Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach

Abstract

Backgorund: The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

Methods: In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

Results: Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

Discussion: This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.

Keywords: Alpha and beta diversity; Climate change; Phytopathogens; Plant growth promoting microorganisms; Vaccinium corymbosum.

Figure 1. Evolutionary tree of the 100 most abundant genera of fungi across the different samples.

Each bar represents the relative abundance of the genus in each sample. Each color of the branches corresponds to one phylum.

Figure 2. Relative abundance of the top 10 most abundant genera identified by ITS sequencing in each sample.

Figure 3. Relative abundance of the top 10 most abundant genera identified by 16S sequencing in each sample.

Figure 4. Evolutionary tree of the 100 most abundant genera of fungi across the different samples.

Each bar represents the relative abundance of the genus in each sample. Each color of the branches corresponds to one phylum.

Figure 5. Multivariate analysis of the fungal communities of each soil sample by non-linear multidimensional scaling (NMDS) to evaluate the dissimilarity between each associated community.

Figure 6. Multivariate analysis of the bacterial communities of each soil sample by non-linear multidimensional scaling (NMDS) to evaluate the dissimilarity between each associated community.

Figure 7. Venn diagram of the common operational taxonomic units (OTUs) of the ITS (A) and 16S (B) metabarcoding.

Each petal in the flower diagram represents for a sample or group, with different colors for different samples. The core number in the center is for the number of OTUs present in all samples, while number in the petals for the unique OTUs only showing in each sample.