Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)

Abstract

Background Drought is global environmental stress that limits crop yields. Plant-associated microbiomes play a crucial role in determining plant fitness in response to drought, yet the fundamental mechanisms for maintaining microbial community stability under drought disturbances in wild rice are poorly understood. We make explicit comparisons of leaf, stem, root and rhizosphere microbiomes from the drought-tolerant wild rice (Oryza longistaminata) in response to drought stress. Results We find that the response of the wild rice microbiome to drought was divided into aboveground–underground patterns. Drought reduced the leaf and stem microbial community diversity and networks stability, but not that of the roots and rhizospheres. Contrary to the aboveground microbial networks, the drought-negative response taxa exhibited much closer interconnections than the drought-positive response taxa and were the dominant network hubs of belowground co-occurrence networks, which may contribute to the stability of the belowground network. Notably, drought induces enrichment of Actinobacteria in belowground compartments, but not the aboveground compartment. Additionally, the rhizosphere microbiome exhibited a higher proportion of generalists and broader habitat niche breadth than the microbiome at other compartments, and drought enhanced the proportion of specialists in all compartments. Null model analysis revealed that both the aboveground and belowground-community were governed primarily by the stochastic assembly process, moreover, drought decreased ‘dispersal limitation’, and enhanced ‘drift’. Conclusions Our results provide new insight into the different strategies and assembly mechanisms of the above and belowground microbial community in response to drought, including enrichment of taxonomic groups, and highlight the important role of the stochastic assembly process in shaping microbial community under drought stress.

Colonization and Interaction of Bacteria Associated With Chinese Chives Affected by Ecological Compartments and Growth Conditions

“…These results are consistent with the research findings of Stouvenakers (Stouvenakers et al, 2020 ). Microbial diversity and interaction among ecological compartments of plants are related to their ability to resist external disturbance (Kusstatscher et al, 2019 ; Xie et al, 2021 ). In this study, the alpha diversity in the Chinese chive rhizosphere was significantly higher than that in other ecological compartments, the rhizosphere microbial network average degree and average clustering coefficient were higher than those in other ecological compartments, and the interaction of the microbial network was more complex.…”

“…As key nodes Proteobacteria and Firmicutes in the phylloplane ecological compartment, they are also key nodes in the root endosphere ( Figure 5 ). Rhizosphere microorganisms could enter the roots of Chinese chives, and some endophytic bacteria migrated from the root endosphere of Chinese chives to the upper stems and leaves (Edwards et al, 2015 ; Xie et al, 2021 ). There were some differences in diversity, bacterial composition, interaction network, and function among the microorganisms in the phylloplane, leaf endosphere, and stem endosphere of Chinese chives ( Figures 1 , 2 , 5 , 6 ).…”

“…oryzae KB88, and Candidaalbicans (Kimura et al, 2018). These results show that the response of microbial communities in the root endosphere to fluctuations in the growth environment was more stable than those in the rhizosphere or soil (Almario et al, 2017;Han et al, 2020;Xie et al, 2021). Bacteroidetes is an important component of the bacterial microbial community (Fernández-Gómez et al, 2013) in a normal aquatic environment (Chen et al, 2011), which is related to the requirement of a strict anaerobic environment as a growth condition for most bacterial strains in this phylum.…”

Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

“…Climate extremes can reorganize networks of associations between co-existing soil microbial taxa (Zhou et al, 2011;de Vries et al, 2018;Bardgett and Caruso, 2020;Yuan et al, 2021) with essential feedback on plant resilience and performance in stress environments. For example, recent studies have shown that WD significantly influences microbial co-existence networks (de Vries et al, 2018;Zhang et al 2021;Xie et al, 2021). These changes in the microbial co-existence network potentially impact the recovery of microbial communities and alter plant-microbe interactions under disturbances.…”

The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis)

“…A 16S rRNA gene amplification was performed for archaea and bacteria. Barcoded primers targeting the variable V4 regions of the 16S rRNA genes were used for amplification using the universal primer pairs, 515F (GGACTACNVGGGTWTCTAAT) and 806R (GGAC-TACHVGGGTWTCTAAT) [72][73][74][75]. Forward and reverse primers were tagged with Illumina adapter, pad, and linker sequences.…”