scholarly journals Microbial Biogeography along the Gastrointestinal Tract Segments of Sympatric Subterranean Rodents (Eospalax baileyi and Eospalax cansus)

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3297
Author(s):  
Daoxin Liu ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Feng Jiang ◽  
Pengfei Song ◽  
...  
Keyword(s):  
Small Intestine ◽  
Community Structure ◽  
Bacterial Community ◽  
Expectation Maximization ◽  
High Throughput Sequencing ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Subterranean Rodents ◽  
Sequencing Technology ◽  
Microbial Biogeography

In this study, based on high-throughput sequencing technology, the biodiversity and the community structure of microbiota in different GIT segments (the stomach, small intestine, cecum and rectum) of plateau zokors and Gansu zokors were studied and compared. A source tracking analysis for the microbial communities of different GIT segments was carried out using the fast expectation–maximization microbial source tracking (FEAST) method. We found that, for both species, the microbial community richness and diversity of the small intestine were almost the lowest while those of the cecum were the highest among the four segments of the GIT. Beta diversity analyses revealed that the bacterial community structures of different GIT segments were significantly different. As for the comparison between species, the bacterial community compositions of the whole GIT, as well as for each segment, were all significantly different. Source tracking conducted on both zokors indicated that the soil has little effect on the bacterial community of the GIT. A fairly high percentage of rectum source for the bacterial community of the stomach indicated that both zokors may engage in coprophagy.

scholarly journals Comparison of Auxin and Cytokinins Concentrations, and the Structure of Bacterial Community between Host Twigs and Lithosaphonecrus arcoverticus Galls

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 982
Author(s):  
Xue-Mei Yang ◽  
Yu Hui ◽  
Lv-Quan Zhao ◽  
Dao-Hong Zhu ◽  
Yang Zeng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Zeatin Riboside ◽  
Insect Galls ◽  
Abnormal Growth ◽  
Liquid Chromatography Tandem Mass ◽  
High Concentrations ◽  
Galling Insects

Insect galls are the abnormal growth of plant tissues induced by a wide variety of galling insects and characterized by high concentrations of auxins and cytokinins. It remains unclear whether the auxins and cytokinins affect the bacterial community structure of insect galls. We determined the concentrations of indoleacetic acid (IAA) as an example of auxin, trans-zeatin riboside (tZR) and isopentenyladenine (iP) as cytokinins in Lithosaphonecrus arcoverticus (Hymenoptera: Cynipidae) galls and the galled twigs of Lithocarpus glaber (Fagaceae) using liquid chromatography–tandem mass spectrometry. Moreover, for the first time, we compared the bacterial community structure of L. arcoverticus galls and galled twigs by high-throughput sequencing, and calculated the Spearman correlation and associated degree of significance between the IAA, tZR and iP concentrations and the bacterial community structure. Our results indicated the concentrations of IAA, tZR and iP were higher in L. arcoverticus galls than in galled twigs, and positively correlated with the bacterial community structure of L. arcoverticus galls. We suggest the high concentrations of IAA, tZR and iP may affect the bacterial community structure of L. arcoverticus galls.

scholarly journals Effects of Continuous Cropping on Bacterial Community Structure in Rhizospheric Soil of Sweet Potato

2020 ◽  
Author(s):  
Zhiyuan Gao ◽  
Yaya Hu ◽  
Meikun Han ◽  
Junjie Xu ◽  
Xue Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sweet Potato ◽  
Soil Ph ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Potato Industry ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Potato Varieties

Abstract Background: Continuous cropping obstacles from sweet potato are widespread, which seriously reduce the yield and quality, restrict the sustainable development of sweet potato industry. Bacteria are the most abundant in rhizospheric soil and have a certain relationship with continuous cropping obstacles. However, there are few reports on how continuous cropping affected the bacterial community structure in the rhizospheric soil of sweet potato. In this study, high-throughput sequencing technique was used to explore the changes of rhizospheric soil bacterial community structure of different sweet potato varieties, and the correlation between soil characteristics and this bacterial community after continuous cropping, so as to provide a theoretical basis for the prevention and control of sweet potato continuous cropping obstacles.Results: After two years of continuous cropping, the results showed that (1) the dominant bacteria phlya in rhizospheric soils from both Xushu18 and Yizi138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. Significant changes in the relative abundance of rhizospheric soil bacteria were observed for two sweet potato varieties. (2) Bacterial richness and diversity indexes of rhizospheric soil from Xushu18 were higher than those from Yizi138 after continuous cropping. Moreover, the beneficial Lysobacter and Bacillus were more prevalent in Xushu18, but Yizi138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis showed that soil pH was significantly correlated with bacterial community. Spearman’s rank correlations coefficients analysis demonstrated that pH was positively correlated with Planctomycetes and Acidobacteria, and negatively correlated with Actinobacteria and Firmicutes.Conclusions: After continuous cropping of sweet potato, the bacterial community structure and physicochemical properties in the rhizospheric soil were unbalanced, and the changes of different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for the development of special microbial fertilizer for sweet potatoes to alleviate continuous cropping obstacle.

