Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Xiong

et al. 2020

Preprint

Background: Plant microbiome is an integral part of the host influencing its growth and health. The increasing evidence indicates that plant rhizosphere may recruit beneficial microbes to suppress soil-borne pathogen, but the ecological mechanisms that govern plant microbiome assembly and functions under disease in both below and aboveground compartments are not fully understood. Here we examined both bacterial and fungal communities from soils (rhizosphere and bulk soil) and multiple plant compartments (e.g. root, stem, and fruit) of chili pepper (Capsicum annuum L.) at two pepper production sites, and explored how Fusarium wilt disease (FWD) affect the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes. Results: Our data demonstrated that FWD had less impact on reproductive organ (fruit) than on vegetative organs (root and stem), with the strongest impact in the stem upper epidermis. Fungal intra-kingdom networks presented lower stabilities and their communities were more sensitive to FWD than the bacterial communities. Moreover, the diseased pepper was more susceptible to colonization by other pathogenic fungi, but they may recruit potential beneficial bacteria to facilitate host or offspring survival, and FWD may enhance the ecological importance of fungal taxa in the interkingdom network. Further, metagenomic analysis revealed that several potential protective functional genes encoding detoxify and biofilm formation were significantly enriched in the diseased pepper.Conclusion: Together, these results significantly advance our understanding of pepper microbiome assembly and functions under biotic stress. Our work highlights the diseased plant and the aboveground compartments harbor a potential of beneficial microbiomes and functions that, in concert, can provide potential critical data for harnessing the plant microbiome for sustainable agriculture.

Section: Disease-induced Changes Of Microbiome Taxonomic Compositionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Disease-induced Changes in Plant Microbiome Assembly and Functional Adaptation

Xiong

et al. 2020

Preprint

“…The numbers of fungal indicator OTUs were signi cantly larger in C. epigeios and P. australis rhizospheres (96 and 49) than the other plant rhizospheres and the bulk soils (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36). The K. foliatum rhizosphere and the bulk soils shared many fungal indicator OTUs (93), most of which belonged to Ascomycota, while the rhizospheres of the six halophytes only shared a small number of fungal indicator OTUs among them (Fig.…”

Section: Rhizosphere Microbial Compositionmentioning

confidence: 99%

“…Soil microbiota plays important roles in sustaining ecosystem functionality [7][8][9][10], remediating degraded land [11][12][13][14] and increasing the ability of plants to resist and/or tolerate stresses (drought, salt, etc.) [15][16][17][18][19] and diseases [20][21][22]. Soil microbial communities are incredibly diverse with complicated associations of microbes that support soil functionality.…”

mentioning

confidence: 99%

Halophytes Increase Rhizosphere Microbial Diversity And Network Complexity In Inland Saline Ecosystem

Qiu

Kong

Zhu

et al. 2021

Preprint

Background: Salinization is an important global environmental problem influencing sustainable development of terrestrial ecosystems. Salt-tolerant halophytes are often used as a promising approach to remedy the saline soils. Yet, how halophytes affect rhizosphere microbial diversity, and microbes’ association and functions in saline ecosystems remains unclear, restricting our ability to assess plant fitness to salt stress and to remediate saline ecosystems. Herein, we examined bacterial and fungal diversities, compositions, and co-occurrence networks in the rhizospheres of six halophytes and bulk soils in a semiarid inland saline ecosystem. We also established the relationship of microbial structure and network complexity to microbial functions.Results: The microbial communities in rhizospheres were more diverse and complex than those the bulk soils. The connections of taxa in the rhizosphere microbial communities increased with fungi-fungi and bacteria-fungi connections and fungal diversity, but decreased with bacteria-bacteria connections and bacterial diversity. The proportion of the fungi-related central connections were larger in the rhizospheres (13-73%) than the bulk soils (3%). Additionally, fungi accounted for 27-63% of the keystone taxa identified in the microbial co-occurrence networks present in the rhizospheres, whereas the keystone taxa identified in the bulk soils were all bacteria/archaea. Moreover, microbial activity and residues were significantly higher in the halophyte rhizospheres than the bulk soils, and were significantly correlated with microbial composition and co-occurrence network complexity.Conclusions: These results indicated that halophytes shaped rhizosphere microbiomes and increased microbial diversity and network complexity in inland saline ecosystem, while fungi enhanced rhizosphere microbiota associations. The increased microbial network complexity contributed to the higher microbial functions in rhizosphere soils.

“…Studies have showed the potential of microbiome adjustment tailored to bring benefits for plant growth and resistance to biotic and abiotic challenges (72). Bioorganic fertilizers promote indigenous soil plant-beneficial consortium to enhance plant disease suppression (73). The design of more efficient biofertilizers to update soil function has important implications for the manipulation of crop microbiomes for sustainable agriculture.…”

Section: Future Prospectsmentioning

confidence: 99%

Network mapping of root-microbe interactions inArabidopsis thaliana

Zhang

Jin

et al. 2020

Preprint

Understanding how plants interact with their colonizing microbiota to determine plant phenotypes is a fundamental question in modern plant science. Existing approaches for genome-wide association studies (GWAS) are based on the association analysis between host genes and the abundance of individual microbes, failing to characterize the genetic architecture of microbial interactions that are thought to a determinant of microbiota structure, organization, and function. Here, we implement a behavioral model to quantify various patterns of microbe-microbe interactions, i.e., mutualism, antagonism, aggression, and altruism, and map host genes that modulate microbial networks constituted by these interaction types. We reanalyze a root-microbiome data involving 179 accessions of Arabidopsis thaliana and find that the four networks differ structurally in the pattern of bacterial-fungal interactions and microbiome complexity. We identify several fungus and bacterial hubs that play a central role in mediating microbial community assembly surrounding A. thaliana root systems. We detect 1142 significant host genetic variants throughout the plant genome and then implement Bayesian networks (BN) to reconstruct epistatic networks involving all significant SNPs and find 91 hub QTLs. Gene annotation shows that a number of the hub genes detected are biologically relevant, playing roles in plant growth and development, resilience against pathogens, root development, and improving resistance against abiotic stress conditions. The new model allows us to better understand the underlying mechanisms that govern the relationships between plants and their entire microbiota and harness soil microbes for plant production.