scholarly journals Effects of continuous cropping of sugar beet (Beta vulgaris L.) on its endophytic and soil bacterial community by high-throughput sequencing

2020 ◽  
Vol 70 (1) ◽  
Author(s):  
Miao Li ◽  
Fuzhen Yang ◽  
Xianyu Wu ◽  
Hai Yan ◽  
Yang Liu
Keyword(s):  
Bacterial Community ◽  
Sugar Beet ◽  
Beta Vulgaris ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Soil Bacterial Community ◽  
Continuous Cropping ◽  
Soil Bacterial

scholarly journals Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4514 ◽  
Author(s):  
Jun Lou ◽  
Li Yang ◽  
Haizhen Wang ◽  
Laosheng Wu ◽  
Jianming Xu
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Laboratory Strain ◽  
Soil Bacterial Community ◽  
Absolute Abundance ◽  
Internal Reference ◽  
Biodegradation Study ◽  
Soil Bacterial

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

scholarly journals Variation of Soil Bacterial Communities during Lettuce Continuous Cropping

2019 ◽  
Vol 131 ◽  
pp. 01091
Author(s):  
Jie Hong ◽  
Yue Yang ◽  
Yi Gao ◽  
LianQuan Zhong ◽  
QuanMing Xu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Continuous Cropping ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Lettuce Yield

The variation of bacterial community in lettuce continuous cropping was determined by high throughput sequencing. During the continuous planting of lettuce, the richness and diversity of bacterial communities in the soil increased, and the ACE index and Chao index increased by 40.21 % and 36.91 %, respectively. The proportion of Actinobacteria, Chloroflexi, Firmicutes and Nitrospirae in the soil increased, while the abundance of Acidobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes and Proteobacteria gradually declined. And the abundance in the soil accounting for 1 % of the dominant bacterial genera increased to 11, among them, Anaerolinea, Bacillus, Nitrosomonas, and Xanthomonas etc became the dominant bacterium genus in the soil after lettuce continuous cropping. After the lettuce had been planted 8 times, the yield decreased by 21.20 % compared to the first harvest. Lettuce continuous cropping had an effect on bacterial community and lettuce yield to some extent.

scholarly journals Dynamic Succession of Soil Bacterial Community during Continuous Cropping of Peanut (Arachis hypogaea L.)

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e101355 ◽  
Author(s):  
Mingna Chen ◽  
Xiao Li ◽  
Qingli Yang ◽  
Xiaoyuan Chi ◽  
Lijuan Pan ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Arachis Hypogaea ◽  
Soil Bacterial Community ◽  
Continuous Cropping ◽  
Arachis Hypogaea L ◽  
Soil Bacterial

scholarly journals Effects of Continuous Cropping of Codonopsis tangshen on Rhizospheric Soil Bacterial Community as Determined by Pyrosequencing

Diversity ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 317
Author(s):  
Meide Zhang ◽  
Yinsheng He ◽  
Wuxian Zhou ◽  
Lunqiang Ai ◽  
Haihua Liu ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Community Structure ◽  
Significant Decline ◽  
Soil Bacterial Community ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Yield And Quality ◽  
Soil Bacterial

Codonopsis tangshen, a perennial herbaceous, has been shown to be affected by continuous cropping, with significant decline in both yield and quality. In this study, we studied the effect of continuous cropping on the abundance and composition of rhizospheric soil bacterial community. Results showed that continuous cropping causes a significant decline in both yield and quality. The nutrient content in continuous cropping soil was higher than that of soil in main cropping. Pyrosequencing analyses revealed Proteobacteria and Acidobacteria as the main phyla in two types of soils. Relative abundance of Acidobacteria, Nitrospirae, TM7, and AD3 phyla was observed to be high in continuous cropping soils, whereas Chloroflexi, Bacteroidetes, and Planctomycetes phyla were richer in main cropping soils. At the genus level, high relative abundance of Pseudomonas (γ-Proteobacteria), Rhodanobacter, Candidatus Koribacter, and Candidatus were observed in continuous cropping soil. Different patterns of bacterial community structure were observed between different soils. Redundancy analysis indicated that organic matter content and available nitrogen content exhibited the strongest effect on bacterial community structure in the continuous cropping soil. Taken together, continuous cropping led to a significant decline in yield and quality, decrease in rhizospheric soil bacterial abundance, and alteration of rhizospheric soil microbial community structure, thereby resulting in poor growth of C. tangshen in the continuous cropping system.

scholarly journals High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12105
Author(s):  
Fangnan Xiao ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Yaling He ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Soil Bacteria ◽  
High Throughput Sequencing ◽  
Soil Bacterial Community ◽  
Tarim River ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
And Function

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

scholarly journals Conservation tillage regulates soil bacterial community assemblies, network structures and ecological functions in black soils

2021 ◽  
Author(s):  
Zhuxiu Liu ◽  
Haidong Gu ◽  
Aizhen Liang ◽  
Lujun Li ◽  
Qin Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Carbon ◽  
High Throughput Sequencing ◽  
Conservation Tillage ◽  
Conventional Tillage ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Tillage Practices ◽  
Degrading Bacteria ◽  
Soil Bacterial

Abstract Aims Conventional tillage is a serious threat to the stability of soil ecosystems. Understanding the response mechanisms of soil microbial community assemblies to anthropogenic activities is a major topic of ecological research. Methods Here, we investigated the bacterial community structures and assemblies in bulk and rhizosphere soils of soybeans grown with conventional tillage (moldboard plow, MP) and with conservation tillage that involved no-tillage (NT) or ridge tillage (RT) using high-throughput sequencing methods. Results We found that soil bacterial community compositions, structures and assembly processes were primarily altered by tillage practices. Briefly, in comparison to MP, NT and RT increased the relative abundances of the nitrogen-fixing bacteria Mesorhizobium sp., Bradyrhizobium sp. and Burkholderia sp., but decreased the abundance of soil carbon-degrading bacteria, especially Blastococcus sp., Streptomyces sp. and Sphingomonas sp. In addition, in comparison to MP, NT and RT resulted in more stable bacterial networks and more lower the relative contribution of homogenizing dispersal. Soil pH was the primary soil factor regulating both the bacterial community structures and assembly processes under the three tillage practices. Conclusions The altered functional bacteria under conservation tillage was mostly affiliated with biomarkers and keystone taxa, inferring that conservation tillage might contribute to biological nitrogen fixation and soil carbon sequestration.

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