scholarly journals Structure of Bacterial Communities in Phosphorus-Enriched Rhizosphere Soils

2020 ◽  
Vol 10 (18) ◽  
pp. 6387
Author(s):  
Yuwei Hu ◽  
Changqun Duan ◽  
Denggao Fu ◽  
Xiaoni Wu ◽  
Kai Yan ◽  
...  
Keyword(s):  
Plant Species ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Nutrient Content ◽  
Illumina Miseq ◽  
Dianchi Lake ◽  
Lake Basin ◽  
Rhizosphere Soils ◽  
Abundance And Diversity ◽  
And Function

Although phytoremediation is the main method for P-removal and maintaining ecosystem balance in geological phosphorus-enriched soils (PES), little is known about the structure and function of microbial communities in PES. Interactions between plants and soil microorganisms mainly occur in the rhizosphere. The aim of this work was to investigate the composition and diversity of bacterial communities found in rhizosphere soils associated with the following three dominant plant species: Erianthus rufipilus, Coriaria nepalensis, and Pinus yunnanensis. In addition, we compared these rhizosphere bacterial communities with those derived from bulk soils and grassland plots in PES from the Dianchi Lake basin of southwestern China. The Illumina MiSeq platform for high-throughput sequencing of 16S rRNA was used for the taxonomy and the analysis of soil bacterial communities. The results showed higher bacterial diversity and nutrient content in rhizosphere soils as compared with bulk soils. Rhizosphere bacteria were predominantly comprised of Proteobacteria (24.43%) and Acidobacteria (21.09%), followed by Verrucomicrobia (19.48%) and Planctomycetes (9.20%). A comparison of rhizosphere soils of the selected plant species in our study and the grassland plots showed that Acidobacteria were the most abundant in the rhizosphere soil of E. rufipilus; Bradyrhizobiaceae and Rhizobiaceae in the order Rhizobiales from C. nepalensis were found to have the greatest abundance; and Verrucomicrobia and Planctomycetes were in higher abundance in P. yunnanensis rhizosphere soils and in grassland plots. A redundancy analysis revealed that bacterial abundance and diversity were mainly influenced by soil water content, soil organic matter, and total nitrogen.

Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site

2017 ◽  
Vol 63 (6) ◽  
pp. 502-515 ◽  
Author(s):  
Natalie P. Blain ◽  
Bobbi L. Helgason ◽  
James J. Germida
Keyword(s):  
Plant Species ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Growth Promotion ◽  
Plant Root ◽  
Gene Copy ◽  
Sampling Location ◽  
Historic Site ◽  
Copy Numbers

The Bitumount Provincial Historic site is the location of 2 of the world’s first oil-extracting and -refining operations. Despite hydrocarbon levels ranging from 330 to 24 700 mg·(kg soil)−1, plants have been able to recolonize the site through means of natural revegetation. This study was designed to achieve a better understanding of the plant-root-associated bacterial partnerships occurring within naturally revegetated hydrocarbon-contaminated soils. Root endophytic bacterial communities were characterized from representative plant species throughout the site by both high-throughput sequencing and culturing techniques. Population abundance of rhizosphere and root endosphere bacteria was significantly influenced (p < 0.05) by plant species and sampling location. In general, members of the Actinomycetales, Rhizobiales, Pseudomonadales, Burkholderiales, and Sphingomonadales orders were the most commonly identified orders. Community structure of root-associated bacteria was influenced by both plant species and sampling location. Quantitative real-time polymerase chain reaction was used to determine the potential functional diversity of the root endophytic bacteria. The gene copy numbers of 16S rRNA and 2 hydrocarbon-degrading genes (CYP153 and alkB) were significantly affected (p < 0.05) by the interaction of plant species and sampling location. Our findings suggest that some of the bacterial communities detected are known to exhibit plant growth promotion characteristics.

scholarly journals Characterization of the salivary microbiome in people with obesity

