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

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.

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The Composition and Assembly of Bacterial Communities across the Rhizosphere and Phyllosphere Compartments of Phragmites Australis

Diversity ◽

10.3390/d11060098 ◽

2019 ◽

Vol 11 (6) ◽

pp. 98 ◽

Cited By ~ 5

Author(s):

Qi Zhou ◽

Xiaomin Zhang ◽

Rujia He ◽

Shuren Wang ◽

Congcong Jiao ◽

...

Keyword(s):

Bacterial Community ◽

Phragmites Australis ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Null Model ◽

Rrna Gene ◽

Rare Taxa ◽

Alpha And Beta Diversity ◽

Deterministic Processes ◽

The Difference

The rhizosphere and the phyllosphere represent two different epiphytic compartments of host plant, which are closely related to plant growth, health, and productivity. However, the understanding of the diversity, composition, and assembly of the bacterial communities in different epiphytic microenvironments of large emerged macrophytes has remained elusive, especially the abundant and rare taxa across rhizosphere and phyllosphere communities. In this study, we collected samples of two different epiphytic compartments (rhizosphere and phyllosphere) of Phragmites australis. Both 16S rRNA gene-based high-throughput sequencing and null-model analysis were employed to determine the difference in the composition and assembly of above-mentioned epiphytic bacterial communities. Our results indicated that bacterial communities of rhizosphere exhibited higher diversity and richness than those of phyllosphere. Deterministic processes dominated the assembly of bacterial community in both compartments, and stochastic processes contributed a certain proportion (30.30%) in the assembly of phyllosphere bacterial community. We also found that rare taxa contributed more significantly to the alpha- and beta-diversity of bacterial community than those of abundant taxa. The obtained data are useful for better understanding the bacterial community of different epiphytic compartments of P. australis.

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Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

mSystems ◽

10.1128/msystems.00721-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Tengxiang Lian ◽

Yingyong Huang ◽

Xianan Xie ◽

Xing Huo ◽

Muhammad Qasim Shahid ◽

...

Keyword(s):

Salt Stress ◽

Bacterial Community ◽

Management Practices ◽

High Throughput Sequencing ◽

Crop Productivity ◽

Soil Salinization ◽

Rrna Gene ◽

Content Type ◽

Rice Mutant ◽

Rhizosphere Bacterial Community

ABSTRACT Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

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

10.14293/s2199-1006.1.sor-.ppeupdd.v2 ◽

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%).

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

Scientific Reports ◽

10.1038/s41598-020-75591-8 ◽

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%).

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Effects of different vegetable rotations on the rhizosphere bacterial community and tomato growth in a continuous tomato cropping substrate

PLoS ONE ◽

10.1371/journal.pone.0257432 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257432

Author(s):

Li Jin ◽

Jian Lyu ◽

Ning Jin ◽

Jianming Xie ◽

Yue Wu ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Crop Rotation ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Total N ◽

Rhizosphere Bacterial Community ◽

Healthy Growth ◽

Dominant Bacteria

In this study, High throughput sequencing was used to analyze the effects of different vegetable rotations on the rhizosphere bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the rhizosphere bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

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

10.14293/s2199-1006.1.sor-.ppeupdd.v1 ◽

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

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Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

Applied and Environmental Microbiology ◽

10.1128/aem.02797-17 ◽

2018 ◽

Vol 84 (12) ◽

pp. e02797-17 ◽

Cited By ~ 15

Author(s):

Dandi Hou ◽

Zhi Lin ◽

Runze Wang ◽

Jun Ge ◽

Shuai Wei ◽

...

Keyword(s):

Bacterial Community ◽

Contaminated Soils ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Sedum Alfredii ◽

Cd Stress ◽

Metal Hyperaccumulation ◽

Content Type

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

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

BioMed Research International ◽

10.1155/2019/4943150 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10 ◽

Cited By ~ 1

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.

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

Jurnal Penelitian Teh dan Kina ◽

10.22302/pptk.jur.jptk.v19i2.114 ◽

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

Bio-imunizer contains an active compound of Chryseobacterium sp. and Bacillus 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 Terminal Restriction Fragment Length Polymorphism 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 Chryseobacterium sp. and Bacillus 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.

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Strong Multivariate Relations Exist Among Milk, Oral, and Fecal Microbiomes in Mother-Infant Dyads During the First Six Months Postpartum

Journal of Nutrition ◽

10.1093/jn/nxy299 ◽

2019 ◽

Vol 149 (6) ◽

pp. 902-914 ◽

Cited By ~ 20

Author(s):

Janet E Williams ◽

Janae M Carrothers ◽

Kimberly A Lackey ◽

Nicola F Beatty ◽

Sarah L Brooker ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Microbial Interactions ◽

Oral Microbiome ◽

Rrna Gene ◽

Sample Type ◽

Fecal Samples ◽

Lactating Women ◽

Fecal Microbiome

ABSTRACT Background Neonatal gastrointestinal (GI) bacterial community structure may be related to bacterial communities of the mother, including those of her milk. However, very little is known about the diversity in and relationships among complex bacterial communities in mother-infant dyads. Objective Our primary objective was to assess whether microbiomes of milk are associated with those of oral and fecal samples of healthy lactating women and their infants. Methods Samples were collected 9 times from day 2 to 6 mo postpartum from 21 healthy lactating women and their infants. Milk was collected via complete breast expression, oral samples via swabs, and fecal samples from tissue (mothers) and diapers (infants). Microbiomes were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene. Alpha and beta diversity indices were used to compare microbiomes across time and sample types. Membership and composition of microbiomes were analyzed using nonmetric multidimensional scaling and canonical correlation analysis (CCA). The contribution of various bacterial communities of the mother-infant dyad to both milk and infant fecal bacterial communities were estimated using SourceTracker2. Results Bacterial community structures were relatively unique to each sample type. The most abundant genus in milk and maternal and infant oral samples was Streptococcus (47.1% ± 2.3%, 53.9% ± 1.3%, and 69.1% ± 1.8%, respectively), whereas Bacteroides were predominant in maternal and infant fecal microbiomes (22.9% ± 1.3% and 21.4% ± 2.4%, respectively). The milk microbiome was more similar to the infant oral microbiome than the infant fecal microbiome. However, CCA suggested strong associations between the complex microbial communities of milk and those of all other sample types collected. Conclusions These findings suggest complex microbial interactions between breastfeeding mothers and their infants and support the hypothesis that variation in the milk microbiome may influence the infant GI microbiome.

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