scholarly journals Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

2016 ◽  
Vol 7 ◽  
Author(s):  
C. Ryan Penton ◽  
Vadakattu V. S. R. Gupta ◽  
Julian Yu ◽  
James M. Tiedje
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sample Size ◽  
Soil Sample ◽  
High Throughput ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Rrna Gene

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 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 the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5583 ◽  
Author(s):  
Ma. Fernanda Sánchez-Soto Jiménez ◽  
Daniel Cerqueda-García ◽  
Jorge L. Montero-Muñoz ◽  
Ma. Leopoldina Aguirre-Macedo ◽  
José Q. García-Maldonado
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gulf Of Mexico ◽  
Microbial Communities ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Hydrocarbon Contamination ◽  
Rrna Gene ◽  
Fold Belt ◽  
Abundant Otus

The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88;H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2;H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded toKordiimonadales, Rhodospirillales,Desulfobacterales(Desulfococcus), Syntrophobacterales and Nitrospirales(GOUTA 19,BD2-6,LCP-6), whilstChromatiales,Oceanospirillales(Amphritea,Alcanivorax),Methylococcales,Flavobacteriales,Alteromonadales(Shewanella,ZD0117) andRhodobacteraleswere the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.

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.

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.

Sign in / Sign up

Export Citation Format

Share Document