scholarly journals Bacterial Composition and Diversity Associated with Rhizosphere of the Chinese Medicinal Herb Dendrobium

2020 ◽  
Author(s):  
Yingdan Yuan ◽  
Mengting Zu ◽  
Lei Liu ◽  
Xiaomei Song
Keyword(s):  
Microbial Community ◽  
Environmental Factor ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Available Phosphorus ◽  
Maturity Stage ◽  
Bacterial Phyla ◽  
Rhizosphere Microorganisms ◽  
Rhizosphere Microbial Community

Abstract Background: Dendrobium is a precious herbal belongs to Orchid and widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most researches still focus on endophytes, and there is still large unknown in rhizosphere microorganisms. In order to investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during maturity stage of three kinds of Dendrobium species.Results: In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, Gemmatimonadetes. We analyzed the environmental factors of the growth of Dendrobium and found that the environmental factor that affects the rhizosphere soil microorganisms of Dendrobium is the soil factor. Among them, soil factors most closely related to the influence of Dendrobium rhizosphere soil microorganisms include total nitrogen, available phosphorus, ammonium nitrogen and pH value.Conclusions: We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, Bacteroidetes. Moreover, the smaller the level of bacterial, the greater the difference among Dendrobium species. Soil is the most important environmental factor affecting the bacterial communities in the rhizosphere soil of Dendrobium. These results fill the gap in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

scholarly journals Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jiajia Zuo ◽  
Mengting Zu ◽  
Lei Liu ◽  
Xiaomei Song ◽  
Yingdan Yuan
Keyword(s):  
Microbial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Maturity Stage ◽  
Chinese Medicinal Herb ◽  
Bacterial Phyla ◽  
Rhizosphere Microorganisms ◽  
The Difference ◽  
Rhizosphere Microbial Community

Abstract Background Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. Results In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. Conclusions We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

scholarly journals Control of Streptomyces alfalfae XY25T Over Clubroot Disease and Its Effect on Rhizosphere Microbial Community in Chinese Cabbage Field Trials

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuanliang Hu ◽  
Lu Qiu ◽  
Zongjie Zhang ◽  
Kai Liu ◽  
Xian Xia ◽  
...  
Keyword(s):  
Microbial Community ◽  
Chinese Cabbage ◽  
Field Experiments ◽  
Available Phosphorus ◽  
Sequencing Analysis ◽  
Clubroot Disease ◽  
Great Ability ◽  
Bacterial Phyla ◽  
Significant Difference ◽  
Rhizosphere Microbial Community

Clubroot caused by Plasmodiophora brassicae is one of the most destructive diseases in cruciferous crops. Streptomyces alfalfae XY25T, a biological control agent, exhibited great ability to relieve clubroot disease, regulate rhizosphere bacterial and fungal communities in Chinese cabbage, and promote its growth in greenhouse. Therefore, field experiments were carried out to investigate the effects of S. alfalfae XY25T on clubroot and rhizosphere microbial community in Chinese cabbage. Results showed that the control efficiency of clubroot by S. alfalfae XY25T was 69.4%. Applying the agent can alleviate soil acidification; increase the contents of soil organic matter, available nitrogen, available phosphorus, and available potassium; and enhance activities of invertase, urease, catalase, and alkaline phosphatase. During Chinese cabbage growth, bacterial diversity decreased first and then increased, and fungal diversity decreased gradually after inoculation with S. alfalfae XY25T. High-throughput sequencing analysis showed that the main bacterial phyla were Proteobacteria, Bacteroidetes, Acidobacteria, and Planctomycetes, and the major fungal phyla were Ascomycota and Basidiomycota in rhizosphere soil. The dominant bacterial genera were Flavobacterium, Candidatus, Pseudomonas, Stenotrophomonas, Sphingomonas, Flavisolibacter, and Gemmatimonbacteria with no significant difference in abundance, and the major fungal genera were Monographella, Aspergillus, Hypocreales, Chytridiaceae, Fusarium, Pleosporales, Agaricales, Mortierella, and Pleosporales. The significant differences were observed among Pleosporales, Basidiomycota, Colletotrichum, two strains attributed to Agaricales, and another two unidentified fungi by using S. alfalfae XY25T. Moreover, quantitative real-time PCR results indicated that P. brassicae content was significantly decreased after the agent inoculation. In conclusion, S. alfalfae XY25T can affect rhizosphere microbial communities; therefore, applying the agent is an effective approach to reduce the damage caused by clubroot.

