Shifts in the diversity of root endophytic microorganisms across the life cycle of the ratooning rice Jiafuzhan

Abstract

The diversity of root endophytic microorganisms, which is closely related to plant life activities, is known to vary with the plant growth stage. This study on the ratooning rice Jiafuzhan explored the diversity of the root endophytic bacteria and fungi and their dynamics during the plant life cycle. By sequencing the 16S ribosomal ribonucleic acid (16S rRNA) and internal transcribed spacer (ITS) genes, 12,154 operational taxonomic units (OTUs) and 497 amplicon sequence variants (ASVs) were obtained, respectively. The root endophytic microorganisms of rice in the seedling, tillering, jointing, heading, and mature stages of the first crop and at 13, 25, and 60 days after regeneration (at the heading, full heading, and mature stages of the second crop, respectively) were analyzed using diversity and correlation analyses. There were significant differences in the α-diversity and β-diversity of root endophytic bacteria and fungi in the growth stage. Additionally, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed biomarker bacteria for each growth stage, but biomarker fungi did not exist in every stage. Moreover, the correlation analysis showed that the bacterial and fungal biomarkers interacted with each other. Furthermore, the nitrogen-fixing genus Bradyrhizobium existed in all growth stages. These findings indicate the pattern of root endophytic microorganisms of ratooning rice at different growth stages, and they provide new insights into the high yield of the second crop of ratooning rice (in light of the abundance of various bacteria and fungi).

Performance of Halo-Alkali-Tolerant Endophytic Bacteria on Hybrid Pennisetum and Bacterial Community under Varying Soil Conditions

“…The abundance of taxa other than the inoculated microbial taxa in analyzed metagenomics samples is still sketchy [34]. These more abundant bacteria in specific samples could represent enriched taxa with significant roles that alter the composition of communities [61].…”

“…These more abundant bacteria in specific samples could represent enriched taxa with significant roles that alter the composition of communities [ 61 ]. According to the study of Dong et al [ 62 ], the correlation of Bacillus sp. with Proteobacteria and Firmicutes may enhance the disease resistance of plants, promote bud growth, and increase overall crop yield since the nitrogen-fixing bacteria become enriched during the mature stages, distributing vital nutrients for the development of transformed axillary buds.…”

Endophytic Fungi in Rice Plants and Their Prospective Uses

“…To explore endophytic fungal communities in the root during the growth of Jiafuzhan ratooning rice, 497 amplicon sequence variants (ASVs) were obtained by sequencing the internal transcribed spacer (ITS) genes, and 12 phyla endophytic fungi were detected. Ascomycota, Basidiomycota, Mortierellomycota, Rozellpmycota, and Mucoromycota were the most abundant fungal phyla [58]. Diverse fungi and unidentified fungi were detected in rice sprouts by ITS1 and ITS2, and Ascomycota and Basidiomycota were the dominant fungal phyla [59].…”

“…Endophytic fungal diversity is affected by many factors, such as environmental factors, cultivation methods, nutrient availability, host plant genotype, and so on [40,49,59,61,62]. The abundance of fungal phyla changes throughout the growth stages of rice [58]. Cooccurrence network analysis showed that the bacterial community exerted a positive influence on fungal endophytes in rice plants [43].…”

“…The Divisive Amplicon Denoising Algorithm (DADA2) and the Quantitative Insights Into Microbial Ecology (QIIME) are helpful for data processing and data analysis [66,67]. Based on clustering the sequences into amplicon variant sequences (ASVs), the taxonomy can be assigned to the ASVs [58,65,68]. Typically, alpha diversity and beta diversity analyses are performed using the diversity plugin.…”