Pyrosequencing assessment of rhizosphere fungal communities from a soybean field

2014 ◽  
Vol 60 (10) ◽  
pp. 687-690 ◽  
Author(s):  
Akifumi Sugiyama ◽  
Yoshikatsu Ueda ◽  
Hisabumi Takase ◽  
Kazufumi Yazaki
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Fungal Communities ◽  
Growth Stages ◽  
Dynamic Changes ◽  
Soybean Field ◽  
Rhizosphere Soils ◽  
Operational Taxonomic Units ◽  
Soil Ecosystems ◽  
Rhizosphere Bacterial Communities

Soil fungal communities play essential roles in soil ecosystems, affecting plant growth and health. Rhizosphere bacterial communities have been shown to undergo dynamic changes during plant growth. This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth. Members of the Ascomycota and Basiodiomycota dominated in all soils. There were no statistically significant changes at the phylum level among growth stages or between bulk and rhizosphere soils. In contrast, the relative abundance of small numbers of operational taxonomic units, 4 during growth and 28 between bulk and rhizosphere soils, differed significantly. Clustering analysis revealed that rhizosphere fungal communities were different from bulk fungal communities during growth stages of soybeans. Taken together, these results suggest that in contrast to rhizosphere bacterial communities, most constituents of rhizosphere fungal communities remained stable during soybean growth.

scholarly journals Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Xiaoning Gao ◽  
Zilin Wu ◽  
Rui Liu ◽  
Jiayun Wu ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Community Characteristics ◽  
Dynamic Changes ◽  
Operational Taxonomic Units ◽  
Total Bacterial Community ◽  
Rhizosphere Bacterial Community ◽  
Rhizosphere Bacterial Communities

To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.

scholarly journals Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field

2022 ◽  
Vol 12 ◽  
Author(s):  
Pei Wang ◽  
Jianping Dai ◽  
Luyun Luo ◽  
Yong Liu ◽  
Decai Jin ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Stage ◽  
Elevational Gradient ◽  
Fungal Communities ◽  
Growth Stages ◽  
Strong Positive Correlation ◽  
Elevation Gradients ◽  
Positive Correlation ◽  
Α Diversity ◽  
Phyllosphere Bacteria

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.

Analysis of bacterial communities in rhizosphere soil of healthy and diseased cotton (Gossypium sp.) at different plant growth stages

2010 ◽  
Vol 339 (1-2) ◽  
pp. 447-455 ◽  
Author(s):  
Yan Zhang ◽  
Bing-Hai Du ◽  
Zhi-gang Jin ◽  
Zheng-hua Li ◽  
Hong-ning Song ◽  
...  
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Growth Stages ◽  
Plant Growth Stages

scholarly journals Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

2021 ◽  
Vol 37 (6) ◽  
pp. 662-672
Author(s):  
Shin Ae Lee ◽  
Hyeon Su Kim ◽  
Mee Kyung Sang ◽  
Jaekyeong Song ◽  
Hang-Yeon Weon
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Soil Salinity ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Tomato Plants ◽  
Rhizosphere Soils ◽  
Salinity Levels

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

scholarly journals Bacterial microbiome associated with the rhizosphere, root interior and aboveground plant organs of wheat and canola at different growth stages

2021 ◽  
Author(s):  
Jorge Cordero Elvia ◽  
Renato Jose de Freitas ◽  
James Germida
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Stem Elongation ◽  
Rhizosphere Bacteria ◽  
Growth Stages ◽  
Crop Species ◽  
Wheat Roots ◽  
Plant Organs ◽  
Bacterial Microbiome ◽  
Plant Growth Stages

Beneficial bacteria associated with agricultural crops may potentially increase crop productivity and health. However, during various plant developmental processes, shifts in the diversity and function of bacterial communities often occur. This study investigated the diversity of bacterial communities associated with the rhizosphere, roots and aboveground plant organs of wheat and canola at stem elongation, flowering and ripening stages. The growth chamber experiment consisted of wheat and canola grown in Orthic Brown Chernozem Calcic Kastanozem and Orthic Black Calcic Chernozem soils from agricultural fields in Saskatchewan, Canada. Rhizosphere bacteria communities of wheat and canola were mainly influenced by soil characteristics, whereas specific root endophytic community associated with each crop species. These results suggest that each crop may select distinct root bacterial endophytes from the rhizosphere. Bacteria associated with aboveground plant organs exhibited high variability among crop species and soils, suggesting that environmental factors influenced bacterial community structure in stem, leaf and seeds. Most abundant bacterial genera associated with the rhizosphere of the crops included Gemmatimonas, Solirubrobacter and Nocardioides, as well as unclassified Commamonadaceae, Chitinophagaceae and Sphingomonadaceae. Other genera e.g., Stenotrophomonas, Streptomyces, Variovorax were predominant in wheat roots, whereas Lentzea and Pantoea were the most abundant root endophytes detected in canola. Bacterial communities associated with aboveground organs consisted mostly of Corynebacterium, Pseudomonas, and unclassified Enterobacteriacaeae. This study also revealed that plant growth stages can modulate the diversity of rhizosphere and endophytic bacteria. The influence of plant growth stages on the bacterial microbiome associated with wheat and canola was crop and organ specific.

scholarly journals Large Rhizosphere Bacterial Diversity Exits Among Wild Progenitor Species of Modern Sugarcane (Saccharum Spp. Inter-Specific Hybrids)

2021 ◽  
Author(s):  
Mukesh Kumar Malviya ◽  
Chnag-Ning Li ◽  
Manoj Kumar Solanki ◽  
Prakash Lakshmanan ◽  
Rajesh Kumar Singh ◽  
...  
Keyword(s):  
Plant Growth ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Wild Progenitor ◽  
Core Microbiome ◽  
Saccharum Spp ◽  
Operational Taxonomic Units ◽  
Plant Growth Promoting ◽  
Related Wild Species ◽  
Growth Promoting

