Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones

被引：32

作者：

Kumar, Mukesh ^{[1
]}

Kumar, Aundy ^{[1
]}

Sahu, Kuleshwar Prasad ^{[1
]}

Patel, Asharani ^{[1
]}

Reddy, Bhaskar ^{[1
]}

Sheoran, Neelam ^{[1
]}

Krishnappa, Charishma ^{[1
]}

Rajashekara, Hosahatti ^{[2
]}

Bhagat, Someshwar ^{[3
]}

Rathour, Rajeev ^{[4
]}

机构：

[1] ICAR Indian Agr Res Inst, New Delhi, India

[2] ICAR Vivekananda Inst Hill Agr, Almora, Uttarakhand, India

[3] ICAR Cent Rainfed Upland Rice Res Stn NRRI, Hazaribagh, Jharkhand, India

[4] CSK Himachal Pradesh Agr Univ, Palampur, Himachal Prades, India

来源：

MICROBIOLOGICAL RESEARCH | 2021年 / 246卷

关键词：

Core-microbiome; Rice leaf; Endophyte; Climate zone; Aromatic rice; mNGS;

D O I：

10.1016/j.micres.2021.126704

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated in-fluence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Aci-netobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice ge-notypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.

引用

页数：19