Comparison and Interpretation of Characteristics of Rhizosphere Microbiomes of Three Blueberry Varieties

Abstract Background: Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carry out various vital functions, and can regulate the growth and improve the yield of plants. However, rhizosphere microbiome of commercial blueberry was only reported by a few study and remains elusive. Comparison and interpretation of the characteristics of rhizosphere microbiome of blueberry are remarkably important to maintain its health. Methods: Hence, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities of 15 rhizosphere soil samples collected from three different blueberry varieties and five bulk soil samples, and compared our results with previous study focused on the rhizosphere microbiome of blueberry varieties. Results: Our results demonstrated significant differences in both alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions: This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.

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Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties

BMC Microbiology ◽

10.1186/s12866-021-02092-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yan Zhang ◽

Wei Wang ◽

Zhangjun Shen ◽

Jingjing Wang ◽

Yajun Chen ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Alpha Diversity ◽

Distribution Patterns ◽

Soil Samples ◽

Bulk Soil ◽

Core Microbiome ◽

Rhizosphere Microbiome ◽

Vital Functions

Abstract Background Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health. Results In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.

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Comparison and Interpretation of Characteristics of Rhizosphere Microbial Communities in Three Blueberry Varieties

10.21203/rs.3.rs-71481/v4 ◽

2021 ◽

Author(s):

Yan zhang ◽

Wei Wang ◽

Zhangjun Shen ◽

Jingjing Wang ◽

Yajun Chen ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Rhizosphere Soil ◽

Alpha Diversity ◽

Distribution Patterns ◽

Soil Samples ◽

Bulk Soil ◽

Core Microbiome ◽

Rhizosphere Microbiome ◽

Vital Functions

Abstract Background: Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health. Results: In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions: This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.

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Comparison and Interpretation of Characteristics of Rhizosphere Microbial Communities in Three Blueberry Varieties

10.21203/rs.3.rs-71481/v3 ◽

2021 ◽

Author(s):

Yan zhang ◽

Wei Wang ◽

Zhangjun Shen ◽

Jingjing Wang ◽

Yajun Chen ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Distribution Patterns ◽

Soil Samples ◽

Bulk Soil ◽

Core Microbiome ◽

Rhizosphere Microbiome ◽

Vital Functions ◽

Sequencing Strategy

Abstract Background: Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health. Methods: In this study, we collected 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, which were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties.Results: Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective. Conclusions: This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.

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Comparison and Interpretation of Characteristics of Rhizosphere Microbial Communities in Three Blueberry Varieties: The Benefits to Blueberry Production

10.21203/rs.3.rs-71481/v1 ◽

2020 ◽

Author(s):

Yan Zhang ◽

Wei Wang ◽

Zhangjun Shen ◽

Jingjing Wang ◽

Yajun Chen ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Critical Role ◽

Alpha Diversity ◽

Distribution Patterns ◽

Soil Samples ◽

Plant Production ◽

Bulk Soil ◽

Rhizosphere Microbiome ◽

Vital Functions

Abstract Background: Rhizosphere microbiota play a critical role in biogeochemical cycles and carry out various vital functions in plant production. Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry remains elusive. Hence, the characteristics of rhizosphere microbial communities of blueberry should be compared and interpreted for improving production. Methods: We collected 15 rhizosphere soil samples of three different blueberry varieties and five bulk soil samples to profile the composition of blueberry microbial communities by high-throughput sequencing. Results: Our results demonstrated significant differences in both alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. We found that the distribution patterns of taxonomical, functional, and phenotypic composition of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, we explored the interactions between OTUs of blueberry rhizosphere microbial communities by constructing the co-occurrence network of OTUs from an ecological perspective. Conclusions: This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which was beneficial to blueberry health and production.

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Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

10.21203/rs.3.rs-159617/v1 ◽

2021 ◽

Author(s):

Jing Zhang ◽

Peter G.L. Klinkhamer ◽

Klaas Vrieling ◽

T. Martijn Bezemer

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Signaling Pathway ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

Soil Microbial Communities ◽

Core Microbiome ◽

Soil Microbial ◽

Soil Bacterial ◽

Sa Signaling

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

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Regular Biochar and Bacteria-Inoculated Biochar Alter the Composition of the Microbial Community in the Soil of a Chinese Fir Plantation

Forests ◽

10.3390/f11090951 ◽

2020 ◽

Vol 11 (9) ◽

pp. 951

Author(s):