Abstract BackgroundRhizosphere is rich in highly diverse and complex microbial communities. Plant growth promoting rhizpbacteria and diazotrops are played crucial role in plant growth and development. In this study, rhizosphere soils were collected from five wild Saccharum species- S. officinarum L. cv Badila (BRS), S. barberi Jesw. cv Pansahi (PRS), S. robustum (RRS), S. spontaneum (SRS), and S. sinense Roxb. cv Uba (URS) for studied of rhizosphere and diazotroph bacterial diversity using 16S rRNA and nifH gene amplification and sequencing.ResultsWe detected a total of 6202 operational taxonomic units (OTUs) specific to the bacterial communities from all species combined. Out of the 107 bacterial communities detected among all samples, we found a core microbiome of 31 rhizobacterial families spread across all the species analyzed. A total of 1099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were distributed across twenty genera-Bradyrhizobium, Dechloromonas, Desulfovibrio, Stenotrophomonas, Xanthobacter, Anaeromyxobacter, Azospirillum, Pseudoacidovorax, Methylobacterium, Azoarcus, Paenibacillus, Ideonella, Beijerinckia, Paraburkholderia, Burkholderia, Ruficoccus, Geobacter, Sinorhizobium, Kosakonia, and Azotobacter. ConclusionThe results presented here advance our understanding of rhizosphere associated bacterial diversity among genetically closely related wild species and provide a knowledge base for studying the evolution of rhizobacteria-host plant association during crop domestication.

scholarly journals Dynamic changes in the rhizosphere bacterial community in monoculture and intercropping maize and soybean during various crop growth stages 

2020 ◽  
Author(s):  
Han Li ◽  
Luyun Luo ◽  
Bin Tang ◽  
Huanle Guo ◽  
Zhongyang Cao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Physicochemical Properties ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Crop Growth ◽  
Soil Samples ◽  
Growth Stages ◽  
Soil Physicochemical Properties ◽  
Crop Growth Stages ◽  
Rhizosphere Bacterial Communities

Abstract Although rhizosphere microorganisms have been studied for a long time, rhizosphere microbial communities based on monoculture and intercropping soybean and maize have rarely been studied. To define the effect of crop monoculture and intercropping on soil physicochemical properties and rhizosphere bacterial communities, field experiments were conducted using maize and soybean cultivars at five different crop growth stages, including monoculture maize, monoculture soybean and maize-soybean intercropping. The rhizosphere bacterial communities were analyzed by using the 16S rRNA Illumina sequencing. The pH and soil organic matter (SOM) were the key factors affecting crop rhizosphere soil bacterial communities. The intercropping soybean-maize increased the available phosphorus (AP) content at five different crop growth stages. And the available potassium (AK) content in the intercropping soybean soil samples was higher than corresponding monoculture soil samples. The content of available cadmium (ACd) in monoculture soybean rhizosphere soil samples decreased and then increased, but the intercropping soybean soil samples indicated an opposite trend. Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and maize rhizosphere soil samples. Crops of the same plant species showed little difference in the bacterial community diversity under the two planting modes. The results indicated the intercropping planting pattern altered the absorption of ACd in the maize and soybean soil since the S2 stage and showed a different change in different crop growth stages. And the maize-soybean intercropping system also changed the bacterial community and soil physicochemical properties.

scholarly journals Nitrogen- and phosphorus-starved Triticum aestivum show distinct belowground microbiome profiles

2018 ◽  
Author(s):  
Antoine P Pagé ◽  
Julien Tremblay ◽  
Luke Masson ◽  
Charles W Greer
Keyword(s):  
Triticum Aestivum ◽  
Bacterial Communities ◽  
Internal Transcribed Spacers ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nitrogen And Phosphorus ◽  
Operational Taxonomic Units ◽  
N Starvation ◽  
Rhizosphere Bacterial Community

Many plants have natural partnerships with microbes that can boost their nitrogen (N) and/or phosphorus (P) acquisition. To assess whether wheat may have undiscovered associations of these types, we tested if N/P-starved Triticum aestivum show microbiome profiles that are simultaneously different from those of N/P-amended plants and those of their own bulk soils. The bacterial and fungal communities of root, rhizosphere, and bulk soil samples from the Historical Dryland Plots (Lethbridge, Canada), which hold T. aestivum that is grown both under N/P fertilization and in conditions of extreme N/P-starvation, were taxonomically described and compared (bacterial 16S rRNA genes and fungal Internal Transcribed Spacers - ITS). As the list may include novel N- and/or P-providing wheat partners, we then identified all the operational taxonomic units (OTUs) that were proportionally enriched in one or more of the nutrient starvation- and plant-specific communities. These analyses revealed: a) distinct N-starvation root and rhizosphere bacterial communities that were proportionally enriched, among others, in OTUs belonging to families Enterobacteriaceae, Chitinophagaceae, Comamonadaceae, Caulobacteraceae, Cytophagaceae, Streptomycetaceae, b) distinct N-starvation root fungal communities that were proportionally enriched in OTUs belonging to taxa Lulworthia, Sordariomycetes, Apodus, Conocybe, Ascomycota, Crocicreas, c) a distinct P-starvation rhizosphere bacterial community that was proportionally enriched in an OTU belonging to genus Agrobacterium, and d) a distinct P-starvation root fungal community that was proportionally enriched in OTUs belonging to genera Parastagonospora and Phaeosphaeriopsis. Our study might have exposed wheat-microbe connections that can form the basis of novel complementary yield-boosting tools.

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