Fertilization alters protistan consumers and parasites in crop‐associated microbiomes

Abstract

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plantsoil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in cropassociated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.

Plant Growth Stage Drives the Temporal and Spatial Dynamics of the Bacterial Microbiome in the Rhizosphere of Vigna subterranea

“…Furthermore, metagenomic analysis in our study revealed that the bacterial diversity in the BGN rhizosphere varied across the four developmental stages. The plant exerts a strong selection mechanism that recruits and selects for specific bacterial taxa during the plant’s development ( Fazal et al, 2021 ; Sun et al, 2021 ). In addition to previous studies of plants shaping their microbiomes through the various compartments and varying genotypes ( Agoussar et al, 2021 ; Stopnisek and Shade, 2021 ; Wagner, 2021 ; Xiong et al, 2021b ), this study further identifies plant development stages as an important process in plant-engineered microbiome assembly and function.…”

18S rRNA gene amplicon sequencing combined with culture‐based surveys of maize rhizosphere protists reveal dominant, plant‐enriched and culturable community members

“…They include parasites, pathogens, predators of other microbes and autotrophs, some of which can impact plant health directly, through nutrient cycling, or indirectly, through predation on or stimulation of other microbes (Bass and del Campo, 2020). Network analyses have pointed to specific taxa, such as the protistan clade Cercozoa, that may influence disease development or abundance of beneficial or pathogenic microbes (Flues et al ., 2017; Xiong et al ., 2020; Sun et al ., 2021). Despite their importance to plant health, challenges posed by high phylogenetic diversity, lack of reference sequences and difficulty in isolation and culturing have historically limited study of the protists in the rhizosphere.…”

“…Methodological advances have addressed some of the technical sequencing limitations for protists (reviewed in Keeling and del Campo, 2017; Geisen and Bonkowski, 2018), facilitating a new taxonomic exploration of protist diversity in plant environments. High‐throughput amplicon sequencing studies have revealed that plant‐associated protistan communities include hundreds of phylotypes, and that protistan community composition is dynamic and shaped by a wide variety of host, soil and environmental factors (Dumack et al ., 2020; Rossmann et al ., 2020; Sun et al ., 2021). These studies represent few locations and hosts, and much work is needed to validate emerging paradigms.…”

“…These studies represent few locations and hosts, and much work is needed to validate emerging paradigms. One question is the role of the plant in protistan community selection; some studies found that the rhizosphere selects a protistan community of reduced diversity relative to that of bulk soil, similar to the selection observed for bacteria and fungi (Sapp et al ., 2018; Dumack et al ., 2020; Ceja‐Navarro et al ., 2021), while others reported little or no rhizosphere effect (Rüger et al ., 2021; Sun et al ., 2021).…”

Organic fertilization regimes suppress fungal plant pathogens through modulating the resident bacterial and protistan communities

“…10,11 Plant-soil microbiome interactions span from deleterious (e.g., fungal plant pathogens) to neutral to highly beneficial (e.g., plant beneficial microbes) to the plant, 12 with far-reaching consequences for plant performance, fitness and ecosystem functioning. 5,13 More importantly, plant-associated beneficial microbes are known to be important contributors to enhancing host's resistance against soil-borne plant pathogens, 12,14,15 possibly through competition with pathogens for niches, direct antagonism via production of antibiotics or volatiles, induction of systemic or induced resistance via production of compounds such as salicylic acid, 16 or directly predating pathogenic microbes. [17][18][19] Given the critical role of plant-microorganism and microorganism-microorganism interactions in disease suppression, 17 it is a promising direction to optimize plant-soil-microbe partnerships to enhance soil protection against fungal pathogens.…”