Liguo Song ◽

Lingyu Hou ◽

Yongqiang Zhang ◽

Zhichao Li ◽

Wenzheng Wang ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Rhizosphere Soil ◽

Soil Microbial Communities ◽

Principal Component ◽

Nutrient Content ◽

Chinese Fir ◽

Bulk Soil ◽

Ecological Processes ◽

Chinese Fir Plantation

Biochar is a promising material for the improvement of soil quality. However, studies on biochar have mostly been carried out in laboratory conditions or have focused on agricultural aspects. The impacts of the application of biochar on soil characteristics and related ecological processes of the forest ecosystem have not been fully resolved. In this study, we investigated the effects of regular biochar and bacteria-loaded biochar on the microbial communities in the bulk soil and the rhizosphere soil of an annual Chinese fir plantation. In early spring (April), the two types of biochar were added to the soil at the rates of 2.22 t·ha−1, 4.44 t·ha−1, 6.67 t·ha−1, 8.89 t·ha−1, and 11.11 t·ha−1 by ring furrow application around the seedlings, and soil samples were collected at the end of autumn (November). The results showed that biochar addition increased the soil nutrient content and promoted the growth and diversity of soil microbial communities. The diversity of soil fungi was significantly increased, and the diversity of soil bacteria was significantly decreased. Principal component analysis under the different biochar types and application rates demonstrated that microbial communities differed significantly between the treatments and controls and that the effect of biochar on the microbial community of the bulk soil was more significant than that of the rhizosphere soil. Under the same dosage, the effect of bacteria-loaded biochar on soil was more significant than that of regular biochar.

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Effects of Cropping Practice on Bupleurum Chinense Rhizosphere Microbial Community

10.21203/rs.3.rs-583121/v1 ◽

2021 ◽

Author(s):

Li Liu ◽

Hailu Cao ◽

Yannan Geng ◽

Ya Fan ◽

Haiyang Feng ◽

...

Keyword(s):

Microbial Communities ◽

Rhizosphere Soil ◽

Soil Microbial Communities ◽

Chemical Properties ◽

Alpha Diversity ◽

Soil Chemical Properties ◽

Continuous Cropping ◽

Factors Affecting ◽

Soil Microbial ◽

Cropping Practices

Abstract It is of great importance to understand the effects of cropping practices of Bupleurum chinense on the properties of rhizosphere soil. Therefore, the chemical properties of rhizosphere soil and the rhizosphere microbiome were assessed in the field trial with Bupleurum and three cropping practices (continuous monocropping, Bupleurum-corn intercropping and Bupleurum-corn rotation). The results showed cropping practices changed the chemical properties of the rhizosphere soil and composition, structure and diversity of the rhizosphere microbial communities. Continuous monocropping of Bupleurum chinense not only decreased soil pH and the contents of NO3--N and available K, but also decreased the alpha diversity of bacteria and beneficial microorganisms. However, Bupleurum-corn rotation improved soil chemical properties and reduced the abundance of harmful microorganisms. Soil chemical properties, especially the contents of NH4+-N, soil organic matter (SOM) and available K, were the key factors affecting the structure and composition of microbial communities in the rhizosphere soil. These findings could provide a new basis for overcoming problems associated with continuous cropping and promote development of B. chinense planting industry by improving soil microbial communities.

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Dynamic changes in the rhizosphere bacterial community in monoculture and intercropped corn and soybean during various crop growth stages

10.21203/rs.3.rs-49276/v2 ◽

2020 ◽

Author(s):

Han Li ◽

Luyun Luo ◽

Bin Tang ◽

Huanle Guo ◽

Zhongyang Cao ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Rhizosphere Soil ◽

Crop Growth ◽

Soil Samples ◽

Community Diversity ◽

Growth Stages ◽

Cadmium Content ◽

Crop Growth Stages ◽

Rhizosphere Bacterial Community

Abstract Although rhizosphere microorganisms have been studied for a long time, rhizosphere microbial communities based on monoculture and intercropped soybean and corn have rarely been studied. To define the effect of crop monoculture and intercropping on soil physicochemical properties and rhizosphere microbial communities, field experiments were conducted using corn and soybean cultivars at five different crop growth stages. The pH and soil organic matter (SOM) were the key factors affecting crop rhizosphere soil microorganisms. The content of available phosphorus (AP) in the intercropped soybean/corn soil samples was higher than that in the monoculture soil samples at five different growth stages. The content of available cadmium (ACd) in monoculture soybean rhizosphere soil samples decreased and then increased, but the intercropped soybean soil samples indicated an opposite trend. Proteobacteria, Chloroﬂexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and corn rhizosphere soil samples. Crops of the same plant species showed little difference in the bacterial community diversity under the two planting modes. The results showed that the cadmium content in cadmium-polluted soil could be reduced by the soybean/corn intercropping system. The crop rhizosphere bacterial community is not only regulated by the crop itself but also influenced by the planting pattern.