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4458 ◽  
Author(s):  
Yujia Wu ◽  
Xiaopei Chi ◽  
Qian Zhang ◽  
Feng Chen ◽  
Xuliang Deng
Keyword(s):  
High Throughput Sequencing ◽  
Periodontal Diseases ◽  
Illumina Miseq ◽  
Normal Weight ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Diseases ◽  
And Function ◽  
Healthy Participants

Background The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs. Methods We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases. Results The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus Prevotella, Granulicatella, Peptostreptococcus, Solobacterium, Catonella, and Mogibacterium were significantly more abundant in the obesity group; meanwhile the genus Haemophilus, Corynebacterium, Capnocytophaga, and Staphylococcus were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls. Discussion Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases.

Comparative analysis of biofilm community on different coloured substrata in relation to mussel settlement

2016 ◽  
Vol 97 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Yi-Feng Li ◽  
Xing-Pan Guo ◽  
Yu-Ru Chen ◽  
De-Wen Ding ◽  
Jin-Long Yang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Significant Difference ◽  
The World ◽  
Community Variability ◽  
Biofilm Community

Mussels are typical macrofouling organisms in the world. In this study, the interaction between the settlement ofMytilus coruscusplantigrades and bacterial community on coloured substrata was determined. Bacterial communities in biofilms developed on seven coloured substrata were analysed by Illumina Miseq sequencing. The mussel settlement response to coloured substrata with no biofilms was also examined.Flavobacteria, AlphaproteobacteriaandGammaproteobacteriawere the first, second and third most dominant groups in seven biofilm samples. The results suggest that the inducing activities of these biofilms on plantigrade settlement varied with coloured substrata and the lowest percentage of settlement was observed on biofilms on the green substratum. High-throughput sequencing showed that bacterial community in biofilms also changed with the substratum colour. No significant difference in the inducing activity on plantigrade settlement was observed between the coloured substrata with no biofilms. Thus, difference in plantigrade settlement response may be correlated to the changes in bacterial community on coloured substrata. This finding extends current knowledge of interaction among mussel settlement and bacterial community variability.

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 Bacterial community evolution along full-scale municipal wastewater treatment processes

2020 ◽  
Vol 18 (5) ◽  
pp. 665-680
Author(s):  
Lei Zhang ◽  
Yanan Cheng ◽  
Chang Qian ◽  
Wenxuan Lu
Keyword(s):  
Wastewater Treatment ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Oxygen Demand ◽  
Illumina Miseq ◽  
Municipal Wastewater Treatment ◽  
Bacterial Assemblage

Abstract Sewage pollution is a major threat to public health because sewage is always accompanied by pathogens. Generally, wastewater treatment plants (WWTP) receive and treat sewage to control pathogenic risks and improve environmental health. This study investigated the changes in the bacterial community over the course of treatment by a WWTP. Illumina MiSeq high-throughput sequencing was performed to characterize the bacterial communities in the WWTP. This study found that potential pathogens in the WWTP, especially the genera Arcobacter and Acinetobacter, were greatly reduced. In addition, high chemical oxygen demand levels provided excessive growth substrates for the genera Hyphomicrobium and Rhodoplanes, the abundance of which could exceed autotrophic bacteria, increasing the ammonium removal. According to the network analysis, the bacterial assemblage was not randomly arranged in the WWTP, and various defined processes led to higher intra-phylum (such as Proteobacteria) coexistence than expected. Moreover, the metabolic functions of bacterial communities significantly improved in the WWTP compared with the influent. Together, the data in this study emphasize the need to understand the bacterial community of WWTPs better. When analyzing the risks of WWTP drainage systems to the environment and human health, these data should be considered.

scholarly journals High-Throughput Sequencing Analysis of the Composition and Diversity of the Bacterial Community in Cinnamomum camphora Soil

2021 ◽  
Vol 10 (1) ◽  
pp. 72
Author(s):  
Deqiang Chen ◽  
Weihong Sun ◽  
Shuang Xiang ◽  
Shuangquan Zou
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bulk Soil ◽  
Slope Position ◽  
Available Phosphorus ◽  
Sequencing Analysis ◽  
Sample Type ◽  
Cinnamomum Camphora ◽  
And Function

