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.

Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Tong-tong Liu ◽  
Hong Yang
Keyword(s):  
Bacterial Community ◽  
Surface Sediment ◽  
Bacterial Communities ◽  
Surface Sediments ◽  
Lake Taihu ◽  
Dynamic Changes ◽  
Dna And Rna ◽  
Close Relationship ◽  
Total Bacterial Community ◽  
Quantitative Results

ABSTRACT Bacterial communities play crucial roles in the biogeochemical cycle of the surface sediments of freshwater lakes, but previous studies on bacterial community changes in this habitat have mostly been based on the total bacterial community (DNA level), while an exploration of the active microbiota at the RNA level has been lacking. Herein, we analysed the bacterial communities in the surface sediments of Lake Taihu at the DNA and RNA levels. Using MiSeq sequencing and real-time quantification, we found that the sequencing and quantitative results obtained at the RNA level compared with the DNA level were more accurate in responding to the spatiotemporal dynamic changes of the bacterial community. Although both sequencing methods indicated that Proteobacteria, Chloroflexi, Acidobacteria, Nitrospirae, Bacteroidetes and Actinobacteria were the dominant phyla, the co-occurrence network at the RNA level could better reflect the close relationship between microorganisms in the surface sediment. Additionally, further analysis showed that Prochlorococcus and Microcystis were the most relevant and dominant genera of Cyanobacteria in the total and active bacterial communities, respectively; our results also demonstrated that the analysis of Cyanobacteria-related groups at the RNA level was more ‘informative’.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang tao ◽  
Wang Zhongke ◽  
Lv Xinhua ◽  
Dang Hanli ◽  
Zhuang Li
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, Ferula sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (Slope position and soil depth) and Found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in Ferula sinkiangensi s rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in Ferula sinkiangensis . In addition, Soil physicochemical factors jointly explained 24.28% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tao Zhang ◽  
Zhongke Wang ◽  
Xinhua Lv ◽  
Hanli Dang ◽  
Li Zhuang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Abstract Ferula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

Comparative analysis of biofilm community on different coloured substrata in relation to mussel settlement

2016 ◽  
Vol 97 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Yi-Feng Li ◽  
Xing-Pan Guo ◽  
Yu-Ru Chen ◽  
De-Wen Ding ◽  
Jin-Long Yang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Significant Difference ◽  
The World ◽  
Community Variability ◽  
Biofilm Community

Mussels are typical macrofouling organisms in the world. In this study, the interaction between the settlement ofMytilus coruscusplantigrades and bacterial community on coloured substrata was determined. Bacterial communities in biofilms developed on seven coloured substrata were analysed by Illumina Miseq sequencing. The mussel settlement response to coloured substrata with no biofilms was also examined.Flavobacteria, AlphaproteobacteriaandGammaproteobacteriawere the first, second and third most dominant groups in seven biofilm samples. The results suggest that the inducing activities of these biofilms on plantigrade settlement varied with coloured substrata and the lowest percentage of settlement was observed on biofilms on the green substratum. High-throughput sequencing showed that bacterial community in biofilms also changed with the substratum colour. No significant difference in the inducing activity on plantigrade settlement was observed between the coloured substrata with no biofilms. Thus, difference in plantigrade settlement response may be correlated to the changes in bacterial community on coloured substrata. This finding extends current knowledge of interaction among mussel settlement and bacterial community variability.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang tao ◽  
Wang Zhongke ◽  
Lv Xinhua ◽  
Dang Hanli ◽  
Zhuang Li
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, Ferula sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (Slope position and soil depth) and Found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in Ferula sinkiangensi s rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in Ferula sinkiangensis . In addition, Soil physicochemical factors jointly explained 24.28% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

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 Analysis of Tea Rhizosphere Bacterial Community at the Seedling Stage Using Terminal Restriction Fragment Length Polymorphism (TRFLP) Techniques

2017 ◽  
Vol 19 (2) ◽  
Author(s):  
Dwi Ningsih Susilowati ◽  
Fani Fauziah ◽  
Eko Pranoto ◽  
Ernin Hidayat ◽  
Mamik Setyowati ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Bacterial Community ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Bacterial Communities ◽  
Fragment Length Polymorphism ◽  
Rhizosphere Bacterial Community ◽  
Tea Plants ◽  
Rhizosphere Bacterial Communities ◽  
Restriction Fragment Length

<em>Bio-imunizer</em><em> contains an active compound of  </em>Chryseobacterium<em> sp. and </em>Bacillus<em> sp. has been developed by PPTK Gambung. This formula has positive effect on the growth of tea plants also potentially increasing resistance of the plant. The purpose of this study was to determine the effects of bacteria in Bio-imunizer to the rhizosphere bacterial communities as well as the consistency of its existence after application on tea plants at the nursery stage. The technique used in this research is </em>Terminal Restriction Fragment Length Polymorphism <em>based on metagenomic and culture dependent approaches. The value of relative abundance, Shannon diversity index, Pielou's evenness index, and Simpson dominance index were calculated. Based on the T-RF profiles of rhizosphere bacterial communities show that </em>Chryseobacterium<em> sp. and </em>Bacillus<em> sp. which is the active compound of  Bio-imunizer consistently found in the tea plant rhizosphere. Application of Bio-imunizer can increase the diversity of rhizosphere bacterial community without affecting the communities that already exist.</em>

scholarly journals Differential Assembly and Shifts of the Rhizosphere Bacterial Community by a Dual Transgenic Glyphosate-Tolerant Soybean Line with and without Glyphosate Application

