scholarly journals Bacterial Diversity in Soybean Rhizosphere Soil at Seedling and Mature Stages

2019 ◽  
Vol 68 (2) ◽  
pp. 281-284
Author(s):  
LIN WANG ◽  
ZHIYING LI ◽  
RUIRUI LIU ◽  
LULU LI ◽  
WEIWEI WANG
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Rhizosphere Soil ◽  
Structural Diversity ◽  
Crop Productivity ◽  
Mature Stage ◽  
Growth Stages ◽  
Abundance And Diversity ◽  
Two Stages ◽  
Dominant Bacteria

Changes in the structural diversity of bacterial communities in soybean rhizospheres play important roles in plant growth and crop productivity. However, there are only a few studies on different soybean growth stages. Here, we investigated the changes in the bacterial community of soybean rhizosphere soil at two stages using Illumina high-throughput sequencing. The results showed that the bacterial abundance and diversity in the seeding stage were higher than those in the mature stage and that the diversity changed significantly. Actinobacteria, Acidobacteria, and Proteobacteria were the dominant bacteria in the soybean rhizosphere soil. Additionally, changes in Actinobacteria and Proteobacteria abundances showed opposite trends.

scholarly journals Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingwu Shi ◽  
Hongmei Yang ◽  
Ming Chu ◽  
Xinxiang Niu ◽  
Ning Wang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Growth Period ◽  
Tianshan Mountains ◽  
Rhizosphere Bacteria ◽  
Microbial Composition ◽  
Ecological Regions ◽  
Rhizosphere Fungi ◽  
Dominant Bacteria ◽  
North And South

The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.

scholarly journals Resuscitation of soil microbiota after > 70-years of desiccation

2020 ◽  
Author(s):  
Jun Zhao ◽  
Dongfeng Chen ◽  
Wei Gao ◽  
Zhiying Guo ◽  
Zhongjun Jia ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Storage Conditions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Osmotic Change ◽  
Abundance And Diversity ◽  
Strong Adaptation

AbstractThe abundance and diversity of bacteria in 24 historical soil samples under air-dried storage conditions for more than 70 years were assessed by quantification and high-throughput sequencing analysis of 16S rRNA genes. All soils contained a measurable abundance of bacteria varying from 103 to 108 per gram of soil and contrasting community compositions were observed in different background soils, suggesting that the bacteria detected were indigenous to the soil. Following a 4-week soil rewetting event, the bacterial abundance significantly increased in soils, indicating strong adaptation of soil bacteria to extreme osmotic change and high resuscitation potential of some bacteria over long periods of desiccation. Paenibacillus, Cohnella and two unclassified Bacillales genera within the phylum Firmicutes represented the most ubiquitously active taxa, which showed growth in the highest number of soils (≥12 soils), while genera Tumebacillus, Alicyclobacillus and Brevibacillus in the phylum Firmicutes displayed the highest growth rates in soils (with >1000-fold average increase) following rewetting. Additionally, some Actinobacteria and Proteobacteria genera showed relatively high activity following rewetting, suggesting that the resilience to long-term desiccation and rewetting is a common trait across phylogenetically divergent microbes. The present study thus demonstrated that diversified groups of microbes are present and potentially active in historically desiccated soils, which might be of importance in the context of microbial ecology.

scholarly journals Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongshuo Xu ◽  
Wenli Jiang ◽  
Dandan Qin ◽  
Taiguo Liu ◽  
Jianmin Zhang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Microbial Composition ◽  
Wheat Varieties ◽  
Resistant Varieties ◽  
Abundance And Diversity ◽  
Dwarf Bunt ◽  
Wheat Tissues

AbstractDwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.

scholarly journals Insights into the Fungal Community and Functional Roles of Pepper Rhizosphere Soil under Plastic Shed Cultivation

Diversity ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 432
Author(s):  
Shi Yao ◽  
Xiaona Li ◽  
Hu Cheng ◽  
Kaining Sun ◽  
Xin Jiang ◽  
...  
Keyword(s):  
Fungal Community ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Crop Productivity ◽  
Fungal Communities ◽  
Functional Roles ◽  
Rhizosphere Soils ◽  
Soil Microbial ◽  
Fungal Community Structure ◽  
Abundance Variation

The rhizosphere fungal community is essential for determining plant health and improving crop productivity. The fungal community structure and functional roles in the plastic shed soils were explored using high throughput sequencing and FUNGuild in this study. The fungal community structures shifted between the rhizosphere and non-rhizosphere soils. The greatest abundance variation was observed for the rare fungal members with relative abundances <0.1%. In the rhizosphere soil of pepper, the abundance of the genera Purpureocillium, Metacorgyceps, Arthrobotrys, Cephalotheca, and Scedosporium increased significantly, among which, Purpureocillium, Arthrobotrys and Metacorgyceps exhibited biocontrol characteristics. Co-occurrence network analysis revealed different interactions of fungal communities in the rhizosphere and non-rhizosphere soils, both of which were dominated by low abundance members. More positive correlation was identified among the rare members, the fungal pathotroph functions and phthalate acid ester in the rhizosphere soil. This study highlights the important niche of the rare fungal members in soil microbial ecology under plastic shed cultivation.