scholarly journals Effects of Phytoremediation Treatment on Bacterial Community Structure and Diversity in Different Petroleum-Contaminated Soils

2018 ◽  
Vol 15 (10) ◽  
pp. 2168 ◽  
Author(s):  
Yuanyuan Shen ◽  
Yu Ji ◽  
Chunrong Li ◽  
Pingping Luo ◽  
Wenke Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Cost Effective ◽  
Northwest China ◽  
Community Response ◽  
Available Nitrogen ◽  
Increased Risk

Increased exploitation and use of petroleum resources is leading to increased risk of petroleum contamination of soil and groundwater. Although phytoremediation is a widely-used and cost-effective method for rehabilitating soils polluted by petroleum, bacterial community structure and diversity in soils undergoing phytoremediation is poorly understood. We investigate bacterial community response to phytoremediation in two distinct petroleum-contaminated soils (add prepared petroleum-contaminated soils) from northwest China, Weihe Terrace soil and silty loam from loess tableland. High-throughput sequencing technology was used to compare the bacterial communities in 24 different samples, yielding 18,670 operational taxonomic units (OTUs). The dominant bacterial groups, Proteobacteria (31.92%), Actinobacteria (16.67%), Acidobacteria (13.29%) and Bacteroidetes (6.58%), increased with increasing petroleum concentration from 3000 mg/kg–10,000 mg/kg, while Crenarchaeota (13.58%) and Chloroflexi (4.7%) decreased. At the order level, RB41, Actinomycetales, Cytophagales, envOPS12, Rhodospirillales, MND1 and Xanthomonadales, except Nitrososphaerales, were dominant in Weihe Terrace soil. Bacterial community structure and diversity in the two soils were significantly different at similar petroleum concentrations. In addition, the dominant genera were affected by available nitrogen, which is strongly associated with the plants used for remediation. Overall, the bacterial community structure and diversity were markedly different in the two soils, depending on the species of plants used and the petroleum concentration.

Bacterial community diversity and dynamics of Dongzhai harbor mangrove soils in China

2019 ◽  
Vol 65 (10) ◽  
pp. 703-712
Author(s):  
Peng Li ◽  
Siyu Wu ◽  
Haoneng Yin ◽  
Hongping Wu ◽  
Qin Peng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Soil Samples ◽  
Community Diversity ◽  
Orthologous Group ◽  
Bacterial Community Diversity ◽  
National Nature Reserve ◽  
Abundant Otus

Dongzhai Harbor National Nature Reserve is the largest mangrove reserve in China, but the bacterial diversity and community structure of soils in the Dongzhai harbor mangrove (DHM) is still not well known. This study was conducted to characterize and compare the bacterial community diversity and composition of DHM soils in three typical sites (YA, entrance of wastewater and sanitary sewage; YB, located in Dongzhai Harbor National Nature Reserve; YC, near the sea) using high-throughput sequencing of the 16S rDNA. Community statistical analyses suggested that the YB and YC soils have a similar community structure, but they differ from the YA soils significantly. Proteobacteria and Chloroflexi were the ubiquitous and dominant groups that made up nearly 80% of total bacterial communities, but it was noted that Chloroflexi had a higher relative abundance in YA soil samples than YB and YC soil samples and that the operational taxonomic units (OTUs) of Anaerolineaceae, Gammaproteobacteria, and Thiogranum reached extremely significant levels. Interaction network analysis of the 50 most abundant OTUs further demonstrated that the OTUs of YA showed few interactions with YB and YC OTUs, and the Cluster of Orthologous Group (COG) involved in lipid transport and metabolism showed significant differences between the YA and YB soil samples. Our results will greatly help to understand the bacterial community variation of the DHM as human activities enhance and grow, and to identify some challenges for the restoration and management of the mangrove ecosystem.

Bacterial Community Analysis of Mine Contaminated Soils in Hechi City

2020 ◽  
Vol 14 (4) ◽  
pp. 476-486
Author(s):  
Tingting Liu ◽  
Caoping Pang ◽  
Fengcai Ye ◽  
Dafei Gong ◽  
Jieling Luo ◽  
...  
Keyword(s):  
Microbial Community ◽  
Genetic Engineering ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Mine Soils ◽  
Sequencing Technology ◽  
Autonomous Region

Four mine contaminated soils located in northwest of Guangxi autonomous region were selected for microbial community analysis. These mine soils were contaminated by chromium (Cr) and cadmium (Cd). Microbial communities were described by high-throughput sequencing technology, which showed 39 different phyla in four samples. Among these phyla, Proteobacteria was the most abundant phylum in all samples. Acidobacteria, Actinobacteria, Planctomycetes, Firmicutes, Gemmatimonadetes, Bacteroidetes and Chloroflexi showed higher relative abundances than other phyla. In addition, a wide diversity of bacteria with the potential of bioremediation, such as Sphingomonas, Lysobacter and Gemmatimonas were detected in the tested mine contaminated soils. The results of microbial community analysis will provide a new target for isolation of microorganisms with the potential of bioremediation and lay the foundation for a great enhancement of bioremediation ability through the genetic engineering modification of indigenous microorganisms in future.