Horticulturae ◽  
2021 ◽  
Vol 7 (10) ◽  
pp. 374
Author(s):  
Minkai Yang ◽  
Zhongling Wen ◽  
Chenyu Hao ◽  
Aliya Fazal ◽  
Yonghui Liao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Economic Benefits ◽  
Rrna Gene ◽  
Soybean Line ◽  
Seed Filling ◽  
Alpha And Beta Diversity ◽  
Rhizosphere Bacterial Community ◽  
Rhizosphere Bacterial Communities

Modern agriculture has gained significant economic benefits worldwide with the use of genetically modified (GM) technologies. While GM crops provide convenience to humans, their biosafety has attracted increasing concern. In this study, the Illumina MiSeq was used to perform a high-throughput sequencing of the V3-V4 hypervariable regions of 16S rRNA gene (16S rDNA) amplicons to compare the rhizosphere bacterial communities of the EPSPS/GAT dual transgenic glyphosate-tolerant soybean line Z106, its recipient variety ZH10, and Z106 with glyphosate application (Z106G) during flowering, seed filling, and maturing stages under field settings. At each of the three stages, the alpha and beta diversity of rhizosphere bacterial communities revealed no significant differences between ZH10, Z106, and Z106G. However, some bacterial taxa demonstrated a greater proportional contribution, particularly the nitrogen-fixing rhizobium Ensifer fredii, in the rhizospheric soil of Z106 at the seed filling and maturing stages, when compared to ZH10 and Z106G. The present study therefore suggests that the EPSPS/GAT dual transgenic line Z106 and exogenous glyphosate application have a minimal effect on the composition of the soybean rhizosphere bacterial community but have no impact on the structure of the rhizosphere microbial community during a single planting season.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang Tao ◽  
Dang Han Li ◽  
Wang Zhong Ke ◽  
Lv Xin Hua ◽  
Zhuang Li
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Environmental Gradients ◽  
Soil Depth ◽  
Community Diversity ◽  
Slope Position ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Abstract Background Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in regulating global biogeochemical cycle, plant growth and adaptability. However, the Ferula sinkiangensis bacterial community and the processes that drive its assembly remain unclear. Results In this study, based on Illumina HiSeq high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions (upper, middle and bottom) and soil depths (0-10 cm, 10-25 cm, 25-40 cm) and their correlation with soil physicochemical properties. Actinobacteria (22.7%), Proteobacteria (18.6%), Acidobacteria (14.0%), Gemmatimonadetes (10.1%), Cyanobacteria (7.9%), Bacteroidetes (6.9%), Planctomycetes (3.9%), Verrucomicrobia (3.5%), Firmicutes (3.4%) and Chloroflexi (3.2%) were the dominant bacterial phyla in Ferula sinkiangensis rhizosphere soil. Variance analysis showed that the diversity and abundance of rhizosphere bacterial community in Ferula sinkiangensis were significantly different at various slope positions and soil depths. Specifically, the diversity of bacterial community was significantly higher at the top than the bottom of the slope, and the diversity and richness of bacterial community were significantly greater in the 0-10cm than the 25-40cm soil layer. Linear discriminant effect size (LEfSe) analysis showed the specific phyla and genera of bacteria affected by slope position and soil depth. For example, Planctomycetes, Sphingomonas , Rubrobacter and Adhaeribacter by slope position and significant impact on soil depth. In addition, distance-based redundancy analysis (db-RDA) and variance analysis showed that soil physicochemical factors jointly explained 29.81% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. There was a significant positive correlation between available phosphorus（AP）and the diversity of Ferula sinkiangensis rhizosphere bacterial community ( p < 0.01), whereas pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%, p < 0.01), followed by altitude (5.53%), total salt (TS, 5.21%) and total phosphorus (TP, 4.90%). Conclusion Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (slope position and depth) and shed new light on the mechanisms of coevolution and interaction between Ferula sinkiangensis and their rhizosphere bacterial communities across environmental gradients.

scholarly journals Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

2020 ◽  
Author(s):  
Zhang tao ◽  
Wang Zhongke ◽  
Lv Xinhua ◽  
Dang Hanli ◽  
Zhuang Li
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Physicochemical Factors ◽  
Rhizosphere Bacterial Community ◽  
Ferula Sinkiangensis ◽  
Rhizosphere Bacterial Communities

Ferula sinkiangensis ( F.sinkiangensis ) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F.sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F.sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F.sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F.sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F.sinkiangensis . In addition, Soil physicochemical factors jointly explained 24.28% of variation in F.sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F.sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

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