial fertilizers. [Objective] To screen the vector with strong adsorption ability of Bacillus velezensis PZ-3. [Methods] We carried out adsorption experiments for B. velezensis PZ-3 with biochar, humic acid, biomass ash, organic fertilizer, mushroom bran, and rice husk powder as carriers. The carrier suitable for the target strain was screened by dilution coating-colony counting method, flow cytometry, and maize pot experiment. Then, we investigated the effects of the adsorbed target strain on the microbial diversity in the rhizosphere soil of maize. [Results] The best colonization effect was achieved in the rhizosphere soil of maize after the adsorption of the target strain by humic acid+mushroom bran. The abundance and number of the target strain in the rhizosphere soil of this treatment peaked at 1.28×105 CFU/g, with a relative abundance of 59.15%, on day 7. Compared with the control (original soil), this treatment increased the plant height, stem diameter, and aboveground dry weight of maize by 28.51%, 19.05%, and 48.65%, respectively. Moreover, this treatment increased the relative abundance of Streptomyces and Pseudomonas (P<0.05) and reduced the relative abundance of Paeniclostridium, Lophotrichus, and Gibberella in the rhizosphere soil of maize. [Conclusion] Humic acid combined with mushroom bran had a strong ability to adsorb B. velezensis PZ-3. The combination significantly promoted the growth of maize, increased the relative abundance of plant growth-promoting strains, and reduced the relative abundance of plant pathogenic fungi in the rhizosphere soil of maize.

Abstract:[Background] Rhizosphere microbial community is closely related to the root rot of Panax notoginseng (PN). However, PN with root rot under natural forest is rarely reported. [Objective] To compare rhizosphere microbial community of PN with root rot under natural forest and in the field and to lay a basis for the control of root rot and wild cultivation of PN. [Methods] Rhizosphere soil of PN with root rot under the natural forest and in the field was respectively collected, and species composition and diversity of soil bacterial and fungal communities were analyzed based on high-throughput sequencing. Moreover, we determined soil physicochemical properties and enzyme activity. [Results] The composition of bacterial and fungal communities in the rhizosphere soil was different between PN with root rot under natural forest and that in the field. The rhizosphere soil of PN under natural forest had abundant Basidiomycota, Acidobacteria, and Verrucomicrobia species, while that of PN in the field boasted abundant Ascomycota, Proteobacteria, and Chloroflexi species. At the genus level, Fusarium was dominant in the rhizosphere soil of PN under natural forest, with relative abundance of 17.30%, and Plectosphaerella dominated the rhizosphere soil of PN in the field, with relative abundance standing at 22.55%. The relative abundance of Candidatus Bacilloplasma in non-PN rhizosphere soil under natural forest was 8.05%, while the figure was quite low for rhizosphere soil of PN (0−1.25%). The organic matter content, enzyme activity, and microbial diversity in the rhizosphere soil of PN with root rot in the field were lower than those under natural forest (P<0.05). Redundancy analysis (RDA) suggested significant differentiation of soil bacterial and fungal communities in the rhizosphere soil of PN under natural forest and in the field, which was closely related to the soil organic matter content and enzyme activity. [Conclusion] The rhizosphere microbial composition of PN with root rot under natural forest was significantly different from that in the field. For the cultivation of PN in the field, efforts should be made to improve soil organic matter content, enzyme activity, and microbial diversity. In addition to pathogenic Fusarium, Plectosphaerella should be emphasized in the cultivation of PN.

Abstract:[Background] Bacterial biofilm is a major factor causing bacterial resistance and recurrent nosocomial infections. But up to now there have been no effective anti-biofilm drugs. Rhizosphere microorganisms of some plants in high-cold, special environment can produce large quantities of active components which can improve the host immunity, and are thought to be a medicinal resource with great anti-biofilm potential. [Objective] To understand the rhizosphere microbial diversity of Astragalus yunnanensis and A. tatsienensis var. incanus growing in Baima Snow Mountain, and to screen cultivable strains with antibacterial and anti-biofilm activities. [Methods] In this study, metagenomics and traditional culture-dependent methods were employed to explore the rhizosphere microbial diversity of A. yunnanensis and A. tatsienensis var. incanus from Baima Snow Mountain in Deqin County, Diqing Tibetan Autonomous Prefecture, Yunnan Province. The microplate assay was conducted for determining the antibacterial and anti-biofilm activity of these cultivable microbes. [Results] Metagenomic sequencing indicated that the rhizosphere microorganisms of A. yunnanensis samples belonged to 6 phyla, 7 classes, 8 orders, 8 families, 9 genera and 10 species, and Thermus was the dominant microflora. The rhizosphere microbes of A. tatsienensis var. incanus samples belonged to 6 phyla, 8 classes, 10 orders, 11 families, 14 genera and 15 species, and Bradyrhizobium was the dominant microflora. A total of 145 cultivable strains were obtained by pure cultivation, including 112 bacteria and 33 fungi. Among them, 59 bacterial strains of 16 genera and 35 species and 19 fungal strains of 4 genera and 5 species were isolated from the rhizosphere soil of A. yunnanensis, with Streptomyces, Pseudomonas and Aspergillus being predominant. The other 53 bacterial isolates of 16 genera and 29 species and 14 fungal isolates of 3 genera and 4 species were derived from the rhizosphere soil of A. tatsienensis var. incanus, among which Bacillus, Stenotrophomonas and Aspergillus were the most abundant genera. For the screened microbes with antibacterial and anti-biofilm activity, 51 bacterial strains and 7 fungal strains were chosen at different species levels as representatives to explore their potential as medicinal resources of natural antibiotics. The crude ethyl acetate extract of the fermentation broth of 5 bacteria and 1 fungus were demonstrated to have moderate to strong activity against Gram-positive pathogens, and 4 strains of them showed anti-biofilm activity against methicillin-resistant Staphylococcus aureus (MRSA). Finally, two microbial strains Streptomyces fulvissimus KTA1 and Aspergillus fumigatus YNF5 were considered as the promising bioactive strains. [Conclusion] It is reported for the first time that there is abundant species community composition in the rhizosphere microorganisms of Astragalus plants distributed in northwestern Yunnan province. These cultivable microorganisms could be regarded as a great medicinal source for the exploitation of natural antibiotics. This study was significant for utilization and protection of characteristic plants-associated microorganisms in high-cold, special environment of northwestern Yunnan.