scholarly journals Effects of plant cultivars on the structure of bacterial and fungal communities associated with ginseng

2020 ◽  
Author(s):  
Huaying Wang ◽  
Xiaoxue Fang ◽  
Hao Wu ◽  
Xinyu Cai ◽  
Hongxing Xiao
Keyword(s):  
Microbial Community ◽  
Bacterial Communities ◽  
Fungal Diversity ◽  
Microbial Community Composition ◽  
Fungal Communities ◽  
Associated Bacteria ◽  
Rhizosphere Microorganisms ◽  
Soil Rhizosphere ◽  
Bacteria And Fungi ◽  
Rhizosphere Microbial Community

Abstract Background There is a growing awareness of the importance of root-associated bacteria and fungi to plant growth. At present, little is known about whether different ginseng cultivars affect the soil rhizosphere microbial community. Results Here, we examined the changes in the microorganismal diversity and composition of the rhizospheres of different ginseng cultivars. We found that fungal communities were more influenced by the cultivars than bacterial communities and revealed differences in the microbial community composition and diversity among the different ginseng cultivars. We found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ; however, TSBT had the lowest bacterial and fungal diversity. We also discovered certain rhizosphere microorganisms that may be associated with pathogenicity and the lifespan of ginseng cultivars, including Bacillus, Alternaria alternata and Cladosporium spp. Conclusions Our results showed that the microbial diversity and community structures under different ginseng cultivars are significantly different and are related to the host cultivar. This result is helpful in providing information that could be used for the breeding of Panax ginseng.

scholarly journals Characteristics of the soil microbial community in the forestland of Camellia oleifera

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9117 ◽  
Author(s):  
Peng Zhang ◽  
Zhiyi Cui ◽  
Mengqing Guo ◽  
Ruchun Xi
Keyword(s):  
Microbial Community ◽  
Species Diversity ◽  
Carbon Source ◽  
Soil Microbial Community ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Rrna Genes ◽  
Camellia Oleifera ◽  
Soil Microbial ◽  
Rhizosphere Microorganisms

Characterizing soil microbial community is important for forest ecosystem management and microbial utilization. The microbial community in the soil beneath Camellia oleifera, an important woody edible oil tree in China, has not been reported before. Here, we used Illumina sequencing of 16S and ITS rRNA genes to study the species diversity of microorganisms in C. oleifera forest land in South China. The results showed that the rhizosphere soil had higher physicochemical properties, enzyme activities and microbial biomass than did the non-rhizosphere soil. The rhizosphere soil microorganisms had a higher carbon source utilization capacity than the non-rhizosphere soil microorganisms, and attained the highest utilization capacity in summer. The soil microbial community of C. oleifera was characterized by rich ester and amino acid carbon sources that played major roles in the principal functional components of the community. In summer, soil microbes were abundant in species richness and very active in community function. Rhizosphere microorganisms were more diverse than non-root systems in species diversity, which was associated with soil pH, Available phosphorous (AP) and Urease (URE). These results indicated that microbial resources were rich in rhizosphere soil. A priority should be given to the rhizosphere microorganisms in the growing season in developing and utilizing soil microorganisms in C. oleifera plantation. It is possible to promote the growth of C. oleifera by changing soil microbial community, including carbon source species, pH, AP, and URE. Our findings provide valuable information to guide microbial isolation and culturing to manage C. oleifera land.

scholarly journals Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

2020 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Soil Bacterial Communities ◽  
Plant Soil ◽  
Soil Bacterial

Abstract Background: The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. Results: OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

scholarly journals Diversity patterns of soil microbial communities in the Sophora flavescens rhizosphere in response to continuous monocropping

2020 ◽  
Author(s):  
Haiying Lei ◽  
Ake Liu ◽  
Qinwen Hou ◽  
Qingsong Zhao ◽  
Jia Guo ◽  
...  
Keyword(s):  
Microbial Community ◽  
Physicochemical Properties ◽  
Microbial Communities ◽  
Crop Production ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Available Phosphorus ◽  
Sophora Flavescens ◽  
Diversity Patterns ◽  
Soil Microbial