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Compartmentalization Rather Than Host Tree Drives Truffle Microbiome

10.21203/rs.3.rs-52941/v1 ◽

2020 ◽

Author(s):

Dong Liu ◽

Jesus Perez-Moreno ◽

Xinhua He ◽

Roberto Garibay-Orijel ◽

Fuqiang Yu

Keyword(s):

Bacterial Community ◽

Fungal Community ◽

Alpha Diversity ◽

Microbial Interactions ◽

Bulk Soil ◽

Edible Fungi ◽

Core Microbiome ◽

Bacterial Phyla ◽

Host Trees ◽

Whole Life Cycle

Abstract Background: Truffles are some of the among the most expensive edible fungi worldwide whose value in international markets is worth billions of US dollars annually. They form ectomycorrhiza which is a symbiotic relationship with host trees and produce hypogeous ascomata. Their whole life-cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host trees are drivers for truffle microbiome is unclear.Methods: To identify and compare bacterial and fungal communities in four truffle-associated compartments (Tuber indicum bulk soil, adhering soil to peridium, peridium and gleba), associated to three host trees we sequenced their ITS (fungal) and 16S (bacterial) rDNA with Illumina MiSeq high throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Results: Tuber indicum microbiome composition was strongly driven by their associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacterial-dominated, and its bacterial community formed a substantially more complex interacting network compared with that of fungal community. Core fungal community changed from Basidiomycota-dominated (in bulk soil) to Rozellomycota-dominated (in interphase soil); while core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. At the truffle and soil interphase, an interphase-sieving process was confirmed by i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi and Planctomycetes) in gleba; ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon and Simpson indices); and iii) a substantial decrease in the complexity of the network from bulk soil, to soil-truffle interphase, to peridium and finally to gleba. The network analysis of microbiome showed a more complex and higher number of positive microbial interactions in truffle tissues than in both bulk soil and peridium-adhering soil. Cupriavidus, Bradyrhizobium, Aminobacter and Mesorhizobium were the keystone network hub genera associated to truffle gleba. Conclusion: This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing than they are more complex than previously thought.

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Dynamic Changes in the Rhizosphere Bacterial Community in Monoculture and Intercropped Corn and Soybean During Various Crop Growth Stages

10.21203/rs.3.rs-49276/v1 ◽

2020 ◽

Author(s):

Han Li ◽

Luyun Luo ◽

Bin Tang ◽

Huanle Guo ◽

Zhongyang Cao ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Rhizosphere Soil ◽

Crop Growth ◽

Soil Samples ◽

Community Diversity ◽

Growth Stages ◽

Cadmium Content ◽

Crop Growth Stages ◽

Rhizosphere Bacterial Community

Abstract Although rhizosphere microorganisms have been studied for a long time, rhizosphere microbial communities based on monoculture and intercropped soybean and corn have rarely been studied. To define the effect of crop monoculture and intercropping on soil physicochemical properties and rhizosphere microbial communities, field experiments were conducted using corn and soybean cultivars at five different crop growth stages. The pH and soil organic matter (SOM) were the key factors affecting crop rhizosphere soil microorganisms. The content of available phosphorus(AP) in the intercropped soybean/corn soil samples was higher than that in the monoculture soil samples at five different growth stages.The content of available cadmium(ACd) in monoculture soybean rhizosphere soil samples decreased and then increased, but the intercropped soybean soil samples indicated an opposite trend.Proteobacteria, Chloroﬂexi, Acidobacteria, Actinobacteria, and Firmicutes were the dominant phyla in the soybean and cornrhizosphere soil samples. Crops of the same plant species showed little difference in the bacterial community diversity under the two planting modes. The results showed that the cadmium content in cadmium-polluted soil could be reduced by the soybean/corn intercropping system. The crop rhizosphere bacterial community is not only regulated by the crop itself but also influenced by the planting pattern.

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