Soil bacterial communities and root-associated microbiomes play important roles in the nutrient absorption and healthy growth of host plants. Cinnamomum camphora is an important timber and special economic forest tree species in Fujian Province. In this study, the high-throughput sequencing technique was used to analyze the composition, diversity, and function of the bacterial communities present in the soil from different samples and slope positions of C. camphora. The results of this analysis demonstrated that the related bacterial communities in C. camphora soil were mainly clustered based on sample type. Bacterial alpha diversity in the rhizosphere and bulk soil of C. camphora growing downhill was higher than that of C. camphora growing uphill. At the phylum level, Bacteroidetes, Proteobacteria, Chloroflexi, and Gemmatimonadetes were positively correlated with pH, available phosphorus, total phosphorus, available potassium, and total potassium, while Acidobacteria and Verrucomicrobia were negatively correlated with alkaline-hydrolyzable nitrogen. These results show that there were remarkable differences in the composition, diversity, and function of related bacterial communities between different sample types of C. camphora soil. The slope position had a marked effect on the bacterial communities in the rhizosphere and bulk soil, while the root endosphere remained unaffected.

scholarly journals Study on the Diversity of Fungal and Bacterial Communities in Continuous Cropping Fields of Chinese Chives (Allium tuberosum)

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Yizhu Gu ◽  
Yuxin Wang ◽  
Pingzhi Wang ◽  
Chaonan Wang ◽  
Jinhai Ma ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Nutrient Content ◽  
Scientific Management ◽  
Continuous Cropping ◽  
Potassium Fertilizer ◽  
Beneficial Bacteria ◽  
Bacterial Phyla ◽  
Chinese Chives

In this study, high-throughput sequencing technology was used to analyse the diversity and composition of fungal and bacterial communities in continuous cropping soil of Chinese chives. The soil nutrient was also measured to explore the rationality of current fertilization management. These results can provide a basis for the prevention and control of the continuous cropping obstacles of Chinese chives and further scientific management. Soil samples from fields continuously cropped with Chinese chives for one year, three years, and five years were collected and analysed. The results showed that the nutrient content of TP, AP, AK and TK increased significantly with increasing continuous cropping years. Short-term continuous cropping soil nutrients have not deteriorated. Alpha-diversity analysis showed that significant differences were not found in the diversity of the fungal and bacterial community among different years. Ascomycota, Basidiomycota and Mortierellomycota were the three most dominant fungal phyla. Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria were the dominant bacterial phyla. Continuous cropping makes Fusarium increase, and the beneficial bacteria Pseudomonas decreased significantly. According to the correlation heat map analysis of environmental factors, excessive phosphorus may lead to the increase of Fusarium, potassium may promote the proliferation of beneficial bacteria in the continuous cropping process, and it is necessary to regulate the application of phosphate and potassium fertilizer.

scholarly journals Tibetan wild asses (Equus Kiang) were superior to domestic donkeys (Equus Asinus) in terms of the composition and function of gut microbial community

2019 ◽  
Author(s):  
Hongjin Liu ◽  
Xinquan Zhao ◽  
Shixiao Xu ◽  
Liang Zhao ◽  
Xueping Han ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Species Interactions ◽  
High Throughput Sequencing ◽  
Acid Metabolism ◽  
Alpha Diversity ◽  
Equus Asinus ◽  
Significant Difference ◽  
And Function ◽  
Gut Microbial Community

Abstract Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibetan Plateau, and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefor, understanding the gut microbita composition and function can provide a theoretical for the situ conservation of wild animals in the future. This study analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA regions. No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla of Bacteroidetes and Firmcutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses were superior to that of domestic in gut bacteria community composition and function, and wild asses should be more suitable to survive in wild than to be domesticated or captive.

Sign in / Sign up

Export Citation Format

Share Document