Abstract Background: Continuous monocropping can affect the physicochemical and biological characteristics of cultivated soil. Sophora flavescens is a valuable herbal medicine and sensitive to continuous monocropping. Currently, diversity patterns of soil microbial communities in soil continuous monocropping with S. flavescens have not been extensively elucidated.Results: In this study, comparative 16S rDNA and internal transcribed spacer (ITS) MiSeq sequencing analyses were used to examine the taxonomic community structure and microbial diversity in nonrhizosphere soil (CK) and rhizosphere soils (SCC, TCC, and FCC) sampled from fields that had undergone two, three, and five years of continuous monocropping, respectively. Among the microbial communities, a decreased abundance of Acidobacteria and increased abundances of Proteobacteria and Bacteroidetes were found with the increase in monocropping years of S. flavescens. As the continuous monocropping time increased, the diversity of the bacterial community decreased, but that of fungi increased. Redundancy analysis also showed that among the properties of the rhizosphere soil, the available phosphorus, organic matter, total nitrogen, and sucrase had the greatest impacts on the diversity of the rhizosphere microbial community. Moreover, a biomarker for S. flavescens soil was also identified using the most differentially abundant bacteria and fungi in soil samples.Conclusions: Our study indicates that long-term monocropping exerted great impacts on microbial community distributions and soil physicochemical properties. The relationship between microbial community and physicochemical properties of rhizosphere soil would help clarify the side effects of continuous S. flavescens monocropping. Our study may aid in uncovering the theoretical basis underlying obstacles to continuous monocropping and provide better guidance for crop production.

scholarly journals Effect ofBacillus velezensis JC-K3 on Endophytic Bacterial and Fungal Diversity in Wheat Under Salt Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Chao Ji ◽  
Xiaohui Wang ◽  
Xin Song ◽  
Qisheng Zhou ◽  
Chaohui Li ◽  
...  
Keyword(s):  
Salt Stress ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Bacterial Communities ◽  
Endophytic Bacteria ◽  
Rhizosphere Soil ◽  
Fungal Communities ◽  
Salt Damage ◽  
Bacteria And Fungi

Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant’s above-ground and underground parts, which may be the cause of the plant’s “Induced Systemic Tolerance.” The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat’s biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.

scholarly journals Impact of long-term industrial contamination on the bacterial communities in urban river sediments

2020 ◽  
Author(s):  
lei zhang ◽  
Demei Tu ◽  
Xingchen Li ◽  
Wenxuan Lu ◽  
Jing Li
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Industrial Pollution ◽  
River Sediments ◽  
Urban River ◽  
Bacterial Phyla ◽  
Different Types

Abstract Background: The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.Results: Although the composition of dominant bacterial phyla in different sediment samples was similar, their relative abundance was different. These dominant bacterial phyla showed significant differences in different types of industrial contaminated sediment. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P <0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.Conclusions: Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

Improved Production of 1-Deoxynojirmiycin via Mixed Cultivation of Bacillus subtilis and Fungi Isolated from Mulberry Rhizosphere

2012 ◽  
Vol 550-553 ◽  
pp. 1491-1495 ◽  
Author(s):  
Qian Huang ◽  
Qiang Li ◽  
Geng Sheng Ji ◽  
Ting Lu Fan ◽  
Xu Ding Gu ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Glucose Consumption ◽  
Dual Culture ◽  
Activity Assay ◽  
Rhizosphere Microorganisms ◽  
Mixed Cultivation ◽  
Dual Culture Assay

To help meet the challenge of 1-Deoxynojirmiycin (DNJ) manufacture from microbial fermentation, optimal condition for the fermentation has attracted substantial research interest. In the case, mix strategy was carried out to cultivate mulberry rhizosphere Bacillus Subtilis BJ-B121 (DNJ producing strain), Rhizopus spp.BJ-F13 and Aspergillus niger BJ-F8 according to the plate dual culture assay and inhibitory activity assay in vitro. We characterized mixed cultivation of Bacillus Subtilis BJ-B121 and mulberry rhizosphere microorganisms on the basis of biochemical data. Rhizosphere soil microorganisms may interact with each other and lead to improvement of DNJ production. Campared with mono culture, the glucose consumption and DNJ production were efficient. DNJ production was improved by 26-32% in mixed cultivation, 100 μg/mL and 308 μg/mL extra DNJ production were obtained. In addition, DNJ did not affect the growth of the mixed cells.

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