Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.).
The objective of this study was to elucidate the endophytic microbiota in rice sprouts, roots, and stems, and their transmission in the plant development. Prior to DNA extraction, roots and stems were treated with 36% formaldehyde and 0.1M NaOH solutions to remove epiphytic bacterial whole 16S rRNA genes. Bacterial and fungal taxa in the sprout, root, and stem samples were analyzed using Illumina-based sequencing of the V3-V4 hyper variable regions of bacterial 16S rRNA genes and the ITS2 regions of fungal rRNA genes, respectively. Results showed that more diverse bacterial OTUs were detected in roots than in stems, while more diverse fungal OTUs were detected in stems than in roots. Compared with the endophytic microbiota in sprouts, the bacterial OTUs increased in roots but decreased in stems, whereas the fungal OTUs in both stems and roots decreased. Sprout-borne bacterial genera Sphingomonas and Pseudomonus, and fungal genera Fusarium, Pestalotiopsis, and Penicillium were detected in stems and roots. The coexistence of these indigenous bacterial and fungal taxa in sprouts, roots, and stems indicated their transmission during the development from sprouts to mature plants. The results from this study should be useful to better understand the plant-microbe interactions and to select suitable microbial taxa for rice production.
School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
Wenfeng
W
Wang
School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
Yanyan
Y
Zhai
School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: lssclx@163.com.
Lixiang
L
Cao
School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
Hongming
H
Tan
School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China. Electronic address: zhangrd@mail.sysu.edu.cn.
Renduo
R
Zhang
D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D060026:Endophytes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D005658:Fungi / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D064307:Microbiota; D012275:Oryza / Q000382:microbiology*; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology*; D018547:Plant Stems / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D036226:Seedlings / Q000382:microbiology*; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004271:DNA, Fungal; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D012336:RNA, Ribosomal, 16S
Endophyte; Plant microbiome; Pseudomonus; Rice; Sphingomonas