Root-Associated Endophytic Bacterial Community Composition of Pennisetum sinese from Four Representative Provinces in China

Abstract

Pennisetum sinese, a source of bio-energy with high biomass production, is a species that contains high crude protein and will be useful for solving the shortage of forage grass after the implementation of “Green for Grain” project in the Loess plateau of Northern Shaanxi in 1999. Plants may receive benefits from endophytic bacteria, such as the enhancement of plant growth or the reduction of plant stress. However, the composition of the endophytic bacterial community associated with the roots of P. sinese is poorly elucidated. In this study, P. sinese from five different samples (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China) were investigated by high-throughput next-generation sequencing of the 16S rDNA V3-V4 hypervariable region of endophytic bacteria. A total of 313,044 effective sequences were obtained by sequencing five different samples, and 957 effective operational taxonomic units (OTUs) were yielded at 97% identity. The phylum Proteobacteria, the classes Gammaproteobacteria and Alphaproteobacteria, and the genera Pantoea, Pseudomonas, Burkholderia, Arthrobacter, Psychrobacter, and Neokomagataea were significantly dominant in the five samples. In addition, our results demonstrated that the Shaanxi province (SX) sample had the highest Shannon index values (3.795). We found that the SX (308.097) and NS (126.240) samples had the highest and lowest Chao1 richness estimator (Chao1) values, respectively. Venn graphs indicated that the five samples shared 39 common OTUs. Moreover, according to results of the canonical correlation analysis (CCA), soil total carbon, total nitrogen, effective phosphorus, and pH were the major contributing factors to the difference in the overall composition of the bacteria community in this study. Our data provide insights into the endophytic bacteria community composition and structure of roots associated with P. sinese. These results might be useful for growth promotion in different samples, and some of the strains may have the potential to improve plant production in future studies.

The Root Endophytic Fungi Community Structure of Pennisetum sinese from Four Representative Provinces in China

“…The root samples were then immediately transferred to the lab for further processing in less than 12 h. At the time of the root collection, soils around the roots were also collected to measure the soil’s physicochemical characteristics. To prevent the contamination of the soil and rhizosphere fungi, the root a surface sterilization procedure was performed, as previously described [11]. In order to verify the effect of surface sterilization, parts of the sterilized roots were rolled on potato dextrose agar (PDA) plates.…”

“…Endophytic microbes include endophytic bacteria and endophytic fungi. Studies on endophytic bacteria of P. sinese from different provinces have shown great differences in different eco-regions of China, and soil properties and climate are the most important reasons behind these differences [11]. However, many studies on endophytes of P. sinese have evidenced a difference in the dominant bacteria [11,12].…”

“…Although some studies on the endophytic bacteria of P. sinese have been reported [11,12], there are still no reports on the root endophytic fungi community of P. sinese. Here, we ae the first to report the endophytic fungi diversity of P. sinese collected from four provinces of China (Shaanxi province, Fujian province, Xinjiang Uygur Autonomous Prefecture, and Inner Mongolia (including sandy and saline–alkali soil) using the high throughput sequencing method.…”

Dynamic Changes in the Bacterial Community During the Fermentation of Traditional Chinese Fish Sauce (TCFS) and their Correlation with TCFS Quality

“…Recently, an increasing number of studies have revealed that approximately 99% of the microbial community in the environment is uncultured, which limits the applications of traditional culture methods. With the development of molecular biology technology, the non-culture method based on high-throughput sequencing technology allows a comprehensive and accurate understanding of microbial community structures in the environment and provides a new way to study their diversity and function [15,16,17]. High-throughput sequencing is mainly performed through sequencing by synthesis (SBS) and the exclusive reversible termination of chemical reactions; therefore, large amounts of data can be obtained in a short time, with high throughput, high accuracy, and low cost.…”

The Role of the Bacterial Community in Producing a Peculiar Smell in Chinese Fermented Sour Soup

“…Library concentrations were detected by Qubit v. 3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). The library was quantified to 10 nM; PE250/FE300 double-end sequencing was performed according to the instructions of the Illumina MiSeq (Illumina, San Diego, CA, USA) instrument, and sequence information was read by MiSeq Control Software (MCS) [ 15 ].…”