scholarly journals The influence of genetically modified glyphosate-tolerant maize CC-2 on rhizosphere bacterial communities revealed by MiSeq sequencing

2020 ◽  
Vol 66 (No. 8) ◽  
pp. 387-394
Author(s):  
Xiaoli Zhou ◽  
Jingang Liang ◽  
Ying Luan ◽  
Xinyuan Song ◽  
Zhengguang Zhang
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Rhizosphere Soil ◽  
Genetically Modified ◽  
Economic Benefits ◽  
Growth Stages ◽  
Safety Issues

Genetically modified (GM) crops have brought huge economic benefits to mankind, however, at the same time, their safety issues are drawing growing attention. This investigation was conducted to assess whether the long-term cultivation of GM glyphosate resistant maize CC-2 effects bacterial communities in the rhizosphere soil. A 2-year follow-up trial was conducted, and soils were sampled at various plant developmental stages. The bacterial community structure of the rhizosphere soil was analysed by the high-throughput sequencing and compared with the near-isogenic non-GM maize Zheng 58. We showed here that long-term cultivation of CC-2 has no significant effect on the structure and diversity of bacterial communities, while different growth stages had significant effect. These results provided a reliable theoretical basis for the future cultivation and increased commercialisation of CC-2.  

scholarly journals Response of Bacterial Community Structure to Different Biochar Addition Dosages in Karst Yellow Soil Planted with Ryegrass and Daylily

2020 ◽  
Vol 12 (5) ◽  
pp. 2124 ◽  
Author(s):  
Songping Luo ◽  
Binghui He ◽  
Dandan Song ◽  
Tianyang Li ◽  
Yaopeng Wu ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Chemical Properties ◽  
Crop Productivity ◽  
Low Fertility ◽  
Available Nitrogen ◽  
Nutrient Contents ◽  
Soil Bacterial

Biochar has been widely used to ameliorate soil quality and increase crop productivity through enhancement of nutrient availability and microbial community. The Karst yellow soil in China is characterized by severe soil degradation owing to intensive nutrient leaching. However, the biochar addition effects on the changes of Karst yellow soil are unclear, and the adequate number of biochar dosages to explain optimum of plant growth in this soil area remains poorly understood. In this study, pot experiments were conducted to examine the effects of biochar addition (1%, 3%, 5%, 7%, and 9% by weight; 0% as a control) on bacterial abundance and community structure via high-throughput sequencing coupled with bioinformatics methods applied to Karst yellow soil with planting ryegrass (Lolium perenne L.) and daylily (Hemerocallis fulva). After adding biochar for 188 days, significantly increased pH, soil organic matter, total nutrient contents, and bacterial abundance, but decreased available nitrogen, were observed. Changed bacterial community structures were found in biochar treatments compared with those without biochar. In both soils of planted ryegrass and daylily, the optimum soil bacterial abundance was found in 7% biochar dosage, but the lowest values were in the controls (0%). Taxonomic analysis identified that Micrococcaceae (24.53%), Oxalobacteraceae (11.87%), and Nocardioidaceae (7.89%) were the dominant family in the soil of ryegrass growth, and Micrococcaceae (16.20%), Xanthomonadaceae (6.94%), and Nocardioidaceae (6.41%) were the dominant family in soil of daylily growth. Canonical correspondence analysis showed that the alterations of soil bacterial abundance and community were highly interrelated with soil chemical properties. The results provided a better understanding of the mechanisms underlying the plant-soil microbe interactions and their responses to biochar dosages in low fertility soil regions.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

Effects of pH shock on microaerobic activated sludge system with a graphene oxide/nano-magnetic powder composite

2020 ◽  
Vol 35 (3) ◽  
pp. 457-463
Author(s):  
Huixia Lan ◽  
Xiangzhi Wang ◽  
Shixin Qi ◽  
Da Yang ◽  
Hao Zhang
Keyword(s):  
Graphene Oxide ◽  
Activated Sludge ◽  
High Throughput Sequencing ◽  
Impact Resistance ◽  
Magnetic Powder ◽  
Blank Group ◽  
Activated Sludge System ◽  
Ph Shock ◽  
Dominant Bacteria ◽  
The Impact

