scholarly journals Community Structure and Function of Epiphytic Bacteria Associated With Myriophyllum spicatum in Baiyangdian Lake, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Lei Sun ◽  
Jiashuo Wang ◽  
Yangyang Wu ◽  
Tianyu Gao ◽  
Cunqi Liu
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Myriophyllum Spicatum ◽  
Epiphytic Bacteria ◽  
Baiyangdian Lake ◽  
Operational Taxonomic Units ◽  
The Common ◽  
And Function

Epiphytic bacteria on the surfaces of submerged macrophytes play important roles in the growth of the host plant, nutrient cycling, and the conversion of pollutants in aquatic systems. A knowledge of the epiphytic bacterial community structure could help us to understand these roles. In this study, the abundance, diversity, and functions of the epiphytic bacterial community of Myriophyllum spicatum collected from Baiyangdian Lake in June, August, and October 2019 were studied using quantitative PCR (qPCR), high-throughput sequencing, and the prediction of functions. An analysis using qPCR showed that the epiphytic bacteria were the most abundant in October and the least abundant in August. High-throughput sequencing revealed that Proteobacteria, Gammaproteobacteria, and Aeromonas were the dominant phylum, class, and genus in all the samples. The common analyses of operational taxonomic units (OTUs), NMDS, and LDA showed that the epiphytic bacterial communities were clustered together based on the seasons. The results of a canonical correlation analysis (CCA) showed that the key water quality index that affected the changes of epiphytic bacterial community of M. spicatum was the total phosphorus (TP). The changes in abundance of Gammaproteobacteria negatively correlated with the TP. Predictive results from FAPROTAX showed that the predominant biogeochemical cycle functions of the epiphytic bacterial community were chemoheterotrophy, nitrate reduction, and fermentation. These results suggest that the epiphytic bacterial community of M. spicatum from Baiyangdian Lake varies substantially with the seasons and environmental conditions.

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 Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

Minerals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 596 ◽  
Author(s):  
Shuang Zhou ◽  
Min Gan ◽  
Jianyu Zhu ◽  
Xinxing Liu ◽  
Guanzhou Qiu
Keyword(s):  
Community Structure ◽  
Next Generation Sequencing ◽  
Microbial Ecology ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Structure And Function ◽  
Next Generation ◽  
Sequencing Technologies ◽  
And Function ◽  
Generation Sequencing

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

scholarly journals Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

2016 ◽  
Vol 82 (12) ◽  
pp. 3525-3536 ◽  
Author(s):  
Nikea Ulrich ◽  
Abigail Rosenberger ◽  
Colin Brislawn ◽  
Justin Wright ◽  
Collin Kessler ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Storm Event ◽  
Rrna Gene ◽  
Content Type

ABSTRACTBacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in whichBetaproteobacteriaandGammaproteobacteriadecreased in 16S rRNA gene relative abundance, while the relative abundance of members of theFirmicutesincreased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains ofLegionella,Campylobacter,Arcobacter, andHelicobacter, as well as bacteria of fecal origin (e.g.,Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.IMPORTANCEIn order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.

scholarly journals Diversity of Endophytic Fungal Community in Leaves of Artemisia argyi Based on High-throughput Amplicon Sequencing

2021 ◽  
Vol 70 (2) ◽  
pp. 273-281
Author(s):  
QIU-FANG WU ◽  
LING-MIN HE ◽  
XIN-QIANG GAO ◽  
MEI-LING ZHANG ◽  
JING-SHUN WANG ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Fungal Community Structure ◽  
Operational Taxonomic Units ◽  
Artemisia Argyi ◽  
Artemisia Species

To investigate the community structure and diversity of endophytic fungi in the leaves of Artemisia argyi, leaf samples were collected from five A. argyi varieties grown in different cultivation areas in China, namely, Tangyin Beiai in Henan (BA), Qichun Qiai in Hubei (QA), Wanai in Nanyang in Henan (WA), Haiai in Ningbo in Zhejiang (HA), and Anguo Qiai in Anguo in Hebei (AQA), and analyzed using Illumina high-throughput sequencing technology. A total of 365,919 pairs of reads were obtained, and the number of operational taxonomic units for each sample was between 165 and 285. The alpha diversity of the QA and BA samples was higher, and a total of two phyla, eight classes, 12 orders, 15 families, and 16 genera were detected. At the genus level, significant differences were noted in the dominant genera among the samples, with three genera being shared in all the samples. The dominant genus in QA was Erythrobasidium, while that in AQA, HA, and BA was Sporobolomyces, and that in WA was Alternaria, reaching a proportion of 16.50%. These results showed that the fungal community structure and diversity in QA and BA were high. The endophytes are of great importance to the plants, especially for protection, phytohormone and other phytochemical production, and nutrition. Therefore, this study may be significant with the industrial perspective of Artemisia species.

scholarly journals Lacustrine Sediments Bacterial Community Structure Vertical Succession of the Linxia Basin, NE Tibetan Plateau: Significance for Paleoenvironment Reconstruction

2022 ◽  
Vol 9 ◽  
Author(s):  
Song Xu ◽  
Jingjing Wang ◽  
Xiaoxia Zhang ◽  
Rong Yang ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Community Structure ◽  
Tibetan Plateau ◽  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Global Climate ◽  
The Tibetan Plateau ◽  
Linxia Basin ◽  
Surrounding Soil

The study on sediments in the marginal basins of the Tibetan Plateau is of great significance for global climate change. The geological information of the Linxia Basin has been intensely investigated; however, the profiles of the microbial communities in this basin remain largely unknown. Here, based on the 16S rRNA high-throughput sequencing method, the bacterial community structure vertical succession is studied with different thicknesses of sedimentary samples. The bacterial community with a total of 1,729,658 paired reads distributed within 1,042 phylogenetic amplicon sequence variants (ASVs) from twenty sediments, and three surrounding soil samples were sequenced. First, high-throughput sequencing results highlight the surrounding soil sample bacterial community structures were significantly different from those recovered from the sediment samples. In addition, as observed in the PCoA and PERMANOVA, there is a dramatic change shift event of the community structure at M311. Our data suggest that shifts in relative abundances of the abundant taxa (˃1%) and the significant variations in the diversity of bacterial community implied community structure responses to changes in different sedimentary layers. Predicted community function changes demonstrate that the sediment bacterial community aerobic chemoheterotrophy has been significantly increased, and we believe that the possible influence of the lithofacies changes from the anaerobic system to the aerobic environment, possibly accompanied by the significant uplift of the plateau that has previously been associated with enhanced aridity in Central Asia at ∼8 Ma. Taken together, these results illustrate the potential for the microbial community as a biological indicator in sediment ecosystems to reconstruct paleoenvironments.

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