Comprehensive analysis of the apple rhizobiome as influenced by different Brassica seed meals in the same soil/plant system

Authors: Somera, Tracey; FREILICH, SHIRI - Agricultural Research Organization, Volcani Center; Mazzola, Mark

Submitted to: Applied Soil Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2020
Publication Date: 1/1/2021
Publication URL: https://handle.nal.usda.gov/10113/7139950
Citation: Somera, T.S., Freilich, S., Mazzola, M. 2021. Comprehensive analysis of the apple rhizobiome as influenced by different Brassica seed meals in the same soil/plant system. Applied Soil Ecology. 157. Article 103766. https://doi.org/10.1016/j.apsoil.2020.103766.
DOI: https://doi.org/10.1016/j.apsoil.2020.103766

Interpretive Summary: Seed meal, a by-product of the oil extraction process from certain Brassicaceae plants, have been used as a pre-plant soil amendment for the control of apple replant disease (ARD). When grown in soils amended with Brassicaceae seed meal, apple roots support a specialized microbiome; one that promotes suppression of apple replant disease (ARD) pathogens through various modes of action. Combining seed meal treatments with specific rootstocks with reported tolerance to ARD may be essential to optimizing the disease-suppressing potential of the seed meal modified microbiome. In previous studies we reported the combined effects of seed meal x rootstock genotype on composition of the apple rhizosphere microbiome in several different orchard soil types. However, the functional significance of these changes in the microbiome remains poorly characterized. In this experiment, we utilized next gen amplicon sequencing to characterize changes in the rhizosphere bacterial, fungal and oomycete communities of a tolerant (G.210) and susceptible (M.26) apple rootstock. The type of seed meal used (that is plant species from which it was sourced) had a dominant influence on structuring the composition of the rhizosphere microbiome, with host genotype having a subordinate role. Different seed meal types resulted in effective or ineffective disease control, with the effective seed meal formulation Brassica juncea + Sinapis alba reducing the incidence of several plant pathogenic fungi and oomycetes. In addition to taxa with the potential to control replant pathogens, The Brassica juncea + Sinapis alba seed meal-structured microbiome was enriched with many microbial groups known to provide biological control of fungal, oomycete and nematode pathogens of plants. In addition, microbial groups with biodegradative and bioremediation potential, including degradation of xenobiotics and uptake of heavy metals, were unique to the seed meal modified microbiome. Brassica juncea + Sinapis alba seed meal-structured microbiomes are likely to contribute to long-term orchard health through a diversity of functional means.

Technical Abstract: Replant disease refers to the poor growth of trees when attempting to establish the same or related species on old orchard sites. Apple replant disease (ARD) results primarily from plant-induced changes in the soil microbiota leading to a build-up of multiple soil-borne pathogens over time prior to removal of the old orchard. One promising strategy for the control of ARD is the use of pre-plant Brassicaceae seed meal (SM) soil amendments. This disease control method requires both biologically- and chemically-based mechanisms that function in response to the seed meal amendment. Optimizing microorganism-driven protection of apple roots from infection by specific ARD pathogens requires a better understanding of how “effective” vs. “ineffective” Brassicaceae seed meal x rootstock genotype disease control systems modulate composition of the rhizosphere microbiome. SM amendment type was a major factor structuring bacterial, fungal and oomycete rhizosphere communities, while rootstock genotype influenced composition of these communities to a lesser degree. Relative abundance of individual fungal and oomycete plant pathogens detected in the apple rhizosphere varied in a treatment x rootstock genotype dependent manner. In addition to taxa with the potential to control replant pathogens, Brassica juncea + Sinapis alba seed meal-structured microbiomes were highly enriched in microbial groups with biodegradative and bioremediation potential. Although amplicon sequencing provided a much more detailed picture of the genetic diversity of specific oomycete groups in the apple rhizosphere than previously appreciated, further oomycete-specific community level studies are likely to improve our understanding of ARD as well as many other soil-borne diseases.