ICAR-Indian Agricultural Research Institute, New Delhi, India.
ICAR-Indian Agricultural Research Institute, New Delhi, India.
Microbiol Res. 2021 May;246:126704. doi: 10.1016/j.micres.2021.126704. Epub 2021 Jan 10.
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 influence 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; Acinetobacter; 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 genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.
我们通过宏基因组 NGS（mNGS）和传统微生物学方法，破译了在印度山区和高原地区生长的芳香型（cv. Pusa Basmati-1）和非芳香型（cv. BPT-5204）水稻基因型的叶片内生微生物组。通过对核糖体基因 V3-V4 区域进行测序的微生物组分析表明，在 Palampur 和 Almora 的山区，细菌操作分类单元（OTU）比 Hazaribagh 的高原区略多。有趣的是，山区水稻叶片内生微生物组与高原区的微生物组分离聚类。Bray-Curtis 不相似性指数表明，地理位置对塑造水稻内生微生物组组成的影响大于基因型本身。在所有三个地点，细菌门，变形菌门其次是拟杆菌门、厚壁菌门和放线菌门都很丰富。核心微生物组分析表明，与叶片内共生有关的有 Acidovorax、Acinetobacter、Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium、Aureimonas、Bradyrhizobium、Burkholderia-Caballeronia-Paraburkholderia、Enterobacter、Pantoea、Pseudomonas、Sphingomonas 和 Stenotrophomonas 与叶片内共生体相关。叶围和种皮围的微生物群似乎对水稻叶片内共生微生物群有贡献。内生微生物组的 SparCC 网络分析显示，微生物群落之间存在复杂的合作和竞争的微生物相互作用。mNGS 数据的微生物学验证进一步证实了核心和瞬态属的存在，如 Acidovorax、Alcaligenes、Bacillus、Chryseobacterium、Comamonas、Curtobacterium、Delftia、Microbacterium、Ochrobactrum、Pantoea、Pseudomonas、Rhizobium、Rhodococcus、Sphingobacterium、Staphylococcus、stenotrophomonas 和 Xanthomonas 在水稻基因型中。我们分离、鉴定并确定了水稻叶片核心内生微生物群落，以便在未来通过微生物组再工程来发展微生物组辅助的作物管理。
