Root Endophyte Shift and Key Genera Discovery in Rice under Barnyardgrass Stress

doi:10.1016/j.rsci.2023.01.008

Abstract

Abstract:

Despite increasing knowledge of barnyardgrass (Echinochloa crus-galli) interference with rice, relatively little is known how endophytes improve the ability of rice against barnyardgrass stress. Here, we provided a detailed temporal characterization of rice root-associated microbiomes during co-cultivation with barnyardgrass and a comparison with the microbiomes of weed-free rice plants. Alpha diversity analysis indicated that barnyardgrass had the opposite effects on endophytic bacteria and fungi in rice roots, in terms of the community diversity, richness and coverage at the rice seedling stage. Principal coordinate analysis showed that barnyardgrass had only a minor effect on the community composition of endophytes in rice roots at the rice seedling stage, but showed a significant and maximum interference at the heading stage. Rice recruited many endophytes to resist biotic stress from barnyardgrass, especially for fungi. PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) predictive analysis indicated that 23 metabolic pathways of bacteria were overrepresented in rice. In addition, the main trophic mode of fungi was pathotroph according to FUNGuild analysis. A positive correlation between bacteria and fungi in rice roots was found via network analysis. Anaeromyxobacter, Azospira and Pseudolabrys were the vital bacteria, Phaeosphaeria and Funneliformis were the dominant fungi in maintaining the stability of the ecological network. These results provided data and a theoretical basis for the in-depth understanding of what role endophytes play in rice resistance to barnyardgrass stress and will have implications on improving the resistance of rice against biotic stress using root microbiota.

Key words: rice, Echinochloa crus-galli, biotic stress, endophytic bacterium, endophytic fungus, phylogenetic investigation of communities by reconstruction of unobserved states, FUNGuild test

Li Shuyan, Yan Qiling, Wang Jieyu, Jiang Huidan, Li Zuren, Peng Qiong. Root Endophyte Shift and Key Genera Discovery in Rice under Barnyardgrass Stress[J]. Rice Science, 2023, 30(2): 160-170.

Figures/Tables 5

Fig. 1. Species diversity, richness and coverage in rice roots at different growth stages for operational taxonomic units constructed at 0.03 dissimilarity for bacterial and fungal sequences. The diversity estimator Shannon, richness estimator Chao and coverage estimator Coverage were calculated at 3% distance. Data are Mean ± SE (n = 6). Statistical analyses were performed with Mann-Whitney U test. Asterisks above the bars indicate significant differences at P < 0.05 between the WFR (weed-free rice) and WSR (weed-stress rice) groups.

Fig. 2. Principal coordinate analysis (PCoA) based on Bray-Curtis distances between weed-free rice (WFR) and weed-stress rice (WSR) for endophytic bacteria and fungi in rice roots at different growth stages. PCoA of unweighted UniFrac distance matrix represents differences in community structures of WFR and WSR microcosms. WFR1?5 and WSR1?5 represent the WFR and WSR samples collected from the five different growth stages of rice (seedling, tillering, jointing, booting and heading), respectively.

Fig. 3. Endophytic bacterial (A) and fungal (B) community structures at genus level in weed-free rice (WFR) and weed-stress rice (WSR) roots among five different growth stages. WFR1?5 and WSR1?5 represent WFR and WSR grown at the rice seedling, tillering, jointing, booting and heading stages, respectively.

Fig. 4. Relative abundance of PICRUSt1 (phylogenetic investigation of communities by reconstruction of unobserved states) inferred function in weed-free rice (WFR) and weed-stress rice (WSR) samples at booting and heading stages.

Fig. 5. Relative abundance of trophic modes (A) and mainly guilds (B?D) assigned by FUNGuild for fungal community. WFR, Weed-free rice (rice grown alone); WSR, Weed-stress rice (rice-barnyardgrass co-planted). Data are Mean ± SE (n = 6).

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