The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

Cristina Lazcano,Gerald Holmes,Alexis Pasulka,Eric Boyd,Shashika Hewavitharana,Kelly Ivors

doi:10.1038/s41598-021-82768-2

Abstract

Microbial-root associations are important to help plants cope with abiotic and biotic stressors. Managing these interactions offers an opportunity for improving the efficiency and sustainability of agricultural production. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Overall, the plants had a distinctive and genotype-dependent rhizosphere microbiome with higher abundances of known beneficial bacteria such as Pseudomonads and Rhizobium. The rhizosphere microbiome played a significant role in the resistance to the two soil-borne pathogens as shown by the differences in microbiome between high and low resistance cultivars. Resistant cultivars were characterized by higher abundances of known biocontrol microorganisms including actinobacteria (Arthrobacter, Nocardioides and Gaiella) and unclassified acidobacteria (Gp6, Gp16 and Gp4), in both pathogen trials. Additionally, cultivars that were resistant to V. dahliae had higher rhizosphere abundances of Burkholderia and cultivars resistant to M. phaseolina had higher abundances of Pseudomonas. The mechanisms involved in these beneficial plant-microbial interactions and their plasticity in different environments should be studied further for the design of low-input disease management strategies.

Highlights

Microbial-root associations are important to help plants cope with abiotic and biotic stressors
After filtering chloroplast and unassigned reads, 3,786,463 sequences were clustered into 5,600 Operational Taxonomic Units (OTUs) representing 33 Archaeal and 5567 Bacterial OTUs from 353 genera
Differences in OTU community structure between sample types in the two pathogen trials were examined via non-metric multidimensional scaling (NMDS) using a Bray–Curtis dissimilarity of the standardized and transformed data (Fig. 1)

Summary

Introduction

Microbial-root associations are important to help plants cope with abiotic and biotic stressors. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Root-associated microorganisms, either symbiotic or free living are key for plant nutrition and health and, because of this, the rhizosphere is frequently compared with the human gut[10] Soil bacteria such as Pseudomonas, Bacillus and Rhizobium can increase the concentration of plant available phosphorus (P) in soil by releasing phosphatase enzymes or organic c helates[11]. Plants with higher resistance will exhibit a different microbiome from plants with low resistance having a higher abundance of beneficial bacteria and archaea; resistance to soil-borne pathogens, growth and nutrient uptake, would be corelated with the composition of the rhizosphere microbiome

Methods

Results

Discussion

Conclusion