Rhizospheric Microbiome Profiling of Capsicum annuum L. Cultivated in Amended Soils by 16S and Internal Transcribed Spacer 2 rRNA Amplicon Metagenome Sequencing.

Ali Asaff-Torres,Raúl Rodríguez-Heredia,Jorge Verdín,Itzamná Baqueiro-Peña,Mariana Armendáriz-Ruiz,Marcos Orozco,Juan Carlos Mateos-Díaz,Manuel Kirchmayr,Luis Figueroa-Yáñez

doi:10.1128/genomea.00626-17

Abstract

ABSTRACTRhizospheric microbiomes of Capsicum annuum L. cultivated either conventionally or amended with a synthetic microbial consortium or a root exudate inductor, were characterized by 16S/internal transcribed spacer 2 (ITS2) rRNA amplicon metagenome sequencing. The most abundant taxa found, although differently represented in each treatment, were Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Bacilli, as well as Chytridiomycetes and Mortierellomycotina.

Highlights

Rhizospheric microbiomes of Capsicum annuum L. cultivated either conventionally or amended with a synthetic microbial consortium or a root exudate inductor, were characterized by 16S/internal transcribed spacer 2 (ITS2) rRNA amplicon metagenome sequencing
Rhizospheres from each plant/treatment were extracted with phosphate-buffered saline (PBS)-Silwet MAXX (0.02% [vol/vol]) (Arysta Life Science, Mexico) and pooled
Rhizosphere and rhizoplane metagenomic DNA was extracted with the PowerSoil DNA isolation kit (Mo Bio, Inc., Carlsbad, CA), and its integrity and concentration were assessed by agarose gel electrophoresis and UV spectroscopy. 16S V3-V4 and ITS2 rRNA genes were amplified with primers 337F/805R [8] and ITS3F/ITS4R [9], respectively

Summary

Introduction

Rhizospheric microbiomes of Capsicum annuum L. cultivated either conventionally or amended with a synthetic microbial consortium or a root exudate inductor, were characterized by 16S/internal transcribed spacer 2 (ITS2) rRNA amplicon metagenome sequencing. C. annuum L. was cultivated in Chihuahua, Mexico (28°42=10ЉN, 105°57=42ЉW), under open-field conditions from May to June 2016. BioFit RTU and ExuRoot amendments were applied five times at days 7, 14, 24, 35, and 46 posttransplantation (4.0 and 3.72 kg/ha/application, respectively). 20 plants/replicate, with two replicates from each of three treatments were sampled, in addition to duplicated control samples consisting of a 19-cm column of bulk soil taken 2 cm beneath the surface.

Results

Conclusion