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

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.

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

10.21203/rs.2.18767/v1 ◽

2019 ◽

Author(s):

Zhang Tao ◽

Dang Han Li ◽

Wang Zhong Ke ◽

Lv Xin Hua ◽

Zhuang Li

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Physicochemical Properties ◽

Bacterial Community Structure ◽

Soil Depth ◽

Community Diversity ◽

Slope Position ◽

Soil Physicochemical Properties ◽

Rhizosphere Bacterial Community ◽

Ferula Sinkiangensis

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 interaction mechanisms between Ferula sinkiangensis rhizosphere bacterial community and soil physicochemical properties.

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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.v3 ◽

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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Bacterial community structure upstream and downstream of cascade dams along the Lancang River in southwestern China

Environmental Science and Pollution Research ◽

10.1007/s11356-020-10159-7 ◽

2020 ◽

Vol 27 (34) ◽

pp. 42933-42947

Author(s):

Xia Luo ◽

Xinyi Xiang ◽

Guoyi Huang ◽

Xiaorui Song ◽

Peijia Wang ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Community Diversity ◽

Spatial Distance ◽

Rrna Gene ◽

Lancang River ◽

Hydroelectric Dam ◽

Cascade Dams

Abstract Extensive construction of dams by humans has caused alterations in flow regimes and concomitant alterations in river ecosystems. Even so, bacterioplankton diversity in large rivers influenced by cascade dams has been largely ignored. In this study, bacterial community diversity and profiles of seven cascade dams along the720 km of the Lancang River were studied using Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Spatiotemporal variations of bacterial communities in sediment and water of the Gongguoqiao hydroelectric dam and factors affecting these variations were also examined. Microbial diversity and richness in surface water increased slightly from upstream toward downstream along the river. A significant positive correlation between spatial distance and dissimilarities in bacterial community structure was confirmed (Mantel test, r = 0.4826, p = 0.001). At the Gongguoqiao hydroelectric dam, temporal differences in water overwhelmed spatial variability in bacterial communities. Temperature, precipitation, and nutrient levels were major drivers of seasonal microbial changes. Most functional groups associated with carbon cycling in sediment samples decreased from winter to summer. Our findings improve our understanding of associations, compositions, and predicted functional profiles of microbial communities in a large riverine ecosystem influenced by multiple cascade dams.

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

Horticulturae ◽

10.3390/horticulturae7100374 ◽

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.

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Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽

10.3390/w13111465 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1465

Author(s):

Chao Shen ◽

Liuyan Huang ◽

Guangwu Xie ◽

Yulai Wang ◽

Zongkai Ma ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Diversity Index ◽

Plastic Substrate ◽

Simpson Index ◽

Plastic Debris ◽

Plastic Substrates ◽

Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

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