AbstractUsing the acclimated activated sludge from the pulping middle-stage effluent, the effect of pH shock on the micro-oxygen activated sludge system with a nano-magnetic powder/graphene oxide composite was studied. The results showed that the removal rates of chemical oxygen demand (CODCr) and ultraviolet adsorption at 254 nm (UV254) decreased. Also, the sludge settling performance was poor due to the impact of pH, but the impact resistance of nano-magnetic powder/graphene oxide group (MGO group) was higher and the recovery was faster. Results of high throughput sequencing indicated that the diversity of microbial community was reduced by the impact of pH, but it was significantly higher in MGO group than in the blank group. The dominant bacteria after pH shock or recovery in both of the system had a large difference. The percentage of the dominant bacteria in the MGO group was higher than that in the blank group. The MGO group had higher electron transfer system (ETS) activity which made the system having a strong pH impact resistance.

scholarly journals Dynamics of Diversity and Abundance of Sulfonamide Resistant Bacteria in a Silt Loam Soil Fertilized by Compost

Antibiotics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 699
Author(s):  
Hui Han ◽  
Mohan Bai ◽  
Yanting Chen ◽  
Yali Gong ◽  
Ming Wu ◽  
...  
Keyword(s):  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Resistant Bacteria ◽  
Arable Soils ◽  
Soil Bacterial Communities ◽  
Sulfonamide Resistance ◽  
Loam Soil ◽  
Abundance And Diversity ◽  
Sulfonamide Resistance Genes

Although composting is effective in deactivating antibiotic substances in manure, the influence of compost fertilization on the occurrence and dissemination of antibiotic resistance in arable soils remains to be controversial. Herein, the abundance and diversity of two sulfonamide resistance genes (sul1 and sul2) in soil fertilized by compost spiked with two concentrations of sulfadiazine (1 and 10 mg kg−1) were studied intensively by qPCR and high throughput sequencing based on a two-month microcosm experiment. The concentration of sulfadiazine decreased rapidly after spiking from 25% at Day 1 to less than 2.7% at Day 60. Relative abundance of both sul1 and sul2 were significantly higher in soil amended with compost than the non-amended control at Day 1 and slightly decreased with incubation time except for sul2 in the S10 treatment. Soil bacterial communities were transiently shifted by compost fertilization regardless of the presence of sulfadiazine. Relative abundance of genera in three hubs positively interlinked with sul1 and sul2 were significantly higher in compost treated soil than the control at Day 1, 7 and 21, but not at Day 60. High throughput sequencing analyses revealed that most detected (>67% in relative abundance) sul1 and sul2 genotypes sharing >99% similarity with those found in gammaproteobacterial pathogens frequently were commonly present in compost and soil. These results indicated that compost fertilization might increase the abundance rather than diversity of sulfadiazine-resistant populations in soil, which may be facilitated by the presence of sulfadiazine.

scholarly journals Denitrifying bacterial communities in surface-flow constructed wetlands during different seasons: characteristics and relationships with environment factors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jia-ming Wei ◽  
Li-juan Cui ◽  
Wei Li ◽  
Yun-mei Ping ◽  
Wan Li
Keyword(s):  
Environmental Factors ◽  
High Throughput Sequencing ◽  
Bacterial Abundance ◽  
Flow Direction ◽  
Denitrifying Bacteria ◽  
Surface Flow ◽  
Strongly Correlated ◽  
Community Structures ◽  
Oxidation Reduction ◽  
Different Seasons

AbstractDenitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. In this study, we explored space–time analysis with high-throughput sequencing to elucidate the relationships between denitrifying bacteria community structures and environmental factors during different seasons. Our results showed that along the flow direction of different processing units, there were dynamic changes in physical and chemical indicators. The bacterial abundance indexes (ACEs) in May, August, and October were 686.8, 686.8, and 996.2, respectively, whereas the Shannon-Weiner indexes were 3.718, 4.303, and 4.432, respectively. Along the flow direction, the denitrifying bacterial abundance initially increased and then decreased subsequently during the same months, although diversity tended to increase. The abundance showed similar changes during the different months. Surface flow wetlands mainly contained the following denitrifying bacteria genus: unclassified Bacteria (37.12%), unclassified Proteobacteria (18.16%), Dechloromonas (16.21%), unranked environmental samples (12.51%), unclassified Betaproteobacteria (9.73%), unclassified Rhodocyclaceae (2.14%), and Rhodanobacter (1.51%). During different seasons, the same unit showed alternating changes, and during the same season, bacterial community structures were influenced by the second genus proportion in different processing units. ACEs were strongly correlated with temperature, dissolved oxygen, and pH. Bacterial diversity was strongly correlated with temperature, electrical conductivity, pH, and oxidation reduction potential. Denitrifying bacteria are greatly affected by environmental factors such as temperature and pH.

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