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

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.

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

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.

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

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.

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

2020 ◽  
Author(s):  
Yan zhang ◽  
Wei Wang ◽  
Zhangjun Shen ◽  
Jingjing Wang ◽  
Yajun Chen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Rhizosphere Soil ◽  
Alpha Diversity ◽  
Distribution Patterns ◽  
Soil Samples ◽  
Ecological Perspective ◽  
Bulk Soil ◽  
Core Microbiome ◽  
Rhizosphere Microbiome ◽  
Vital Functions

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.

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

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.

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

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.

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

Forests ◽  
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.

Diversity and function of microbial communities in the sand sheath of Agropyron cristatum by metagenomic analysis

2021 ◽  
pp. 1-13
Author(s):  
Yuehua Wang ◽  
Meixiao Wu ◽  
Yijing Wang ◽  
Xuefei Wang ◽  
Ming Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Polyketide Synthase ◽  
Phosphorus Uptake ◽  
Agropyron Cristatum ◽  
Bulk Soil ◽  
Phosphorus Cycle ◽  
Mannitol Dehydrogenase ◽  
Microbial Composition ◽  
Illumina Hiseq

The roots of most gramineous plants are surrounded by a variety of microorganisms; however, few studies have focused on the rhizosheath of psammophytes. Therefore, in this study, we used Illumina HiSeq high-throughput sequencing technology to analyse the composition and functional diversity of microbial communities in the rhizosheath of sand-grown Agropyron cristatum (L.) Gaertn. We found that the number of species and functions of microbial communities gradually decreased from the rhizosheath to the bulk soil. Thus, the microbial composition of the rhizosheath was richer and more diverse, and the abundance of bacteria, including Sphingosinicella, Rhizorhabdus, Friedmanniella, Geodermatophilus, Blastococcus, and Oscillatoria, was higher, and the abundance of fungi, such as Mycothermus, was higher. The abundance of CO2 fixation-related genes (acsA, Pcc, and cbbL) in the carbon cycle; NO3–, NO2–, NH2OH, and N2 transformation genes (nrtP, nirS, hao, and nifK) in the nitrogen cycle; soxB/A/C, Sat, and dsrB genes in the sulphur cycle; and 1-phosphate mannitol dehydrogenase (MtlD) gene and polyketide synthase gene (pks) were higher in the rhizosheath than in the bulk soil, as well as genes related to phosphorus uptake in the phosphorus cycle. Our findings showed that the rhizosheath may host the predominant microbial species related to the formation of a rhizosheath.

scholarly journals Effects of Soil Microbiomes and Enzymatic Activities on Glechoma longituba

HortScience ◽  
2020 ◽  
Vol 55 (4) ◽  
pp. 515-521
Author(s):  
Li Liu ◽  
Lin Jin ◽  
Qiaosheng Guo
Keyword(s):  
Bioactive Compounds ◽  
Soil Enzymes ◽  
High Throughput Sequencing ◽  
Soil Microbes ◽  
Rhizosphere Soil ◽  
Plant Morphology ◽  
Soil Samples ◽  
Medicinal Uses ◽  
Glechoma Longituba ◽  
Morphological Indices

Soil microbes and enzymes play important roles in plant growth and metabolism. However, for Glechoma longituba (Nakai) Kupr., an important crop with edible and medicinal uses in China, their effects are not well elucidated. To explore their impacts on plant morphology and bioactive compounds, the plant samples and rhizosphere soil of five different G. longituba populations were collected and investigated in this study. After high-throughput sequencing combined with data analyses, high microbial diversity and richness in the rhizosphere soil of each G. longituba population were observed, and the variations on bacterial and fungal community compositions among these soil samples were also proved. The activities of urease, neutral phosphatase, sucrase, protease, and polyphenol oxidase were significantly different among the rhizosphere soils from different G. longituba populations. Among the major microbial communities and soil enzymes we studied, the genera of Tomentella, Sebacina, Fusarium, Nitrospira, and the activity of soil sucrase were remarkably correlative with both the morphological indices and the contents of bioactive compounds of G. longituba by redundancy analysis. These findings would help guide the scientific plantation of G. longituba to promote its medicinal quality.

scholarly journals Starch Degradation by Microbial Communities in Soils from Oldupai Gorge (Tanzania)

2019 ◽  
Author(s):  
Tolutope Akeju ◽  
Peter Dunfield ◽  
Julio Mercader
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Fungal Species ◽  
Soil Samples ◽  
Model Organisms ◽  
Starch Degradation ◽  
Soil Conditions ◽  
Soil Microbial ◽  
Specific Species ◽  
Microbial Dna

The taphonomy behind ancient starch preservation is very poorly understood in archaeological contexts. This understanding could be aided by biogeochemical experimentation in controlled laboratory environments to isolate degradation pathways in soils, and how this degradation is affected by biotic and abiotic variables. The aims of this project were to:1) Identify and characterize bacterial and fungal species responsible for the degradation of starch in Tanzanian soils2) Determine how factors such as the starch source, soil water, and soil aeration affect the activity of these microbes3) Observe the alterations of starch granules inflicted by degradation by different microbial communities. Field and laboratory studies were designed to achieve these objectives:In the field, bulk soil samples (not adjacent to plant roots/tubers) and tubersphere soil samples (attached to starchy plant tubers) were collected for analysis of microbial communities via high-throughput sequencing of soil microbial DNA. Laboratory analysis of these samples is ongoing, but initial results suggest that particular starch-degrading microbes associate with particular starchy tubers. Secondly, controlled laboratory microcosms of soils amended with various starch types were incubated under different conditions. The microbial communities degrading the starch were followed over time via DNA sequencing and the starch taphonomy observed microscopically. These studies have shown that hardy, spore-forming bacteria of the phylum Firmicutes dominate starch-degrading microbial communities in the Tanzanian soils, but that the specific species change depending on experimental variables. The soil conditions and the source of the starch dramatically affected both the degradation rate and the specific microbial species involved. These findings suggest that starch degradation and taphonomy may be site-specific, that certain starches may be more prone to preservation than others may, and that starch-degradation studies using model organisms may not always be representative of the field conditions.

scholarly journals Effects of Cropping Practice on Bupleurum Chinense Rhizosphere Microbial Community

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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