Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype

Abstract

Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting plant health and disease. The plant microbiome is shaped by plant species, plant genotype, soil and environmental conditions, but the contributions of these variables are hard to disentangle from each other in natural systems. We used bioassay common garden experiments to decouple plant genotype and soil property impacts on fungal and bacterial community structure in the Populus rhizobiome. High throughput amplification and sequencing of 16S, ITS, 28S and 18S rDNA was accomplished through 454 pyrosequencing. Co-association patterns of fungal and bacterial taxa were assessed with 16S and ITS datasets. Community bipartite fungal-bacterial networks and PERMANOVA results attribute significant difference in fungal or bacterial communities to soil origin, soil chemical properties and plant genotype. Indicator species analysis identified a common set of root bacteria as well as endophytic and ectomycorrhizal fungi associated with Populus in different soils. However, no single taxon, or consortium of microbes, was indicative of a particular Populus genotype. Fungal-bacterial networks were over-represented in arbuscular mycorrhizal, endophytic, and ectomycorrhizal fungi, as well as bacteria belonging to the orders Rhizobiales, Chitinophagales, Cytophagales, and Burkholderiales. These results demonstrate the importance of soil and plant genotype on fungal-bacterial networks in the belowground plant microbiome.

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

“…An increasing number of studies characterize plant microbiomes, moving us toward a more mechanistic and synergistic understanding of factors structuring these communities. Nevertheless, while many studies have looked at spatial variation or plant genetic variation, most studies do not simultaneously examine both soil origin and plant genotype in the same design, making direct comparisons among these effects di cult (but see [33,[62][63][64]). Our design, combined with sequencing microbial communities from both endosphere (root, nodule, leaf) and rhizosphere compartments, allows us to directly compare the effects of soil and genotype across these distinct "organs".…”

Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi

“…Some endophytic species are known to protect their host plant against disease, while others contribute to plant host growth, health and overall survival (Shakya et al, 2013;Liao et al, 2019). However, relationships between microbes in the endosphere are complex, as they are multipartite and as may have indirect effects on the host and other microbes (Yang et al, 2013;Bonito et al, 2019). Further, identification of these microorganisms and understanding their interactions and dynamics is difficult due to methodological limitations in their cultivatability or detection (Appuhn and Joergensen, 2006;Lee et al, 2008;Compant et al, 2010;Podolich et al, 2015).…”

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato

“…These differences could be explained by the diverse sets of available microorganisms with varied abilities to attach to the nematode cuticle. We also consider that the rhizobiome composition could be affected by the physicochemical conditions of the soil (Bonito et al, 2019;Saad et al, 2019). Wolfgang et al (2019) proposed that changes in physiological conditions of plant cells is the cause by a microbial structure shift, and this is influenced by the ability of some bacteria to adhere to the nematode cuticle (Elhady et al, 2017).…”