scholarly journals Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

2021 ◽  
Author(s):  
Soo-In Sohn ◽  
Jae-Hyung Ahn ◽  
Subramani Pandian ◽  
Young-Ju Oh ◽  
Eun-Kyoung Shin ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Root Nodules ◽  
Growth Stages ◽  
Sequencing Analysis ◽  
Biolog Ecoplate ◽  
Metabolic Capability ◽  
Increasing Trend

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max L.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

scholarly journals Application of Broccoli Residues to Soil can Suppress Verticillium Wilt of Cotton by Regulating the Bacterial Community Structure of the Rhizosphere

2021 ◽  
Author(s):  
Weisong Zhao ◽  
Qinggang Guo ◽  
Shezeng Li ◽  
Xiuyun Lu ◽  
Peipei Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput ◽  
Verticillium Wilt ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Field Experiments ◽  
Cotton Seeds ◽  
Relative Abundances ◽  
And Control

Abstract [Aims] Verticillium wilt (VW) of cotton was effectively controlled by application of broccoli residues (BR) to soil. Information regarding the variation in bacterial communities in rhizosphere of cotton cultivars with different VW resistance levels under BR treatment is still lacking and finally to provide guidance for screening effective biocontrol bacteria. [Methods] Real-time fluorescence quantitative PCR was used to determine the population of Verticillium dahliae, the effects of BR on the bacterial community structure in rhizosphere were determined by high-throughput sequencing technology. [Results] Results showed that control effects for susceptible cultivar (cv. EJ-1) and resistant cultivar (cv. J863) on VW after BR treatment were 51.76% and 86.15%, the population of V. dahliae decreased by 18.88% and 30.27%, respectively. High-throughput sequencing showed that ACE and Chao1 indices were increased by application of BR. Actinobacteria, Proteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, and Firmicutes were the most dominant phyla, and relative abundances of these bacterial taxa significantly differed between cultivars. Additionally, Bacillus stably increased in rhizosphere following BR treatment. Redundancy analysis (RDA) showed that relative abundances of Bacillus, Lysobacter, Streptomyces, Rubrobacter, Gemmatimonas, Bryobacter and Nocardioides were correlated with occurrence of VW. Field experiments demonstrated that dressing cotton seeds with Bacillus subtilis NCD-2 could successfully reduce occurrence of VW, and control effects for EJ-1 and J863 were 35.26% and 31.02%, respectively. [Conclusions] The application of BR changed the bacterial community structure in cotton rhizosphere, decreased the population of V. dahliae in soil, and increased the abundance of beneficial microorganisms, thus significantly reducing the occurrence of VW.

scholarly journals Application of Tea Polyphenols and Their Effects on Ultrafiltration Effluent Disinfection and Microbial Risk

Water ◽  
2021 ◽  
Vol 13 (18) ◽  
pp. 2559
Author(s):  
Cuimin Feng ◽  
Tong Wei ◽  
Shan Qing ◽  
Fang Han ◽  
Xingcheng Tao
Keyword(s):  
Bacterial Community ◽  
Virulence Factors ◽  
High Throughput Sequencing ◽  
Tea Polyphenols ◽  
Sequencing Technology ◽  
Microbial Risk ◽  
Pathogen Virulence ◽  
Disinfection Process ◽  
By Products ◽  
Number Of Bacteria

To reduce the risk of by-products from traditional disinfection technology and to ensure safe water quality, tea polyphenols (TP) were used as disinfectants after the ultrafiltration (UF) process. The disinfectant effect of TP was tested on the total number of bacteria and changes in bacterial community structure, and pathogen virulence factors were detected by Illumina’s high-throughput sequencing technology. The results showed that the recommended dosage of TP for water treatment after UF was 5 mg/L, which can effectively inhibit bacterial growth and maintain the disinfectant effect for up to 48 h later. In the disinfection process, the degradation of the tea polyphenols concentration was fitted to the equation of the second order reaction kinetics. The lower the initial concentration and the higher the reaction temperature, the faster the TP decay. The metagenomic analysis of the microorganisms indicated that disinfection with tea polyphenols reduced the diversity of microorganisms in the water and altered the structure of the bacterial community. The existence of tea polyphenols also significantly inhibited the growth of potential common Gram-negative pathogens, especially Mycobacterium. TP disinfectant can also reduce the diversity and abundance of pathogenic bacterial virulence factors and improve biological safety in drinking water.

scholarly journals Different Soil Salinity Imparts Clear Alteration In Rhizospheric Bacterial Community Dynamics In Rice And Peanut.

2021 ◽  
Author(s):  
Md Majharul Islam ◽  
Rajarshi Bhattacharya ◽  
Biraj Sarkar ◽  
Pulak Kumar Maiti ◽  
Shouvik Mahanty ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Host Plant ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Bacterial Community Composition ◽  
Chemical Properties ◽  
Alpha Diversity ◽  
Rhizospheric Soil ◽  
Bacterial Community Dynamics

Abstract The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in overall health of the host-plant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community-dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence-analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community-structure is related to both the adjoining soil characters and the type of the hosts.

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